Contacts of the strand formed by residues 536 - 551 (chain B) in PDB entry 2C11
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 GLU 536 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532B VAL 4.9 0.3 - - - +
534B GLY 3.7 0.9 - - - -
535B LEU* 1.3 90.9 + - + +
537B ASN* 1.3 65.1 + - - +
538B TRP* 3.4 19.9 - - + -
591B SER* 4.2 8.0 + - - -
592B ASN* 4.3 3.1 + - + +
671B GLY* 3.0 27.4 - - - +
672B LYS* 3.4 7.9 - - - -
673B ASP 5.3 0.4 - - - +
1H NAG 6.0 2.9 - - - +
5H FUC 6.0 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 537 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530B LEU 3.7 12.1 - - - +
532B VAL* 2.7 53.0 + - - +
534B GLY 3.4 9.3 + - - +
535B LEU 3.0 18.2 - - - +
536B GLU* 1.3 80.4 + - - +
538B TRP* 1.3 65.3 + - - +
589B LEU* 4.4 7.0 - - + -
590B ALA 3.1 18.8 + - - +
591B SER* 4.0 0.2 - - - +
671B GLY 3.1 15.1 + - - -
672B LYS 2.9 8.9 + - - +
674B LEU* 3.0 28.6 + - + +
1741B CA 4.1 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 538 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536B GLU* 3.4 22.4 - - + -
537B ASN* 1.3 79.0 - - - +
539B VAL* 1.3 66.1 + - - +
540B TRP* 3.8 16.5 + + - +
568B LEU* 3.9 27.2 - - + +
588B TYR 3.5 0.9 - - - +
589B LEU* 3.0 4.9 - - - -
590B ALA 2.8 36.9 + - - +
591B SER 4.0 2.5 - - - +
592B ASN* 3.2 47.8 - - + -
669B ILE 4.0 3.1 - - - -
670B ALA* 3.3 33.7 + - + +
671B GLY* 3.2 23.6 - - - -
674B LEU* 4.2 0.4 - - - -
5H FUC 4.7 17.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 539 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538B TRP* 1.3 74.9 - - - +
540B TRP* 1.3 62.3 + - - +
568B LEU* 3.5 6.6 - - - +
569B LEU* 3.0 49.4 + - + +
575B ALA* 5.0 1.3 - - + -
587B LEU* 3.6 27.1 - - + -
588B TYR 3.4 6.5 - - - +
589B LEU* 3.4 25.4 - - + -
634B VAL* 3.9 19.1 - - + -
669B ILE* 3.8 19.3 + - + +
674B LEU* 3.8 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 540 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538B TRP* 4.1 18.8 - + + +
539B VAL* 1.3 73.8 - - - +
541B ALA* 1.3 62.3 + - - +
542B GLU* 4.0 1.8 - - + -
566B ARG* 4.0 24.5 - - + -
567B LYS 3.6 18.4 - - - -
568B LEU* 3.5 45.8 - - + -
569B LEU* 4.8 0.2 - - - -
587B LEU* 3.0 20.1 - - - +
588B TYR* 2.8 65.0 + + + +
590B ALA* 3.9 16.0 - - + +
591B SER 5.0 1.8 + - - -
600B PRO* 4.2 19.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 541 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540B TRP* 1.3 76.0 - - - +
542B GLU* 1.3 60.6 + - - +
543B ASP* 5.5 0.4 - - - +
565B THR 3.3 4.3 - - - +
567B LYS* 2.8 41.9 + - + +
569B LEU* 4.1 17.3 - - + -
577B PHE* 5.9 0.4 - - + -
584B PRO* 3.9 24.9 - - + -
586B TYR 3.5 5.6 - - - -
587B LEU* 4.0 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 542 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A ASN* 4.4 1.7 - - - +
685A ILE* 3.8 13.2 - - + +
540B TRP 4.0 0.4 - - - -
541B ALA* 1.3 76.4 - - - +
543B ASP* 1.3 63.7 + - - +
564B VAL* 4.3 4.3 - - + -
565B THR 2.9 6.1 - - - +
566B ARG* 3.0 48.4 + - + -
584B PRO* 4.1 1.4 - - - +
585B ARG 3.8 1.0 + - - -
586B TYR* 2.8 44.0 + - + +
588B TYR* 3.1 30.9 + - + +
708B TYR* 2.6 35.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 543 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613A GLU* 4.4 1.7 - - - +
