Contacts of the strand formed by residues 77 - 84 (chain A) in PDB entry 1DG3
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 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A ILE 3.3 7.9 - - - -
16A ASN* 3.8 16.8 - - - +
76A LYS* 1.3 77.7 - - - +
78A ILE* 1.3 64.4 + - - +
79A TRP* 4.1 2.0 - - - -
97A ASP 3.6 0.5 - - - +
98A THR* 3.4 5.5 - - - -
99A GLU* 2.8 37.4 + - - +
115A ILE* 3.9 13.0 - - - +
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Residues in contact with ILE 78 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A CYS* 3.8 0.5 - - - -
13A LEU* 2.8 31.2 + - + +
14A ILE* 2.9 32.4 + - + +
77A GLY* 1.3 76.5 - - - +
79A TRP* 1.3 73.5 + - - +
96A LEU* 4.0 28.7 - - + -
97A ASP 3.4 6.3 - - - +
98A THR* 4.7 5.4 - - + -
115A ILE* 3.7 38.8 - - + +
118A LEU* 4.0 19.5 - - + -
119A ALA* 4.0 13.9 - - + +
122A LEU* 4.9 4.7 - - + -
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Residues in contact with TRP 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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10A PRO* 3.7 28.0 - - + -
11A MET* 3.3 14.4 - - - -
12A CYS* 3.3 35.4 - - + -
55A MET* 5.4 0.4 - - - -
74A HIS* 3.9 30.5 - + - -
75A THR* 2.8 46.4 + - - -
76A LYS 4.3 0.8 + - - -
77A GLY 4.2 4.5 - - - -
78A ILE* 1.3 81.7 - - - +
80A MET* 1.3 60.8 + - - +
95A LEU 3.6 0.3 - - - +
96A LEU* 3.2 5.0 - - - -
97A ASP* 2.8 44.2 + - + +
99A GLU* 3.3 28.8 - - + +
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Residues in contact with MET 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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7A MET* 3.8 14.1 - - + +
10A PRO* 3.2 3.4 - - - +
11A MET* 2.7 42.2 + - + +
13A LEU* 3.1 32.5 - - + -
27A ALA* 3.1 45.5 - - + +
30A ILE* 5.4 2.0 - - - -
31A LEU* 3.7 25.1 - - + -
55A MET* 5.4 0.2 - - - -
78A ILE 4.2 0.4 + - - -
79A TRP* 1.3 75.4 - - - +
81A TRP* 1.3 62.0 + - - +
82A CYS* 4.0 12.3 - - - -
94A VAL* 4.7 4.7 - - + -
95A LEU 3.1 4.9 - - - +
96A LEU* 3.8 19.5 - - + -
293A LEU* 5.9 0.2 - - - -
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Residues in contact with TRP 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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7A MET* 3.6 20.2 + - + -
8A THR 3.9 7.6 - - - -
9A GLY* 3.5 32.9 - - - -
10A PRO* 3.3 31.9 - - + -
55A MET* 3.9 17.0 - - + -
56A ASN* 3.3 20.6 - - - -
59A ALA* 3.6 31.9 - - + -
61A LYS* 3.4 35.4 - - + -
80A MET* 1.3 75.9 - - - +
82A CYS* 1.3 63.9 + - - +
83A VAL* 3.8 16.4 + - + +
93A LEU 3.5 4.0 - - - +
95A LEU* 2.9 44.5 + - + +
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Residues in contact with CYS 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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6A HIS* 4.1 11.7 + - + +
7A MET* 3.3 34.6 + - + +
30A ILE* 5.2 0.7 - - - -
31A LEU* 4.1 4.7 - - - -
34A ILE* 3.9 26.9 - - + -
80A MET* 4.0 26.0 - - - -
81A TRP* 1.3 71.1 - - - +
83A VAL* 1.3 67.8 + - - +
92A ILE* 4.1 11.9 - - + -
93A LEU 3.5 5.2 - - - -
94A VAL* 4.1 22.4 - - - +
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Residues in contact with VAL 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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6A HIS* 4.4 2.0 - - - -
7A MET 5.2 2.9 - - - +
58A LEU 4.8 0.4 - - - +
59A ALA* 4.3 31.0 - - + +
81A TRP* 4.0 26.2 - - + +
82A CYS* 1.3 81.0 - - - +
84A PRO* 1.3 82.0 - - + +
86A PRO* 5.3 0.4 - - + -
92A ILE* 3.3 8.7 - - - +
93A LEU* 2.7 58.3 + - + +
95A LEU* 5.5 0.9 - - + -
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Residues in contact with PRO 84 (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 HIS* 3.9 18.8 - - + +
83A VAL* 1.3 97.0 - - + +
85A HIS* 1.3 66.3 + - - +
86A PRO* 3.3 9.0 - - - +
91A HIS 4.1 6.3 - - - +
92A ILE* 4.1 9.9 - - + -
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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