Contacts of the strand formed by residues 75 - 83 (chain A) in PDB entry 2D7Q
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 GLY 75 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A PRO* 4.4 11.4 - - - -
73A ALA 3.3 6.2 + - - -
74A PRO* 1.3 74.8 - - - +
76A ASN* 1.3 64.3 - - - -
77A TYR* 4.0 6.9 + - - -
96A ALA 3.4 2.1 - - - +
97A LYS* 3.4 6.2 - - - +
98A VAL 2.9 31.2 + - - +
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Residues in contact with ASN 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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49A ASP 3.7 6.6 - - - +
50A GLY* 4.1 6.9 - - - -
51A PRO* 4.5 4.0 - - - +
75A GLY* 1.3 74.6 - - - -
77A TYR* 1.3 63.7 + - - +
78A LEU 3.8 1.0 + - - -
95A LYS* 3.2 43.6 + - + -
96A ALA 3.3 5.8 - - - +
97A LYS* 4.3 8.1 - - + +
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Residues in contact with TYR 77 (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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48A ILE* 3.7 27.4 - - + -
49A ASP 3.2 4.0 - - - -
50A GLY* 3.6 21.8 - - - -
51A PRO* 3.9 8.0 - - + +
52A SER 3.3 25.4 + - - -
54A VAL* 3.3 13.9 - - + -
69A TYR* 5.2 7.9 - + + +
71A PRO* 4.5 4.7 - - + -
72A MET 3.7 6.4 + - - -
73A ALA* 2.7 45.0 + - - +
75A GLY 4.0 11.9 - - - -
76A ASN* 1.3 72.4 - - - +
78A LEU* 1.3 63.3 + - - +
79A ILE* 3.3 5.5 + - + +
95A LYS* 3.7 1.5 - - - -
96A ALA* 2.8 52.3 + - + +
98A VAL* 4.2 19.1 - - + -
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Residues in contact with LEU 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A THR 3.4 2.1 - - - +
48A ILE* 3.3 6.2 - - - -
49A ASP* 2.8 41.5 + - + +
76A ASN 3.8 1.8 + - - +
77A TYR* 1.3 69.6 - - - +
79A ILE* 1.3 66.1 + - - +
80A ALA* 3.6 8.3 + - + +
88A HIS* 5.5 0.4 - - + -
93A PRO* 3.3 39.9 - - + -
94A PHE 3.9 0.4 - - - +
95A LYS* 4.2 33.9 - - + +
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Residues in contact with ILE 79 (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 GLY 3.0 33.9 - - - +
21A LEU* 3.8 15.0 - - + -
32A PHE* 3.8 33.2 - - + -
46A VAL* 4.6 3.1 - - + -
47A THR 3.3 9.0 - - - +
48A ILE* 4.1 16.8 - - + -
69A TYR* 4.2 9.2 - - + -
77A TYR* 3.9 7.4 - - + +
78A LEU* 1.3 73.5 - - - +
80A ALA* 1.3 62.3 + - - +
81A ILE* 3.8 11.6 + - + +
93A PRO* 3.9 0.2 - - - +
94A PHE* 2.8 40.6 + - + +
96A ALA* 3.7 11.2 - - + -
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Residues in contact with ALA 80 (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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45A SER 3.3 6.8 - - - +
46A VAL* 3.4 2.4 - - - +
47A THR* 3.1 43.4 + - - +
78A LEU* 3.6 10.5 + - + +
79A ILE* 1.3 69.5 - - - +
81A ILE* 1.3 67.3 + - - +
82A LYS* 5.0 8.3 - - - +
88A HIS* 3.7 26.2 - - + -
93A PRO* 4.5 0.9 - - - -
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Residues in contact with ILE 81 (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 VAL* 5.6 0.4 - - + -
16A ALA* 3.7 17.7 - - + -
21A LEU* 3.7 30.5 - - + -
32A PHE* 4.1 9.9 - - + -
34A VAL* 4.5 11.7 - - + -
44A LEU* 3.6 22.7 - - + -
45A SER 3.5 2.7 - - - +
46A VAL* 4.8 4.9 - - + -
79A ILE* 4.0 9.6 - - + +
80A ALA* 1.3 80.9 - - - +
82A LYS* 1.3 66.6 + - - +
88A HIS* 3.8 3.0 + - - -
89A ILE* 3.2 40.7 + - + +
92A SER* 3.4 16.3 + - - +
94A PHE* 3.8 13.2 - - + -
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Residues in contact with LYS 82 (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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44A LEU* 3.0 23.5 - - - +
45A SER* 3.1 38.3 + - - +
47A THR* 5.7 1.4 + - - -
80A ALA* 5.0 7.2 - - - +
81A ILE* 1.3 81.3 - - - +
83A TYR* 1.3 61.3 + - - +
85A GLY 3.9 6.7 - - - +
86A PRO* 3.4 21.3 - - + +
87A GLN 3.2 22.4 - - - +
88A HIS* 3.4 34.0 + - + +
89A ILE* 3.9 4.9 - - - -
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Residues in contact with TYR 83 (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 GLY* 5.7 0.2 - - - -
10A ASP 4.9 7.2 - - - -
11A PRO* 3.6 18.2 - - + +
14A VAL* 3.8 23.1 - - + -
36A THR* 3.7 32.1 + - + -
39A ALA* 3.9 17.5 - - + -
40A GLY 4.6 0.9 - - - -
41A SER* 2.9 25.5 + - - -
42A GLY* 2.7 41.1 + - - -
43A ALA 2.9 22.7 - - - -
44A LEU* 3.9 13.5 - - + -
65A HIS* 4.8 5.7 + + - -
82A LYS* 1.3 75.5 - - - +
84A GLY* 1.3 74.0 + - - +
85A GLY* 3.0 5.3 + - - -
87A GLN 4.5 1.9 + - - +
89A ILE* 3.7 17.4 - - + +
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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