Contacts of the helix formed by residues 536 - 559 (chain B) in PDB entry 7CR3
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 536 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B TRP* 6.1 0.2 - - + -
364B GLU* 5.5 14.1 - - + +
535B GLY* 1.3 71.0 - - - +
537B LYS* 1.3 80.6 + - + +
539B SER* 3.5 8.7 - - - -
540B ILE* 3.0 39.7 + - + +
19C LEU* 5.3 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 537 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B TRP* 3.2 47.6 - - + -
535B GLY 3.2 7.5 - - - +
536B LEU* 1.3 89.9 - - + +
538B VAL* 1.3 58.2 + - - +
540B ILE* 3.4 2.3 + - - +
541B ARG* 2.9 61.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 538 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B GLY* 3.2 13.4 + - - +
537B LYS* 1.3 75.2 - - - +
539B SER* 1.3 64.0 + - - +
541B ARG* 3.6 15.2 - - + +
542B ALA* 2.8 29.3 + - - +
12C GLU* 3.1 41.1 - - - +
13C PHE* 3.6 28.9 - - + -
15C GLU* 5.4 0.2 - - - +
16C ALA* 3.6 25.9 - - + +
69C PHE* 4.9 2.2 - - + -
73C MET* 4.2 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 539 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B GLY 2.4 29.5 + - - -
536B LEU* 3.5 9.8 - - - -
537B LYS 3.2 0.2 - - - -
538B VAL* 1.3 79.9 - - - +
540B ILE* 1.3 64.5 + - - +
542B ALA* 3.9 1.7 - - - +
543B VAL* 3.1 25.8 + - - +
16C ALA* 5.5 2.3 - - - -
19C LEU* 3.4 23.6 - - - +
20C PHE* 4.2 17.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 540 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B THR* 4.4 8.7 - - + -
360B TRP* 5.5 10.3 - - + +
363B TYR* 3.6 55.0 - - + +
364B GLU* 5.0 1.6 - - - +
536B LEU* 3.0 26.5 + - + +
537B LYS* 4.0 2.2 - - - +
539B SER* 1.3 77.2 - - - +
541B ARG* 1.3 57.8 + - - +
543B VAL* 3.2 12.1 - - + +
544B CYS* 2.9 33.2 + - + +
547B ARG* 5.3 2.0 - - - +
40C LEU* 3.8 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 541 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B THR* 2.3 50.9 + - - +
350B ASN* 4.1 1.3 + - - +
351B LEU* 3.4 40.0 - - - +
360B TRP* 3.3 20.7 - - + -
537B LYS* 2.9 56.9 + - - +
538B VAL* 3.5 15.0 - - - +
539B SER 3.1 0.2 - - - -
540B ILE* 1.3 76.7 - - - +
542B ALA* 1.3 58.2 + - - +
544B CYS* 3.1 2.6 + - - +
545B VAL* 2.8 36.6 + - + +
9C GLN* 5.7 3.6 - - - +
12C GLU* 6.3 0.2 - - - -
73C MET* 4.3 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 542 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538B VAL 2.8 20.7 + - - +
539B SER 3.9 0.2 - - - +
541B ARG* 1.3 72.8 - - - +
543B VAL* 1.3 64.2 + - - +
545B VAL* 3.1 3.6 + - - +
546B MET* 3.0 30.7 + - + +
20C PHE* 3.7 18.8 - - + -
69C PHE* 3.5 33.0 - - + -
72C MET* 3.6 0.4 - - - +
73C MET* 3.7 14.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 543 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539B SER 3.1 12.7 + - - +
540B ILE* 3.2 21.1 - - + +
542B ALA* 1.3 80.1 - - - +
544B CYS* 1.3 60.2 + - - +
546B MET* 3.5 11.9 + - + +
547B ARG* 2.9 49.6 + - - +
20C PHE* 4.2 8.0 - - + -
33C LEU* 5.6 1.8 - - + +
36C VAL* 5.3 9.2 - - + -
37C MET* 4.1 31.9 - - + -
40C LEU* 5.4 3.6 - - + -
