Contacts of the helix formed by residues 102 - 112 (chain A) in PDB entry 1HJV
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 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A GLY 4.5 0.2 + - - -
99A TRP 4.0 5.1 + - - -
100A ASN 3.1 5.5 + - - -
101A PHE* 1.3 89.7 - - - +
103A SER* 1.3 67.0 + - - +
104A GLN* 3.1 7.5 + - - -
105A ARG* 3.3 14.5 + - - -
106A PHE* 3.3 10.2 + - - +
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Residues in contact with SER 103 (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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99A TRP 5.4 1.0 + - - -
102A GLY* 1.3 72.2 - - - +
104A GLN* 1.3 66.9 + - - +
106A PHE* 3.6 0.6 + - - -
107A SER* 3.5 15.4 + - - -
139A TRP* 3.5 17.0 + - - +
140A LEU 3.6 23.9 + - - +
141A TYR 3.1 22.6 + - - -
143A GLY* 5.3 0.9 + - - -
146A ASP* 5.4 0.3 - - - +
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Residues in contact with GLN 104 (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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102A GLY* 4.7 3.4 - - - -
103A SER* 1.3 74.9 - - - +
105A ARG* 1.3 67.6 + - - +
106A PHE 3.0 1.8 - - - -
107A SER* 2.9 20.1 + - - -
108A LYS* 3.2 12.8 + - - +
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Residues in contact with ARG 105 (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* 2.6 25.2 + - - -
61A ILE* 3.1 25.7 + - - +
69A TRP* 4.7 3.8 - - - -
101A PHE* 3.2 47.8 + - + +
102A GLY* 3.3 11.3 + - - +
104A GLN* 1.3 78.8 - - - +
106A PHE* 1.3 62.3 + - - +
108A LYS* 3.3 23.8 - - + +
109A ILE* 3.5 17.1 - - + +
1384A NAG 3.6 30.0 + - - +
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Residues in contact with PHE 106 (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 ILE* 4.4 14.6 - - + -
96A VAL* 3.9 23.1 - - + -
97A GLY* 3.6 26.2 - - - -
101A PHE* 3.7 25.7 - + + -
102A GLY 3.3 5.5 + - - +
103A SER 3.7 3.6 - - - +
104A GLN 2.9 0.8 + - - -
105A ARG* 1.3 76.9 - - - +
107A SER* 1.3 66.7 + - - +
109A ILE* 3.1 10.4 + - + +
110A ALA* 2.9 18.4 + - + +
119A PHE* 4.7 6.5 - + - -
137A LEU* 4.5 10.1 - - + -
139A TRP* 3.5 67.1 - + + +
140A LEU 5.1 0.7 - - - -
153A LEU* 4.5 13.9 - - + -
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Residues in contact with SER 107 (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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103A SER 3.5 6.7 + - - -
104A GLN* 2.9 15.3 + - - -
106A PHE* 1.3 74.8 - - - +
108A LYS* 1.3 53.9 + - - +
110A ALA* 2.9 5.4 + - - +
111A SER* 2.8 42.0 + - - -
139A TRP* 3.6 12.5 - - - -
145A ARG* 4.0 13.3 + - - -
146A ASP* 2.8 35.3 + - - -
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Residues in contact with LYS 108 (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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104A GLN 3.2 8.0 + - - +
105A ARG* 3.3 20.0 - - + +
107A SER* 1.3 76.9 - - - +
109A ILE* 1.3 64.1 + - + +
111A SER* 3.9 4.5 + - - -
112A ASN* 3.3 27.9 + - + +
115A SER* 4.1 5.0 - - - +
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Residues in contact with ILE 109 (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 ILE* 3.0 47.3 - - + +
64A ASP* 3.5 16.6 - - + +
101A PHE* 4.9 3.1 - - + -
105A ARG* 3.5 21.3 - - + +
106A PHE* 3.1 10.4 + - + +
108A LYS* 1.3 78.4 - - + +
110A ALA* 1.3 64.5 + - - +
112A ASN 3.6 2.1 - - - +
115A SER* 3.5 30.7 - - - +
116A ARG* 3.1 30.6 + - - +
119A PHE* 4.0 22.0 - - + -
153A LEU* 6.1 0.4 - - - -
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Residues in contact with ALA 110 (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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106A PHE* 2.9 8.4 + - + +
107A SER* 2.9 8.4 + - - +
109A ILE* 1.3 79.0 - - - +
111A SER* 1.3 52.4 + - - +
116A ARG* 2.6 38.1 + - - +
139A TRP* 3.4 38.1 - - + -
149A HIS* 3.9 22.2 - - + +
153A LEU* 5.2 10.3 - - + -
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Residues in contact with SER 111 (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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107A SER* 2.8 27.7 + - - -
108A LYS* 3.9 4.3 + - - -
110A ALA* 1.3 73.2 - - - +
112A ASN* 1.3 61.2 + - - +
113A THR* 3.4 5.4 + - - -
116A ARG* 4.4 4.2 + - - +
149A HIS* 3.6 36.1 - - - -
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Residues in contact with ASN 112 (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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108A LYS* 3.3 15.9 + - + +
109A ILE 3.8 0.2 + - - -
110A ALA 3.5 0.4 - - - -
111A SER* 1.3 77.1 - - - +
113A THR* 1.3 64.2 + - - +
114A GLN* 2.6 35.7 + - - +
115A SER* 2.9 34.0 + - - +
116A ARG* 3.0 24.6 + - - +
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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