Contacts of the strand formed by residues 10 - 17 (chain A) in PDB entry 3IE7
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 ALA 10 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A PRO* 1.3 78.1 - - - +
11A ILE* 1.3 65.0 + - - +
12A ASP* 4.2 7.4 - - - +
36A CYS* 3.6 2.9 - - - -
37A GLY* 2.6 45.3 + - - +
68A LEU* 4.2 7.3 - - - +
89A THR* 3.5 3.6 - - - -
90A ARG* 3.2 37.5 - - + +
92A CYS* 4.7 5.2 - - + -
501A GOL 4.5 1.6 - - - +
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Residues in contact with ILE 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ALA* 1.3 75.3 - - - +
12A ASP* 1.3 63.0 + - - +
34A PHE* 4.0 19.1 - - + -
35A ASP 3.8 3.4 - - - -
36A CYS* 4.8 0.2 - - - +
64A ASN* 3.8 24.7 - - - +
67A LYS* 3.6 37.0 - - + -
68A LEU* 4.0 24.9 - - + +
71A ILE* 3.6 24.7 - - + -
89A THR* 4.4 6.7 - - + -
90A ARG 2.9 7.2 + - - +
91A GLU* 3.2 23.8 - - + +
92A CYS 2.9 20.3 + - - -
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Residues in contact with ASP 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ALA* 4.0 0.7 - - - +
11A ILE* 1.3 72.5 - - - +
13A ARG* 1.3 59.9 + - - +
14A LEU* 3.9 15.2 + - + -
34A PHE* 3.3 9.5 - - - -
35A ASP* 2.8 42.9 + - + +
36A CYS 3.1 20.9 - - - +
37A GLY* 3.7 4.1 - - - -
42A HIS* 3.8 3.1 + - - -
92A CYS* 3.2 24.0 - - - +
94A VAL* 4.6 5.6 - - + -
287A SER* 4.8 1.6 + - - -
501A GOL 2.6 42.4 + - - -
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Residues in contact with ARG 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ILE 3.8 1.2 + - - -
12A ASP* 1.3 73.4 - - - +
14A LEU* 1.3 60.4 + - - +
15A LEU* 3.5 24.5 + - + +
32A THR* 3.4 28.9 + - + +
33A GLU 3.5 2.9 - - - -
34A PHE* 3.4 32.7 - - + -
67A LYS* 4.5 8.1 - - - +
91A GLU* 3.0 36.0 + - - +
92A CYS 2.9 7.0 + - - +
93A PHE* 3.6 26.0 - - + -
94A VAL* 3.0 22.2 + - - -
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Residues in contact with LEU 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ASP* 4.1 21.8 - - + +
13A ARG* 1.3 73.3 - - - +
15A LEU* 1.3 61.2 + - - +
16A PHE* 3.8 29.5 + - + -
31A LYS 3.7 1.0 - - - +
32A THR* 3.3 9.7 - - - +
33A GLU* 2.7 46.9 + - + +
34A PHE 4.8 0.2 - - - -
35A ASP* 4.2 15.7 - - + +
94A VAL* 3.3 22.4 - - + +
96A LEU* 4.2 9.6 - - + -
286A ASP* 3.8 30.1 - - + -
287A SER* 5.3 4.9 - - - +
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Residues in contact with LEU 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ARG* 3.7 34.3 - - + +
14A LEU* 1.3 71.6 - - - +
16A PHE* 1.3 61.5 + - - +
17A ILE* 3.7 2.6 + - + +
29A VAL* 4.2 23.6 - - + -
31A LYS 4.0 2.2 - - - -
32A THR* 3.9 17.0 - - - +
93A PHE* 4.4 23.6 - - + -
94A VAL 2.7 11.3 + - - +
95A VAL* 3.4 26.5 - - + +
96A LEU* 3.1 24.8 + - - +
106A ILE* 6.3 0.2 - - + -
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Residues in contact with PHE 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LEU* 3.8 25.1 - - + -
15A LEU* 1.3 71.0 - - - +
17A ILE* 1.3 56.9 + - - +
29A VAL* 3.4 3.3 - - - +
30A ILE* 2.6 39.1 + - + +
31A LYS* 3.1 53.7 + - + +
33A GLU* 3.3 37.7 - - + -
96A LEU* 3.1 37.9 - - + -
97A SER* 4.8 2.2 - - - -
98A ASP* 4.0 24.0 - - - +
285A GLN* 4.3 14.6 - - + -
286A ASP* 6.0 0.7 - - + -
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Residues in contact with ILE 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A LEU* 4.1 8.1 - - + +
16A PHE* 1.3 80.0 - - - +
18A ARG* 1.3 60.5 + - - +
19A GLY 3.8 15.9 - - - +
20A GLU 3.9 3.6 - - - +
21A LEU* 3.7 28.9 - - + +
27A ASN* 4.0 27.1 - - + +
28A ARG 3.5 22.4 - - - +
29A VAL* 4.3 7.6 - - + -
30A ILE* 4.2 5.0 - - - +
95A VAL* 3.7 23.1 - - + -
96A LEU 2.9 17.4 + - - +
97A SER* 2.7 28.2 + - - -
98A ASP 4.3 1.6 + - - -
99A ASP* 4.3 0.2 - - - +
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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