Contacts of the strand formed by residues 23 - 31 (chain A) in PDB entry 7EHH
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 THR 23 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A VAL* 3.7 0.3 - - - -
19A VAL* 2.9 29.3 + - + -
20A ASN* 2.6 44.0 + - - +
21A GLU 3.7 0.2 - - - -
22A GLN* 1.3 81.8 + - - +
24A VAL* 1.3 70.6 + - - +
79A THR* 3.3 30.1 - - + -
80A VAL 3.3 7.9 - - - +
81A THR* 3.8 16.7 - - + +
128A PHE* 3.9 0.8 - - - -
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Residues in contact with VAL 24 (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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17A TYR 3.2 11.4 - - - +
18A VAL* 4.0 6.7 - - + -
19A VAL* 4.2 2.2 - - - +
23A THR* 1.3 80.6 - - - +
25A ASN* 1.3 62.6 + - - +
26A ILE* 4.4 5.8 - - + -
78A VAL 4.0 0.3 - - - +
79A THR* 3.4 5.6 - - - +
80A VAL* 2.8 45.7 + - + +
87A LEU* 3.8 28.0 - - + -
125A MET* 3.6 31.2 - - + -
128A PHE* 3.6 29.6 - - + -
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Residues in contact with ASN 25 (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 MET 4.8 0.2 - - - -
16A ALA* 3.2 6.2 + - - -
17A TYR* 2.9 69.4 + - + -
19A VAL* 3.5 19.3 - - + +
24A VAL* 1.3 71.6 - - - +
26A ILE* 1.3 61.3 + - - +
27A ARG* 5.6 0.7 - - + -
77A GLN* 3.9 14.1 - - - +
78A VAL 3.6 2.9 - - - +
79A THR* 2.8 36.7 + - - +
426A ASP* 3.6 14.8 + - - +
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Residues in contact with ILE 26 (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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9A HIS* 4.0 4.7 - - + -
15A MET 3.2 8.7 - - - +
16A ALA* 4.5 8.1 - - + -
24A VAL* 4.4 9.6 - - + -
25A ASN* 1.3 80.3 - - - +
27A ARG* 1.3 65.7 + - - +
40A LEU* 3.8 21.3 - - + -
64A MET* 3.6 2.5 - - + +
77A GLN* 3.3 3.8 - - - +
78A VAL* 2.9 42.4 + - + +
80A VAL* 4.5 2.5 - - + -
87A LEU* 3.8 28.5 - - + -
89A TYR* 3.9 19.1 - - + -
91A PHE* 3.6 34.1 - - + -
125A MET* 4.5 1.3 - - - -
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Residues in contact with ARG 27 (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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9A HIS* 2.8 27.2 + - - -
14A GLU* 3.7 25.3 + - - +
15A MET* 2.7 30.6 + - + +
17A TYR* 4.3 4.7 + - + -
25A ASN 5.6 1.1 - - - -
26A ILE* 1.3 78.8 - - - +
28A LEU* 1.3 60.9 + - - +
64A MET* 4.2 2.2 - - - -
75A PHE* 5.8 5.2 - - + -
76A TRP 3.1 12.6 - - - +
77A GLN* 2.8 26.6 + - + +
91A PHE* 4.0 1.9 - - - -
421A LEU 4.4 0.8 + - - -
422A MET* 3.2 48.2 + - - +
424A TYR 2.8 30.9 + - - -
425A ARG* 3.8 1.8 - - - +
426A ASP* 2.8 34.6 + - - +
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Residues in contact with LEU 28 (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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7A ILE* 4.1 3.1 - - + -
8A MET 3.5 18.4 - - - +
9A HIS* 3.8 9.0 - - + -
15A MET* 3.6 3.8 - - - -
27A ARG* 1.3 74.8 - - - +
29A ARG* 1.3 66.6 + - - +
30A THR* 3.9 14.8 - - + -
38A VAL* 3.7 28.0 - - + -
64A MET* 4.1 7.2 - - + +
75A PHE* 3.5 4.3 - - - -
76A TRP* 2.9 39.4 + - + +
91A PHE* 3.9 20.4 - - + -
93A VAL* 3.8 19.7 - - + -
103A TYR* 3.8 27.4 - - + -
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Residues in contact with ARG 29 (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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6A GLY 3.8 8.6 + - - +
7A ILE* 3.2 5.4 - - - +
8A MET* 3.0 65.7 + - - +
15A MET* 3.5 15.3 - - + +
28A LEU* 1.3 72.4 - - - +
30A THR* 1.3 67.5 + - - +
73A SER* 3.6 30.2 + - - +
74A ASP 3.4 4.0 - - - +
75A PHE* 3.7 27.7 - - + -
706A SO4 2.8 33.3 + - - -
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Residues in contact with THR 30 (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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6A GLY 3.3 12.1 - - - -
7A ILE* 4.1 9.4 - - + +
28A LEU* 3.9 20.6 - - + -
29A ARG* 1.3 79.9 - - - +
31A ALA* 1.3 63.7 + - - +
35A ILE* 3.7 32.9 - - + +
73A SER* 3.1 10.4 - - - -
74A ASP* 2.8 37.0 + - - +
76A TRP* 3.0 30.9 + - + +
93A VAL* 5.1 0.4 - - + -
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Residues in contact with ALA 31 (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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3A ASN* 3.6 34.3 - - + +
6A GLY* 3.5 14.1 + - - -
7A ILE* 4.8 2.0 - - - +
30A THR* 1.3 82.5 + - - +
32A LYS* 1.3 68.7 + - - +
33A ASP 3.2 0.9 + - - -
34A ASP* 3.1 31.8 + - + +
35A ILE 4.1 0.5 + - - -
72A ILE 4.0 6.1 - - - +
73A SER* 4.4 1.1 - - - +
74A ASP* 3.9 0.9 - - - +
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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