Contacts of the helix formed by residues 538 - 552 (chain B) in PDB entry 1IGN
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 538 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526B PHE* 3.7 28.1 - - + +
527B LYS* 3.8 24.0 + - - +
530B ALA* 3.4 17.8 - - + +
537B THR* 1.3 74.3 - - - +
539B ASN* 1.3 69.7 + - - +
541B TRP* 3.4 2.8 + - - +
542B ARG* 3.1 23.5 + - + +
20F C 3.4 40.5 + - - +
21F C 4.9 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 539 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537B THR* 3.2 1.0 + - - -
538B GLU* 1.3 86.9 - - - +
540B ALA* 1.3 64.5 + - - +
542B ARG* 3.5 5.0 + - - +
543B ASP* 3.3 23.9 + - - +
14E C 4.0 2.0 - - + -
15E A 3.3 69.1 + - + +
16E C 4.4 17.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 540 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B PHE* 3.6 8.0 - - + -
536B HIS* 3.9 6.1 - - + +
537B THR* 3.0 27.3 + - - +
539B ASN* 1.3 77.5 - - - +
541B TRP* 1.3 63.4 + - - +
543B ASP* 3.6 1.7 + - - +
544B ARG* 3.2 24.1 + - - +
13E A 4.3 3.7 - - + +
14E C 3.2 47.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 541 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B PHE* 3.5 23.6 - + - -
453B GLU* 3.5 46.7 - - + -
454B ASP* 5.3 0.2 - - - -
456B THR* 5.8 0.7 - - - -
457B LEU* 4.1 19.6 - - + +
526B PHE* 4.0 17.0 - - + +
529B PHE* 3.6 32.5 - + + -
530B ALA* 3.7 17.4 - - + +
533B HIS* 3.0 35.5 + - + -
535B ALA* 5.1 1.3 - - + -
536B HIS* 3.3 34.2 + + + +
537B THR 3.0 26.5 + - - +
538B GLU* 3.8 4.5 - - - +
540B ALA* 1.3 77.0 - - - +
542B ARG* 1.3 63.7 + - - +
544B ARG* 3.4 4.3 + - - +
545B PHE* 3.1 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 542 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526B PHE* 3.8 41.0 - - + -
538B GLU* 3.1 17.4 + - + +
539B ASN* 4.0 5.8 - - - +
540B ALA 3.3 0.2 - - - -
541B TRP* 1.3 76.8 - - - +
543B ASP* 1.3 57.7 + - - +
545B PHE* 3.0 4.7 + - - +
546B ARG* 2.9 58.6 + - + +
16E C 4.2 9.1 - - - +
17E C 4.5 0.6 - - - +
21F C 6.0 1.1 - - - -
22F T 3.6 51.0 + - - +
23F G 2.5 42.2 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
539B ASN 3.3 10.4 + - - +
540B ALA 4.2 2.0 - - - +
542B ARG* 1.3 78.2 - - - +
544B ARG* 1.3 55.8 + - - +
546B ARG* 4.0 10.1 + - - +
547B LYS* 2.7 76.7 + - - +
548B PHE* 5.1 0.8 - - - -
13E A 4.4 5.7 - - + +
14E C 2.9 43.3 + - + -
15E A 3.2 14.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 544 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B PHE* 3.5 41.7 + - + +
454B ASP* 2.8 43.8 + - - +
457B LEU* 4.3 9.6 - - + -
540B ALA 3.2 17.8 + - - +
541B TRP* 3.6 6.5 - - - +
543B ASP* 1.3 76.4 - - - +
545B PHE* 1.3 57.0 + - - +
548B PHE* 3.1 51.0 + - + +
549B LEU* 2.9 23.2 + - - +
573B PRO* 4.1 3.4 - - - +
574B MET* 2.9 24.7 + - + +
575B LYS* 5.9 0.6 - - - +
13E A 2.9 34.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 545 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457B LEU* 4.1 6.7 - - + +
461B VAL* 3.8 31.0 - - + -
465B PHE* 4.8 0.7 - + - -
