Contacts of the strand formed by residues 61 - 68 (chain A) in PDB entry 3VY7
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 ILE 61 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A VAL* 3.7 34.1 - - + -
55A ARG 3.7 1.8 - - - -
56A VAL* 4.2 4.5 - - + -
60A TYR* 1.3 70.8 - - - +
62A VAL* 1.3 59.9 + - - +
63A GLY 4.0 5.6 - - - +
64A LEU* 4.3 5.4 - - + -
105A LEU* 2.9 42.0 + - + +
106A LYS* 3.7 27.6 - - - +
107A LYS* 4.0 3.1 - - - +
108A LEU* 4.6 4.3 - - + +
120A PHE* 3.8 22.0 - - + +
121A GLY* 4.2 4.5 - - - -
149A LEU* 3.9 5.2 - - - +
150A ILE* 3.0 40.6 + - + +
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Residues in contact with VAL 62 (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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55A ARG* 2.7 22.6 + - + +
56A VAL 4.0 1.6 - - - -
57A ASN* 3.6 36.3 - - - +
61A ILE* 1.3 75.0 - - - +
63A GLY* 1.3 56.9 + - - +
77A GLY* 3.3 2.9 - - - -
78A GLY 2.9 48.1 + - - +
80A ASN* 3.3 35.0 - - + +
81A GLY* 4.2 0.2 - - - -
148A SER 3.7 9.6 - - - +
149A LEU* 3.3 23.7 - - + -
150A ILE* 4.0 1.3 - - - -
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Residues in contact with GLY 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ARG 4.7 0.2 - - - -
54A VAL* 3.5 4.5 - - - -
55A ARG* 2.9 27.8 + - - +
61A ILE* 3.6 2.9 - - - +
62A VAL* 1.3 81.9 - - - +
64A LEU* 1.3 68.8 + - - +
75A TYR* 3.4 17.9 - - - -
76A VAL 3.1 13.2 - - - -
77A GLY* 4.0 0.2 - - - -
150A ILE* 4.0 3.8 - - - -
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Residues in contact with LEU 64 (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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38A PHE* 4.4 6.1 - - + -
40A HIS* 5.3 1.1 - - + -
53A ARG 3.5 4.3 - - - +
54A VAL* 3.8 31.4 - - + -
61A ILE* 4.3 1.8 - - + -
63A GLY* 1.3 78.0 - - - +
65A GLN* 1.3 63.4 + - - +
66A VAL* 5.6 1.8 - - + -
74A ASP 4.3 0.9 - - - +
75A TYR* 3.9 5.4 - - - -
76A VAL* 2.9 44.2 + - + +
105A LEU* 4.7 2.5 - - + -
108A LEU* 4.0 15.9 - - + -
110A PHE* 5.4 2.9 - - + -
142A ILE* 4.1 20.9 - - + -
150A ILE* 3.8 33.8 - - + +
153A ILE* 4.0 21.3 - - + -
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Residues in contact with GLN 65 (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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40A HIS* 5.1 0.9 - - - -
52A LEU* 3.8 0.9 - - - +
53A ARG* 2.9 77.8 + - + +
64A LEU* 1.3 73.0 - - - +
66A VAL* 1.3 67.6 + - - +
72A TRP* 3.9 16.2 - - + +
73A SER* 3.0 34.7 + - - +
74A ASP* 4.8 0.2 - - - +
75A TYR* 3.7 38.2 - - + +
83A LEU* 5.3 0.9 - - - +
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Residues in contact with VAL 66 (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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40A HIS* 4.1 3.8 - - + +
49A ILE* 3.6 34.5 - - + -
51A ALA 3.8 4.9 - - - +
52A LEU* 4.2 13.7 - - + -
64A LEU* 5.6 2.2 - - + -
65A GLN* 1.3 79.5 - - - +
67A ARG* 1.3 58.6 + - - +
68A TYR* 3.4 37.1 - - + +
72A TRP* 3.5 4.3 - - - -
73A SER* 2.8 40.2 + - - -
110A PHE* 6.2 1.1 - - + -
142A ILE* 3.9 32.3 - - + -
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Residues in contact with ARG 67 (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 ILE* 3.3 5.9 - - - -
50A THR* 2.9 57.7 + - - +
51A ALA* 3.1 20.7 + - + -
66A VAL* 1.3 70.5 - - - +
68A TYR* 1.3 59.3 + - - +
69A GLY 3.5 13.1 + - - +
70A LYS* 3.6 32.5 + - - +
71A VAL 3.5 16.6 - - - -
72A TRP* 3.4 33.8 - - + +
87A PHE* 3.8 29.9 - - - -
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Residues in contact with TYR 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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40A HIS* 2.8 41.1 + + + +
43A ASN* 3.2 50.9 - - + +
44A GLN 4.3 0.2 - - - -
46A ASP* 3.2 17.7 - - + +
47A GLY 3.5 13.7 - - - +
48A PRO 3.4 2.7 - - - -
49A ILE* 3.6 20.9 - - + +
66A VAL* 3.4 31.6 - - + +
67A ARG* 1.3 70.7 - - - +
69A GLY* 1.3 65.1 + - - +
70A LYS 3.2 0.5 + - - -
71A VAL 2.9 23.2 + - - +
73A SER* 4.0 2.2 - - - -
140A ARG 3.3 27.1 - - - -
141A PHE* 3.6 4.8 - - + -
142A ILE* 3.5 13.3 + - - +
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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