52C MET* 4.3 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 544 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B SER* 3.7 1.9 + - - -
345B ARG* 3.3 48.9 - - - -
346B PHE* 3.4 13.7 - - - -
349B THR* 3.6 9.6 - - + +
540B ILE* 2.9 21.2 + - + +
541B ARG 3.5 3.6 - - - +
542B ALA 3.1 0.2 - - - -
543B VAL* 1.3 76.9 - - - +
545B VAL* 1.3 61.7 + - - +
547B ARG* 3.1 22.8 + - - +
548B PHE* 2.8 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 545 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B PHE* 3.7 33.0 - - + -
349B THR* 5.8 0.2 - - - +
541B ARG* 2.8 23.1 + - + +
542B ALA 3.6 6.5 - - - +
544B CYS* 1.3 76.1 - - + +
546B MET* 1.3 58.4 + - - +
548B PHE* 3.2 8.4 + - + +
549B LEU* 2.9 35.2 + - + +
72C MET* 3.6 41.3 - - + +
73C MET* 4.2 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 546 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542B ALA* 3.0 38.5 + - + +
543B VAL* 3.6 6.3 - - - +
545B VAL* 1.3 78.4 - - - +
547B ARG* 1.3 56.1 + - - +
549B LEU* 3.2 5.7 + - - +
550B VAL* 3.0 31.2 + - - +
20C PHE* 3.8 26.2 - - + -
33C LEU* 4.5 5.8 - - - -
52C MET* 3.4 39.4 - - + +
55C GLU* 4.4 0.8 - - + +
56C VAL* 3.5 29.6 - - + -
64C ILE* 4.2 17.9 - - + -
69C PHE* 4.9 4.0 - - + -
72C MET* 3.6 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 547 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B SER* 3.5 7.6 + - - +
345B ARG* 3.0 38.9 - - - +
363B TYR* 3.7 19.3 + - - -
540B ILE* 4.9 1.8 + - - +
543B VAL* 2.9 51.7 + - + +
544B CYS* 3.1 32.6 + - - +
546B MET* 1.3 76.0 - - - +
548B PHE* 1.3 57.9 + - - +
550B VAL* 3.1 11.7 - - + +
551B SER* 3.0 27.5 + - - -
37C MET* 4.2 23.3 - - - +
40C LEU* 5.2 4.0 - - - +
52C MET* 3.8 15.0 - - + -
115C GLU* 5.2 5.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 548 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B LEU* 3.4 29.2 - - + -
342B SER* 3.1 22.4 + - - +
343B ALA* 3.5 30.1 - - + -
346B PHE* 4.3 26.5 - + + -
544B CYS 2.8 17.6 + - - +
545B VAL* 3.7 9.4 - - + +
547B ARG* 1.3 70.7 - - - +
549B LEU* 1.3 63.4 + - + +
551B SER* 3.3 2.9 + - - -
552B LYS* 2.8 61.3 + - + +
77C MET* 4.9 10.1 - - + -
80C THR* 5.7 5.2 - - + -
82C SER* 5.7 8.7 - - - -
86C ILE* 5.9 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 549 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545B VAL* 2.9 23.5 + - + +
546B MET* 3.7 2.0 - - - +
548B PHE* 1.3 76.6 - - + +
550B VAL* 1.3 59.8 + - - +
552B LYS* 3.2 31.7 + - + +
553B ARG* 3.0 24.6 + - - +
55C GLU* 3.0 50.6 - - + +
72C MET* 3.6 35.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 550 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546B MET 3.0 10.9 + - - +
547B ARG* 3.1 27.1 - - + +
549B LEU* 1.3 76.0 - - - +
551B SER* 1.3 56.5 + - - +
553B ARG* 4.1 0.3 - - - +
554B LYS* 2.8 41.2 + - + +
48C GLU 4.5 0.9 - - - +
51C ASP* 3.5 16.8 - - + -
52C MET* 3.5 36.3 - - + +
55C GLU* 3.4 25.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 551 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B PRO* 4.6 2.3 + - - +
338B GLY* 3.2 25.8 + - - -
339B LEU* 3.2 18.6 + - - +
342B SER* 4.3 4.9 - - - -
