Contacts of the strand formed by residues 67 - 76 (chain A) in PDB entry 2A1A
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 ASN 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A MET* 4.2 11.3 - - - +
21A VAL 3.2 5.2 - - - +
22A ASN* 2.9 34.6 - - - +
36A LEU* 3.4 22.2 - - - +
66A LYS* 1.3 91.9 + - - +
68A ASP* 1.3 66.1 + - - +
101A TYR* 4.4 12.5 + - - -
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Residues in contact with ASP 68 (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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20A MET* 3.4 6.2 - - - +
21A VAL* 2.7 48.1 + - + +
23A VAL* 4.5 9.3 - - + +
45A ILE* 5.2 2.9 - - + -
62A ILE* 3.3 22.3 - - - +
63A ARG 5.2 0.5 + - - -
66A LYS* 4.9 6.3 + - - -
67A ASN* 1.3 78.6 - - - +
69A VAL* 1.3 68.6 + - - +
86A LYS* 2.8 44.2 + - - -
94A ILE* 6.2 0.3 - - - +
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Residues in contact with VAL 69 (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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18A ILE* 3.1 34.3 - - + -
19A VAL 3.5 2.7 - - - -
20A MET* 4.1 22.9 - - + -
68A ASP* 1.3 85.5 + - - +
70A ALA* 1.3 60.2 - - - +
86A LYS* 3.5 22.2 - - - +
89A VAL* 4.2 12.3 - - + +
94A ILE* 4.2 38.1 - - + +
97A CYS* 3.7 20.4 - - + -
98A GLU* 5.0 3.1 - - + +
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Residues in contact with ALA 70 (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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18A ILE* 3.2 2.9 - - - -
19A VAL* 2.7 42.2 + - + +
21A VAL* 4.8 4.9 - - + -
45A ILE* 4.5 16.2 - - + -
68A ASP 4.3 0.2 - - - -
69A VAL* 1.3 76.2 - - - +
71A VAL* 1.3 60.9 + - - +
84A LEU* 4.0 27.4 - - + -
85A SER 3.4 14.6 - - - +
86A LYS* 4.9 0.2 - - - -
89A VAL* 3.7 7.6 - - - -
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Residues in contact with VAL 71 (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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16A ASP* 3.6 34.1 - - - +
17A ASP 3.3 2.7 - - - +
18A ILE* 4.4 7.0 - - + +
70A ALA* 1.3 73.0 - - - +
72A VAL* 1.3 70.7 + - - +
73A LEU* 5.6 1.3 - - + -
84A LEU* 3.2 7.4 - - - +
85A SER* 2.7 45.6 + - - +
88A ARG* 4.0 18.4 - - + -
89A VAL* 3.1 37.2 - - + +
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Residues in contact with VAL 72 (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 PRO* 3.8 24.2 - - + -
14A GLU 3.4 24.5 - - - +
15A ILE* 4.0 2.9 - - - +
16A ASP* 3.0 24.4 + - - +
17A ASP* 2.8 22.1 + - + +
19A VAL* 3.9 7.9 - - + -
71A VAL* 1.3 75.2 - - - +
73A LEU* 1.3 62.7 + - - +
74A ARG 4.0 4.5 - - - +
75A VAL* 3.4 32.8 - - + -
82A ILE* 4.1 11.0 - - + -
84A LEU* 3.7 17.9 - - + -
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Residues in contact with LEU 73 (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 ILE* 3.7 23.8 - - - +
46A LEU* 4.2 19.7 - - + -
71A VAL* 4.4 2.5 - - + +
72A VAL* 1.3 76.3 - - - +
74A ARG* 1.3 76.5 + - + +
83A ASP* 2.9 16.0 + - + +
84A LEU* 3.3 34.1 - - - +
85A SER* 3.5 17.3 - - - +
87A ARG* 4.8 2.0 - - - +
88A ARG* 3.5 44.9 - - - +
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Residues in contact with ARG 74 (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 ILE* 4.4 8.5 - - + -
46A LEU* 5.1 4.8 - - - +
72A VAL* 3.7 1.2 - - - +
73A LEU* 1.3 98.3 - - - +
75A VAL* 1.3 65.7 + - - +
76A ASP 4.1 0.7 - - - -
81A TYR 4.7 0.2 - - - -
82A ILE* 3.4 7.6 - - - +
83A ASP* 2.9 63.2 + - + +
379B GLU* 3.0 31.7 + - - +
382B ARG* 3.5 22.8 - - - +
486B ASP 3.2 22.2 + - - -
487B THR* 4.3 6.1 - - + -
488B ALA* 4.7 3.2 - - - +
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Residues in contact with VAL 75 (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 TYR* 4.1 35.0 - - + -
13A PRO* 3.4 21.1 - - + +
15A ILE* 4.6 13.2 - - + +
72A VAL* 3.4 21.3 - - + -
74A ARG* 1.3 79.6 - - - +
76A ASP* 1.3 60.5 - - - +
77A LYS* 3.8 19.6 + - + +
81A TYR 3.7 2.7 - - - +
82A ILE* 4.3 12.8 - - + -
487B THR* 5.1 0.4 - - - -
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Residues in contact with ASP 76 (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 TYR* 5.9 0.2 - - - -
74A ARG 4.1 0.6 - - - -
75A VAL* 1.3 71.8 - - - +
77A LYS* 1.3 58.9 + - - +
78A GLU* 3.1 22.2 + - - +
79A LYS* 3.1 27.8 + - - +
80A GLY* 2.8 24.6 + - - -
81A TYR* 2.9 23.4 + - + +
486B ASP* 3.6 28.9 - - + +
487B THR* 3.8 17.4 + - + +
490B GLU* 4.2 4.0 - - - +
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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