518B ARG 3.7 21.3 - - - -
521B ILE* 4.0 24.9 - - + -
526B PHE* 3.7 23.3 - + + -
541B TRP 3.1 11.4 + - - +
542B ARG 3.0 9.9 + - - +
544B ARG* 1.3 76.9 - - - +
546B ARG* 1.3 78.8 + - + +
549B LEU* 3.3 25.1 + - + -
550B LEU* 2.8 62.2 + - + +
554B ILE* 4.3 4.0 - - + -
22F T 5.6 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 546 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518B ARG* 4.3 14.2 + - - +
542B ARG* 2.9 53.2 + - + +
543B ASP* 3.8 12.1 + - - +
545B PHE* 1.3 90.6 - - + +
547B LYS* 1.3 82.9 + - - +
550B LEU* 3.7 20.2 - - - +
551B ALA* 4.7 2.1 + - - +
15E A 4.6 0.8 - - - +
16E C 4.6 0.4 - - - +
23F G 3.4 40.4 + - - +
24F G 2.9 49.3 + - - -
25F T 3.9 5.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 547 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543B ASP* 2.7 56.2 + - - +
546B ARG* 1.3 100.9 - - - +
548B PHE* 1.3 75.4 + - + +
551B ALA* 3.5 19.2 - - - +
577B LEU* 4.3 12.3 - - - +
578B THR* 5.9 4.9 - - - -
14E C 4.8 1.6 - - - +
25F T 2.9 35.4 + - - +
26F G 5.5 0.2 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
543B ASP* 5.8 0.7 - - - -
544B ARG* 3.1 53.7 + - - +
546B ARG 3.7 0.2 - - - -
547B LYS* 1.3 94.3 - - + +
549B LEU* 1.3 68.0 + - - +
550B LEU 3.3 0.7 - - - -
551B ALA* 3.1 2.1 + - - +
552B TYR* 2.9 21.0 + - - +
574B MET* 3.5 22.8 - - + +
575B LYS* 4.5 5.2 - - - -
577B LEU* 3.8 28.6 - - + +
578B THR* 4.0 8.1 - - - -
12E C 3.6 56.8 - - + -
13E A 3.8 10.8 - + - -
----------------------------------------------------------
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
----------------------------------------------------------
454B ASP 4.7 1.8 - - - +
457B LEU* 3.6 35.4 - - + +
458B ALA* 3.7 29.8 - - + +
461B VAL* 4.2 3.4 - - + -
544B ARG 2.9 10.0 + - - +
545B PHE* 3.5 30.1 - - + +
548B PHE* 1.3 72.4 - - - +
550B LEU* 1.3 60.0 + - - +
553B GLY* 2.8 32.2 + - - +
554B ILE* 3.7 29.5 + - + -
557B TYR* 4.7 6.3 - - + -
574B MET* 3.7 20.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 550 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465B PHE* 5.8 0.2 - - + -
517B ARG 4.7 4.5 - - - +
518B ARG* 3.4 58.8 - - + +
545B PHE* 2.8 62.8 + - + +
546B ARG* 3.7 12.3 - - + +
549B LEU* 1.3 73.3 - - - +
551B ALA* 1.3 61.9 + - - +
553B GLY* 4.1 6.7 + - - -
554B ILE* 4.5 14.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 551 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546B ARG 4.7 1.3 + - - +
547B LYS 3.5 23.8 + - - +
548B PHE* 3.1 4.6 + - - +
550B LEU* 1.3 78.3 - - - +
552B TYR* 1.3 61.9 + - - +
577B LEU* 4.6 17.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 552 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548B PHE 2.9 15.3 + - - +
549B LEU 4.3 0.2 - - - +
551B ALA* 1.3 78.6 - - - +
553B GLY* 1.3 57.4 + - - +
556B ASP* 3.3 25.0 - - + +
557B TYR* 3.5 46.2 - + + -
560B TYR* 3.9 23.8 - + - +
574B MET* 3.6 27.4 - - + -
577B LEU* 4.3 17.0 - - + +
----------------------------------------------------------
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