547B ARG 3.0 19.5 + - - -
548B PHE* 3.5 9.8 - - - -
549B LEU 3.2 0.2 - - - -
550B VAL* 1.3 78.4 - - - +
552B LYS* 1.3 57.0 + - - +
554B LYS* 3.8 4.9 - - - +
555B PHE* 2.9 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 552 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B LEU* 3.5 23.6 - - + -
548B PHE* 2.8 54.0 + - + +
549B LEU* 3.2 27.7 + - + +
551B SER* 1.3 72.5 - - - +
553B ARG* 1.3 59.9 + - + +
555B PHE* 3.4 1.2 + - - +
556B LYS* 2.9 19.6 + - - +
80C THR* 4.2 28.5 + - + +
82C SER* 4.8 9.0 - - - -
85C GLU* 2.9 36.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 553 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549B LEU 3.0 7.3 + - - +
550B VAL 4.1 1.3 - - - +
552B LYS* 1.3 76.9 - - + +
554B LYS* 1.3 60.7 + - - +
556B LYS* 3.1 10.7 + - + +
557B GLU* 2.9 42.9 + - - +
54C ASN* 2.6 43.6 + - - +
55C GLU* 2.8 49.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 554 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B PRO* 4.2 13.9 - - + +
550B VAL* 2.8 26.3 + - + +
551B SER* 3.9 5.2 - - - +
553B ARG* 1.3 74.6 - - - +
555B PHE* 1.3 63.4 + - - +
557B GLU* 3.2 29.1 + - - +
558B SER* 3.0 26.7 + - - -
51C ASP* 6.0 8.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 555 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B ARG* 4.4 9.9 - - + -
335B PRO* 3.6 19.9 - - + +
336B ALA* 3.6 40.4 - - + -
339B LEU* 4.0 9.9 - - + -
551B SER 2.9 18.9 + - - +
552B LYS 3.5 3.6 - - - +
554B LYS* 1.3 76.3 - - - +
556B LYS* 1.3 56.4 + - - +
558B SER 3.5 1.2 + - - -
559B LEU* 2.9 69.8 + - + +
85C GLU* 3.3 40.2 - - + -
88C GLU* 4.1 3.6 - - + -
89C ALA* 3.5 26.9 - - + -
92C VAL* 5.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 556 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552B LYS 2.9 11.5 + - - +
553B ARG* 3.1 13.4 + - + +
555B PHE* 1.3 74.6 - - - +
557B GLU* 1.3 63.9 + - + +
559B LEU* 3.3 17.2 - - + +
560B ARG* 2.4 49.6 + - - +
81C ASP 5.6 1.5 + - - -
84C GLU* 4.3 13.7 + - - +
85C GLU* 3.2 48.1 - - - +
88C GLU* 4.7 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 557 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553B ARG* 2.9 34.2 + - - +
554B LYS* 3.2 32.7 + - - +
556B LYS* 1.3 79.2 - - + +
558B SER* 1.3 59.3 + - - +
559B LEU 3.2 4.0 + - - -
560B ARG* 3.5 15.4 + - - +
51C ASP* 5.1 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 558 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B LYS 4.2 3.5 + - - -
332B ARG* 3.4 31.6 - - - +
335B PRO* 3.5 26.0 - - - +
554B LYS* 3.0 10.7 + - - -
555B PHE 3.7 1.8 - - - -
557B GLU* 1.3 72.0 - - - +
559B LEU* 1.3 60.3 + - - +
560B ARG 3.1 7.1 + - - -
561B PRO* 3.3 18.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 559 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B GLN* 5.5 0.3 + - - -
332B ARG* 2.4 57.8 + - - +
555B PHE* 2.9 52.3 + - + +
556B LYS* 3.3 24.2 - - + +
557B GLU 3.1 1.0 - - - -
558B SER* 1.3 76.6 - - - +
560B ARG* 1.3 88.7 + - - +
561B PRO* 3.4 2.5 - - - -
88C GLU* 4.0 30.5 - - + +
91C ARG* 5.3 1.1 - - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il