Contacts of the helix formed by residues 28 - 37 (chain S) in PDB entry 6Y5D
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 VAL 28 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18S ARG* 3.6 43.3 - - + +
19S SER* 3.7 12.6 + - - +
22S ALA* 4.2 4.0 - - + -
24S LEU* 4.1 24.2 - - + -
26S PHE 4.1 0.4 - - - +
27S PRO* 1.3 76.5 - - - +
29S GLY* 1.3 63.6 + - - +
30S ARG 3.1 1.6 - - - -
31S VAL* 3.1 5.7 + - - +
32S HIS* 2.9 25.1 + - - +
49S PRO* 3.6 14.9 - - + +
50S VAL* 3.6 28.9 - - + +
53S ALA* 4.2 3.6 - - + -
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Residues in contact with GLY 29 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18S ARG* 3.7 28.7 - - - +
28S VAL* 1.3 78.6 - - - +
30S ARG* 1.3 56.3 + - - +
32S HIS* 3.3 3.3 + - - +
33S ARG* 3.0 27.9 + - - +
33V G 5.2 11.2 + - - -
34V A 4.4 9.2 + - - -
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Residues in contact with ARG 30 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27S PRO* 3.8 25.5 - - + +
28S VAL 3.1 0.6 - - - +
29S GLY* 1.3 74.3 - - - +
31S VAL* 1.3 60.3 + - - +
33S ARG* 3.2 24.3 + - - +
34S LEU* 2.8 41.8 + - + +
36T GLU* 3.9 23.5 + - - +
37T SER* 2.6 34.8 + - - +
38T TYR* 4.0 20.6 - - - +
40T VAL* 5.9 0.2 - - - +
41T TYR* 3.5 29.3 + - - -
125U G 4.9 4.4 + - - -
126U C 3.3 24.5 + - - -
33V G 4.7 11.7 + - - +
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Residues in contact with VAL 31 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26S PHE* 5.7 0.2 - - + -
27S PRO* 3.1 26.5 - - + +
28S VAL 3.1 8.1 + - - +
30S ARG* 1.3 77.0 - - - +
32S HIS* 1.3 54.2 + - - +
34S LEU* 3.1 7.7 + - + +
35S LEU* 2.7 34.4 + - + +
49S PRO* 3.5 26.0 - - + +
52S MET* 3.5 31.2 - - + -
53S ALA* 4.3 8.7 - - + -
56S LEU* 4.5 12.8 - - + -
38T TYR* 4.5 15.0 - - + +
71T PHE* 4.4 1.8 - - + -
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Residues in contact with HIS 32 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18S ARG* 3.0 33.9 + - - +
28S VAL 2.9 6.0 + - - +
29S GLY 3.4 9.4 - - - +
31S VAL* 1.3 75.3 - - - +
33S ARG* 1.3 62.9 + - - +
35S LEU* 3.2 2.7 + - - +
36S ARG* 3.1 49.7 + - - +
44S VAL* 3.1 40.3 + - + +
45S GLY 4.1 3.1 + - - -
46S ALA* 4.7 8.7 - - + -
49S PRO* 3.3 32.0 - - + +
116U A 4.8 4.0 + - - -
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Residues in contact with ARG 33 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29S GLY 3.0 14.2 + - - +
30S ARG* 3.3 25.0 + - - +
32S HIS* 1.3 77.4 - - - +
34S LEU* 1.3 67.0 + - - +
36S ARG* 3.1 21.7 - - - +
37S LYS* 3.0 65.1 + - - +
36T GLU* 2.8 33.1 + - - -
32V G 4.7 5.9 - - - -
33V G 3.9 30.8 + - - +
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Residues in contact with LEU 34 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30S ARG* 2.8 31.9 + - + +
31S VAL* 3.6 4.3 - - - +
33S ARG* 1.3 88.8 - - - +
35S LEU* 1.3 60.4 + - - +
37S LYS* 2.8 49.4 - - - +
40S TYR* 3.6 6.1 - - - -
38T TYR* 2.9 32.1 - - + +
68T ASN* 5.4 2.7 - - - +
71T PHE* 3.4 30.3 - - + -
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Residues in contact with LEU 35 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31S VAL* 2.7 22.7 + - + +
32S HIS 3.2 4.2 + - - +
34S LEU* 1.3 72.7 - - - +
36S ARG* 1.3 62.2 + - - +
37S LYS 3.1 7.3 - - - +
40S TYR* 3.3 22.6 + - + +
41S ALA 4.3 1.0 + - - -
44S VAL* 3.8 26.4 - - + +
48S ALA* 3.8 11.2 - - + +
49S PRO* 3.6 37.0 - - + -
52S MET* 3.7 31.4 - - + -
71T PHE* 4.2 1.1 - - + -
75T ALA* 3.9 17.7 - - + -
90T ILE* 4.6 8.2 - - + +
95T ILE* 4.1 12.3 - - + -
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Residues in contact with ARG 36 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18S ARG* 5.6 1.0 - - - +
32S HIS* 3.1 55.3 + - - +
33S ARG* 3.1 26.0 - - - +
35S LEU* 1.3 76.0 - - - +
37S LYS* 1.3 63.6 + - + +
39S ASN* 4.1 7.1 + - - +
41S ALA 3.9 16.4 - - - +
42S GLU 5.8 2.7 - - - +
43S ARG 5.7 0.4 - - - -
44S VAL* 3.6 18.6 - - + +
116U A 4.4 19.5 + - - +
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Residues in contact with LYS 37 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83P HIS* 5.6 0.9 - - - -
33S ARG* 3.0 50.9 + - - +
34S LEU* 2.8 36.9 - - + +
35S LEU 3.1 0.5 - - - +
36S ARG* 1.3 80.0 - - + +
38S GLY* 1.3 59.9 + - - +
39S ASN 2.9 9.5 + - - +
40S TYR* 2.9 14.6 - - - -
702S PTD 1.3 82.1 - - + +
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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
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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) + - + + + + + -
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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