Contacts of the strand formed by residues 31 - 37 (chain E) in PDB entry 1Y62
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 GLN 31 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25E TYR* 3.5 8.8 - - - -
26E ASN* 2.8 36.3 + - - +
29E ARG* 3.2 25.9 - - - +
30E LYS* 1.3 84.4 - - - +
32E CYS* 1.3 62.6 + - - +
33E LEU* 3.6 26.7 + - + +
54E GLN* 5.3 6.7 + - - -
58E LEU* 5.0 10.2 - - - +
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Residues in contact with CYS 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E ILE* 3.5 11.6 - - + +
24E TYR 3.3 5.6 - - - -
25E TYR* 4.0 12.6 - - - -
31E GLN* 1.3 76.2 + - - +
33E LEU* 1.3 65.7 + - - +
50E THR* 3.8 25.9 - - + +
53E CYS* 2.0 61.9 - - + -
54E GLN* 3.6 13.0 - - + +
58E LEU* 5.1 3.4 - - - +
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Residues in contact with LEU 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E ILE* 3.3 6.7 - - - -
24E TYR* 2.9 54.1 + - + +
26E ASN* 3.7 27.8 - - + -
29E ARG* 3.6 33.0 - - - +
31E GLN* 3.6 21.2 + - + +
32E CYS* 1.3 81.2 - - - +
34E ARG* 1.3 64.4 + - - +
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Residues in contact with ARG 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E LYS* 3.8 41.8 - - + +
22E ARG 3.2 7.6 - - - +
23E ILE* 3.5 21.3 - - + +
24E TYR* 3.4 8.1 - - - -
33E LEU* 1.3 80.0 - - - +
35E PHE* 1.3 66.4 + - - +
109E SO4 5.1 14.1 + - - -
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Residues in contact with PHE 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E ALA* 4.1 13.9 - - + -
12E ASP 3.3 31.0 - - - -
13E SER* 4.6 1.6 - - - -
21E LYS* 3.6 7.3 - - - +
22E ARG* 3.1 60.9 + - + -
23E ILE 3.7 15.0 - - - -
24E TYR* 3.5 31.0 - + + -
34E ARG* 1.3 77.1 - - - +
36E ASP* 1.3 87.4 + - - +
37E TYR* 4.1 7.2 - - + -
45E ASN 4.2 6.7 - - - -
46E ASN* 3.6 25.6 - - + -
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Residues in contact with ASP 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E SER* 2.8 30.9 + - - +
19E ALA* 5.2 7.4 - - - +
20E GLU 3.4 13.2 + - - +
21E LYS* 3.3 30.1 + - - -
35E PHE* 1.3 83.2 - - - +
37E TYR* 1.3 59.5 + - - +
38E THR* 5.8 0.4 - - - -
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Residues in contact with TYR 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E ASP 3.8 14.1 - - - -
13E SER 3.3 18.6 - - - -
18E LYS 3.6 1.1 - - - +
20E GLU* 2.8 43.9 + - + +
22E ARG* 3.3 52.3 - - + -
35E PHE* 3.7 4.7 + + + -
36E ASP* 1.3 74.6 - - - +
38E THR* 1.3 59.5 + - - +
39E GLY* 3.3 27.3 + - - -
40E GLN* 3.3 21.5 + - - -
41E GLY 2.6 31.2 + - - -
42E GLY* 4.5 0.2 - - - -
46E ASN* 3.4 25.6 - - - -
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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
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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