Contacts of the strand formed by residues 14 - 23 (chain E) in PDB entry 2PY2
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 ARG 14 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10E MET* 3.5 5.0 - - - +
11E PHE 2.9 30.3 + - - +
12E ASN 4.7 7.2 - - - +
13E GLY* 1.3 83.6 - - - +
15E CYS* 1.3 66.1 + - - +
16E PHE* 3.5 38.4 - - + -
41E SER* 2.6 43.1 + - - +
43E HIS* 3.6 12.9 + - - -
47E GLU* 3.4 29.7 + - - -
79E ASP* 4.6 5.1 + - - -
81E THR* 5.9 2.6 - - - +
126E ALA* 4.5 7.3 - - - +
127E LYS* 3.4 15.0 - - - +
128E PRO* 4.3 8.3 - - + -
129E LEU* 4.1 0.6 - - - +
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Residues in contact with CYS 15 (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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4E CYS* 2.0 50.0 - - + -
5E PRO* 4.0 7.9 - - + -
8E TRP* 3.5 19.7 - - + -
9E LYS 3.3 5.6 - - - -
14E ARG* 1.3 73.7 - - - +
16E PHE* 1.3 61.8 + - - +
126E ALA* 3.1 6.2 - - - +
127E LYS* 2.8 36.5 + - + +
128E PRO 4.7 1.8 - - - -
129E LEU* 3.4 25.1 - - - -
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Residues in contact with PHE 16 (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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7E ASP 4.5 0.5 - - - +
8E TRP* 3.4 6.5 - - - -
9E LYS* 2.7 40.4 + - - +
11E PHE* 3.6 28.3 - + + -
14E ARG* 3.5 57.0 - - + -
15E CYS* 1.3 76.7 - - - +
17E LEU* 1.3 61.7 + - - +
40E ALA* 4.2 9.9 - - + -
41E SER 4.5 1.8 - - - -
47E GLU* 5.3 5.2 - - + -
50E PHE* 3.4 20.2 - + + -
51E VAL* 4.0 25.8 - - + -
54E LEU* 3.7 21.2 - - + +
124E ILE* 4.4 2.7 - - + -
125E CYS 3.2 6.7 - - - +
126E ALA* 3.7 15.5 - - + -
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Residues in contact with LEU 17 (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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7E ASP* 3.2 33.4 - - + +
8E TRP* 3.7 40.8 - - + +
16E PHE* 1.3 75.9 - - - +
18E PHE* 1.3 77.1 + - - +
19E ASN* 3.7 5.1 + - + +
35E GLU* 5.6 4.5 - - + -
54E LEU* 4.8 4.0 - - - -
124E ILE* 3.6 3.1 - - - -
125E CYS* 2.8 45.3 + - + +
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Residues in contact with PHE 18 (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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17E LEU* 1.3 86.9 - - - +
19E ASN* 1.3 58.1 + - - +
20E PRO* 3.4 34.6 - - + +
54E LEU* 3.4 33.9 - - + +
55E THR* 3.9 16.2 - - + -
56E SER* 5.9 0.7 - - - -
60E ILE* 3.8 27.6 - - + -
62E SER* 3.4 23.1 - - - -
122E SER* 3.6 27.1 - - - -
123E SER 3.6 6.3 - - - -
124E ILE* 3.7 21.3 - - + -
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Residues in contact with ASN 19 (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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17E LEU* 3.7 6.0 + - + +
18E PHE* 1.3 72.3 - - - +
20E PRO* 1.3 66.9 - - - +
21E LEU* 3.0 31.1 + - - +
23E LEU* 4.0 9.7 - - - +
28E ALA 5.2 0.2 - - - +
31E SER* 3.4 26.9 + - - -
122E SER* 3.2 3.1 - - - -
123E SER* 2.8 51.2 + - - +
125E CYS* 4.7 12.5 - - - -
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Residues in contact with PRO 20 (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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18E PHE* 3.4 33.2 - - + +
19E ASN* 1.3 86.0 - - - +
21E LEU* 1.3 65.0 + - + +
22E GLN* 2.8 22.0 + - - +
60E ILE* 6.1 0.7 - - + -
122E SER* 3.1 8.5 + - - +
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Residues in contact with LEU 21 (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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19E ASN* 3.0 24.9 + - - +
20E PRO* 1.3 82.5 - - + +
22E GLN* 1.3 61.2 + - - +
23E LEU* 3.4 32.1 + - + +
31E SER* 5.3 4.0 - - - +
34E LYS* 6.2 2.0 - - - +
121E HIS 3.2 14.0 - - - +
122E SER* 3.3 5.0 - - - -
123E SER* 4.6 1.0 + - - -
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Residues in contact with GLN 22 (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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20E PRO 2.8 25.6 + - - +
21E LEU* 1.3 71.2 - - - +
23E LEU* 1.3 66.3 + - - +
60E ILE* 5.4 1.6 - - - +
120E LEU* 3.8 36.9 - - + +
121E HIS* 3.6 7.4 + - - -
122E SER* 2.9 20.9 + - - +
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Residues in contact with LEU 23 (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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19E ASN* 4.0 18.8 - - - +
21E LEU* 4.0 30.7 - - + +
22E GLN* 1.3 83.1 - - - +
24E HIS* 1.3 68.7 + - - +
27E ASP* 3.7 37.0 - - + +
28E ALA* 3.9 13.5 - - + +
31E SER* 4.1 7.6 - - - -
63E TRP* 3.0 10.7 + - - -
120E LEU* 3.8 8.5 - - - -
121E HIS 3.0 26.8 + - - +
123E SER* 5.5 0.7 - - - +
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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