Contacts of the helix formed by residues 77 - 87 (chain A) in PDB entry 1VYH
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 THR 77 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A GLY 4.2 5.2 - - - +
76A ASP* 1.3 78.0 - - - +
78A THR* 1.3 64.2 + - - +
79A ARG* 2.8 21.2 + - + +
80A HIS* 3.1 32.4 + - + +
81A VAL* 3.0 23.4 + - - +
102A VAL* 4.7 3.6 - - - -
103A GLY 5.7 0.2 - - - +
105A ASN* 4.9 6.7 - - - +
106A ASN* 2.9 27.8 + - - +
109A ASN* 5.9 0.4 - - - -
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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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9A ALA* 3.0 24.8 + - - +
77A THR* 1.3 73.9 + - - +
79A ARG* 1.3 55.8 + - - +
80A HIS 3.2 0.2 + - - -
81A VAL* 3.3 2.3 + - - +
82A LEU* 2.8 34.0 + - - +
102A VAL* 4.6 11.7 - - + +
103A GLY* 4.8 5.2 - - - -
106A ASN* 2.7 33.4 + - - +
114A VAL* 4.3 6.7 - - + +
117A GLY* 3.9 6.7 - - - -
118A ILE* 3.8 31.2 - - + +
121A ILE* 4.0 15.8 - - + +
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Residues in contact with ARG 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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8A PRO* 2.5 46.5 + - - +
9A ALA* 3.4 14.7 - - - +
11A ILE* 2.6 34.3 + - - +
13A HIS* 3.4 55.0 + - + +
77A THR* 2.8 15.0 + - - +
78A THR* 1.3 75.4 - - - +
80A HIS* 1.3 61.2 + - + +
82A LEU* 3.3 6.6 - - - +
83A TRP 3.2 16.8 + - - -
106A ASN* 5.5 0.7 - - - +
109A ASN* 4.8 8.9 + - - +
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Residues in contact with HIS 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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13A HIS* 3.0 53.2 - + - -
15A ALA* 3.6 28.6 - - + +
24A TRP* 4.1 8.8 - - + -
75A GLY 4.6 3.3 + - - -
76A ASP* 3.6 32.0 + - - +
77A THR* 3.1 37.1 + - + +
79A ARG* 1.3 74.0 - - - +
81A VAL* 1.3 67.2 + - - +
83A TRP* 3.0 4.4 + - - +
84A ARG* 2.8 24.6 + - - +
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Residues in contact with VAL 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A VAL* 4.8 11.9 - - + -
46A GLY* 4.0 9.4 - - - +
76A ASP* 4.0 5.6 + - + +
77A THR 3.0 13.1 + - - +
78A THR 3.7 3.4 - - - +
80A HIS* 1.3 75.0 - - - +
82A LEU* 1.3 67.3 + - - +
84A ARG* 3.3 30.0 + - - +
85A LEU* 3.0 34.8 + - + +
102A VAL* 3.3 30.3 - - + -
121A ILE* 3.5 25.6 - - + -
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Residues in contact with LEU 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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9A ALA 4.5 2.2 - - - +
10A ALA* 3.3 41.7 - - - +
11A ILE 4.2 0.9 - - - +
12A PRO* 4.0 18.8 - - + -
78A THR* 2.8 18.0 + - - +
79A ARG* 3.3 5.6 - - - +
81A VAL* 1.3 76.5 - - - +
83A TRP* 1.3 65.5 + - - +
85A LEU* 2.8 9.3 + - - +
86A LYS* 2.7 34.9 + - + +
117A GLY 5.1 0.4 - - - +
120A ALA* 4.5 11.7 - - + +
121A ILE* 4.1 22.0 - - + +
124A LEU* 4.4 19.5 - - + -
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Residues in contact with TRP 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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12A PRO* 3.7 14.5 - - + +
13A HIS* 3.4 32.8 - - - +
14A ALA* 3.6 22.4 - - + +
24A TRP* 3.6 33.9 - + - -
25A MET* 3.8 23.8 - - + -
28A HIS* 3.9 22.9 - + - -
79A ARG 3.2 1.9 + - - +
80A HIS 3.0 7.0 + - - +
82A LEU* 1.3 78.5 - - - +
84A ARG* 1.3 59.4 + - - +
86A LYS* 3.1 3.2 + - + +
87A ASN* 2.5 73.7 + - + +
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Residues in contact with ARG 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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24A TRP* 3.8 21.5 - - + -
28A HIS* 3.6 20.7 - - - +
45A VAL* 5.3 3.6 - - - +
46A GLY 3.4 15.8 + - - +
71A PHE* 3.2 19.1 + - - +
73A ILE* 3.2 35.5 - - - +
76A ASP* 2.6 28.4 + - - -
80A HIS 2.8 10.5 + - - +
81A VAL* 3.6 18.1 + - - +
83A TRP* 1.3 83.6 - - - +
85A LEU* 1.3 61.7 + - - +
87A ASN 3.5 7.4 + - - -
88A GLY 3.7 1.0 + - - -
89A GLU* 2.8 69.1 + - - +
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Residues in contact with LEU 85 (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 VAL* 4.5 22.0 - - + -
81A VAL* 3.0 23.1 + - + +
82A LEU* 2.8 11.5 + - - +
84A ARG* 1.3 69.9 - - + +
86A LYS* 1.3 65.8 + - - +
87A ASN 3.3 0.9 + - - -
88A GLY* 3.4 8.8 + - - -
89A GLU* 3.8 21.3 + - + +
90A LEU* 3.6 40.3 - - + +
121A ILE* 3.7 30.3 - - + -
124A LEU* 3.5 18.3 - - + +
125A ILE* 4.0 18.6 - - + -
128A ARG* 4.9 3.5 + - - -
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Residues in contact with LYS 86 (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 PRO* 4.2 25.4 - - + +
82A LEU* 2.7 25.1 + - + +
83A TRP* 3.4 12.8 - - + +
85A LEU* 1.3 78.5 - - - +
87A ASN* 1.3 62.5 + - - +
88A GLY 3.4 3.3 + - - -
124A LEU* 4.0 24.4 - - + +
128A ARG* 3.1 37.2 + - - +
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Residues in contact with ASN 87 (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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28A HIS* 3.6 17.5 + - - +
32A VAL* 4.4 4.0 - - - +
83A TRP* 2.5 87.7 + - + +
84A ARG 3.7 5.4 - - - +
85A LEU 3.2 0.4 - - - -
86A LYS* 1.3 81.0 - - - +
88A GLY* 1.3 56.8 + - - +
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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