683A LEU* 3.9 15.4 - - - +
685A ILE* 4.1 1.2 - - - +
542B GLU* 1.3 75.0 - - - +
544B MET* 1.3 81.4 + - - +
564B VAL* 3.5 12.1 - - - +
565B THR* 2.6 35.5 + - - +
583B THR 4.3 2.4 - - - +
584B PRO* 3.6 10.6 - - + +
585B ARG* 2.7 57.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 544 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A VAL* 5.7 0.9 - - + -
521A THR* 3.9 10.3 - - + -
612A GLY* 3.7 11.4 - - - -
613A GLU* 3.3 59.3 - - + +
683A LEU* 3.7 26.7 - - + -
543B ASP* 1.3 99.2 + - - +
545B VAL* 1.3 70.9 + - - +
546B PHE* 3.7 11.2 - - + -
562B LEU* 3.3 32.5 - - + -
563B GLN 3.4 9.4 - - - +
565B THR* 3.5 8.1 + - - +
585B ARG* 3.8 6.7 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
613A GLU* 4.1 11.2 - - - +
544B MET* 1.3 80.0 - - - +
546B PHE* 1.3 75.0 + - - +
547B VAL* 4.6 5.8 - - + +
561B ARG 3.6 1.0 - - - +
562B LEU* 3.4 5.8 - - - +
563B GLN* 2.9 53.7 + - + +
564B VAL 4.8 0.2 - - - +
565B THR* 3.3 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 546 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A ILE* 4.1 16.6 - - + -
383A ARG* 4.6 0.7 - - - -
521A THR* 5.6 1.3 - - - -
613A GLU* 3.4 31.7 + - + -
614A PRO 3.8 3.1 - - - -
615A LEU* 3.7 33.9 - - + -
616A PRO* 3.5 31.1 - - + +
544B MET* 3.7 13.0 - - + -
545B VAL* 1.3 80.1 - - - +
547B VAL* 1.3 61.4 + - - +
548B PRO* 3.3 11.8 - - - +
560B GLN* 3.6 28.6 + - + +
561B ARG 3.5 0.4 - - - -
562B LEU* 3.4 36.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 547 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545B VAL* 4.6 10.8 - - + -
546B PHE* 1.3 72.8 - - - +
548B PRO* 1.3 77.3 - - + +
549B MET* 3.3 19.6 + - + +
560B GLN* 4.1 0.4 - - - -
561B ARG* 2.7 42.8 + - + +
563B GLN* 2.9 39.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 548 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618A ASN* 5.8 3.1 - - + +
546B PHE 3.3 9.9 - - - +
547B VAL* 1.3 90.1 - - + +
549B MET* 1.3 60.8 - - - +
558B GLN* 3.3 22.4 - - - +
559B LEU 3.4 7.6 - - - +
560B GLN* 3.1 24.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 549 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A TYR* 5.6 0.4 - - - +
547B VAL* 3.5 32.3 - - + +
548B PRO* 1.3 72.9 - - - +
550B ALA* 1.3 64.6 + - - +
552B PRO* 6.4 1.3 - - - -
558B GLN* 3.3 9.4 + - - -
559B LEU* 2.8 45.5 + - + +
561B ARG* 3.6 39.9 - - + +
563B GLN* 4.7 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 550 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549B MET* 1.3 82.2 - - - +
551B VAL* 1.3 64.3 + - - +
552B PRO* 3.2 11.6 - - - +
555B PRO* 4.1 24.0 - - + +
557B HIS 3.5 14.6 - - - +
558B GLN* 3.6 4.9 + - - +
559B LEU* 4.2 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 551 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A LEU* 4.2 12.6 - - + -
381A THR* 5.6 1.3 - - + -
550B ALA* 1.3 72.4 - - - +
552B PRO* 1.3 69.1 - - + +
553B TRP* 2.8 50.4 + - + +
554B SER* 2.8 30.7 + - - +
555B PRO* 3.2 5.8 - - - +
557B HIS* 3.2 32.6 + - + +
558B GLN 4.0 13.7 - - - +
559B LEU* 4.0 12.8 - - + -
----------------------------------------------------------
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