Contacts of the strand formed by residues 75 - 84 (chain A) in PDB entry 1VCW
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 GLU 75 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A ARG* 3.0 5.2 - - - -
65A GLY 2.8 30.7 + - - -
68A THR* 3.5 36.6 - - + +
69A ASN* 2.9 36.0 + - - +
73A GLN 3.1 0.8 + - - -
74A LEU* 1.3 75.2 - - - +
76A ILE* 1.3 67.0 + - + +
77A ARG* 2.9 4.7 + - - +
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Residues in contact with ILE 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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62A TYR* 4.4 21.8 - - + -
63A ASN 3.7 5.6 - - - +
64A ARG* 3.8 21.3 - - + +
68A THR* 5.7 0.7 - - - -
75A GLU* 1.3 77.4 - - + +
77A ARG* 1.3 64.9 + - - +
78A THR* 3.1 21.3 + - - +
79A LEU* 4.4 13.9 - - + -
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Residues in contact with ARG 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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63A ASN* 2.9 20.7 + - - +
65A GLY* 3.2 24.8 - - - +
67A ASN 5.9 0.7 - - - -
68A THR* 3.1 34.5 - - + +
75A GLU 2.9 1.6 + - - +
76A ILE* 1.3 71.0 - - - +
78A THR* 1.3 70.0 + - - +
99A ASN* 2.9 28.5 + - - +
100A ASP* 2.9 30.9 + - - +
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Residues in contact with THR 78 (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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63A ASN* 3.2 29.5 + - - +
76A ILE* 3.1 19.5 + - - +
77A ARG* 1.3 90.0 + - - +
79A LEU* 1.3 88.0 + - - +
96A HIS* 5.0 9.4 - - + +
97A VAL* 4.1 10.5 + - + +
198A HIS* 5.0 14.1 - - + +
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Residues in contact with LEU 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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61A VAL 3.2 13.9 - - - +
62A TYR* 3.7 21.1 - - + +
63A ASN 4.4 0.4 - - - +
76A ILE* 4.4 9.0 - - + -
78A THR* 1.3 92.6 - - - +
80A GLY* 1.3 63.9 + - - +
97A VAL* 3.8 9.5 - - - +
160A ASN* 4.8 9.9 - - - +
162A TYR* 5.7 0.9 - - - +
163A ASN* 3.0 45.8 - - + +
198A HIS* 4.6 16.6 + - + +
199A GLY* 4.8 7.5 - - - -
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Residues in contact with GLY 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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60A ASN* 3.6 7.1 + - - +
61A VAL* 2.8 27.6 + - - +
79A LEU* 1.3 79.9 - - - +
81A SER* 1.3 65.9 + - - -
97A VAL* 3.5 15.5 - - - +
160A ASN* 5.1 3.5 - - - +
199A GLY* 4.3 10.5 - - - -
201A SER* 3.9 7.2 - - - -
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Residues in contact with SER 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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58A VAL* 5.6 1.6 - - - -
59A VAL 3.1 12.3 - - - -
60A ASN* 5.6 0.2 - - - -
61A VAL* 3.7 5.2 - - - -
80A GLY* 1.3 74.4 + - - -
82A GLY* 1.3 60.6 + - - +
93A THR* 3.1 12.8 + - - -
159A GLY* 3.7 3.5 - - - -
160A ASN* 3.0 17.5 + - - +
199A GLY 2.6 28.2 + - - -
201A SER 2.7 7.8 + - - +
202A GLY* 2.9 21.0 - - - -
203A GLY* 3.5 24.9 - - - -
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Residues in contact with GLY 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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58A VAL* 3.2 4.9 - - - +
59A VAL* 2.6 40.3 + - - +
61A VAL* 3.8 13.5 - - - +
81A SER* 1.3 77.0 - - - +
83A VAL* 1.3 63.8 + - - -
91A ILE* 4.0 8.1 - - - -
92A ILE 3.2 13.0 - - - -
202A GLY 3.5 3.8 - - - -
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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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57A ALA 3.9 4.0 - - - +
58A VAL* 4.6 3.6 - - + -
82A GLY* 1.3 73.4 - - - +
84A ILE* 1.3 58.3 + - - +
85A MET* 3.1 15.1 + - - +
91A ILE* 3.9 2.9 - - - -
92A ILE 2.9 31.0 + - - +
141A ILE* 3.2 48.2 - - + -
202A GLY 3.5 16.4 - - - +
203A GLY* 3.8 5.2 - - - +
204A ALA* 3.6 26.5 - - + -
212A LEU* 4.6 3.6 - - + -
215A ILE* 3.9 17.5 - - + -
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Residues in contact with ILE 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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56A PRO 5.2 0.2 - - - +
57A ALA 3.1 11.8 + - - +
59A VAL* 3.5 30.3 - - + -
82A GLY 4.0 0.4 + - - -
83A VAL* 1.3 68.7 - - - +
85A MET* 1.3 59.0 + - - +
86A ASP 3.9 17.7 - - - +
89A GLY 5.4 0.4 - - - -
90A TYR 3.8 7.0 - - - +
91A ILE* 3.9 18.8 - - + -
108A LEU* 3.7 20.6 - - + -
132A ILE* 4.7 1.3 - - + -
138A LEU* 4.4 17.7 - - + -
139A PRO* 3.0 45.5 - - + +
140A THR* 3.6 2.2 - - + -
141A ILE* 3.0 27.2 + - - +
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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