Contacts of the helix formed by residues 110 - 121 (chain B) in PDB entry 3IIV
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 PRO 110 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B ALA 2.9 17.9 - - - +
107B VAL 3.7 8.5 - - - +
108B GLU 4.1 1.1 - - - +
109B ASN* 1.3 81.8 - - - +
111B SER* 1.3 60.3 + - - +
112B LEU 3.0 1.8 - - - -
113B ILE* 3.0 34.4 + - + +
114B THR 3.8 0.3 + - - -
156B TRP* 4.1 12.6 - - + -
159B GLU* 3.4 27.1 - - - +
163B ARG* 3.5 26.4 - - + +
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Residues in contact with SER 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B ASN* 3.0 19.4 + - - -
110B PRO* 1.3 76.4 - - - +
112B LEU* 1.3 62.4 + - - +
113B ILE 3.2 0.2 - - - -
114B THR* 3.1 11.6 + - - -
115B GLN* 3.0 42.1 + - - +
163B ARG* 4.0 18.6 - - - +
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Residues in contact with LEU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B ILE* 4.2 15.9 - - + -
84B TYR 4.6 1.8 - - - +
85B ASP* 3.5 12.6 - - - +
86B PHE* 3.3 39.7 - - + +
102B ILE* 4.3 10.1 - - + -
105B ALA* 4.1 31.2 - - + +
109B ASN* 2.9 27.6 + - + +
111B SER* 1.3 76.8 + - - +
113B ILE* 1.3 64.4 + - - +
115B GLN* 3.4 9.2 + - - +
116B ILE* 3.1 41.4 + - + +
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Residues in contact with ILE 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B ILE* 4.0 14.5 - - + +
106B ALA* 4.3 12.3 - - + -
110B PRO* 3.0 20.0 + - + +
112B LEU* 1.3 77.9 - - - +
114B THR* 1.3 61.2 + - - +
116B ILE* 3.5 0.4 + - - -
117B ALA* 3.1 21.5 + - - +
125B VAL* 3.9 14.0 - - + +
127B VAL* 3.8 26.9 - - + -
156B TRP* 4.6 2.2 - - + -
160B VAL* 4.0 20.6 - - + -
163B ARG* 3.5 25.6 - - + +
164B GLY 3.7 0.9 - - - -
165B ALA* 3.3 34.5 - - - +
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Residues in contact with THR 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B SER* 3.1 13.0 + - - -
113B ILE* 1.3 78.3 - - - +
115B GLN* 1.3 58.5 + - - +
117B ALA* 3.3 3.4 + - + +
118B GLN* 2.8 59.9 + - + +
163B ARG* 2.7 44.5 + - - +
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Residues in contact with GLN 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B PHE* 3.3 45.5 + - + +
109B ASN* 4.3 8.1 - - - +
111B SER* 3.0 41.3 + - - +
112B LEU* 3.4 12.2 + - - +
114B THR* 1.3 73.7 - - - +
116B ILE* 1.3 65.1 + - - +
118B GLN* 3.4 7.6 + - - +
119B THR* 3.4 14.9 + - - -
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Residues in contact with ILE 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B PHE* 3.9 13.0 - - + -
89B ALA* 3.5 30.1 - - + -
93B ILE* 4.1 17.7 - - + -
100B VAL* 4.0 22.4 - - + -
102B ILE* 4.3 15.3 - - + -
112B LEU* 3.1 39.4 + - + +
113B ILE 4.9 0.2 - - - +
115B GLN* 1.3 76.4 - - - +
117B ALA* 1.3 58.3 + - - +
119B THR 3.3 1.6 + - - -
120B PHE* 2.9 34.7 + - + +
124B ALA* 4.7 1.3 - - + +
125B VAL* 3.5 22.0 - - + -
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Residues in contact with ALA 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B ILE 3.1 18.0 + - - +
114B THR* 3.7 5.8 - - + +
116B ILE* 1.3 78.6 - - - +
118B GLN* 1.3 59.2 + - + +
121B GLY* 2.8 37.1 + - - -
122B SER* 3.8 14.3 + - - +
125B VAL* 3.7 4.6 - - + +
164B GLY* 3.6 27.1 - - - +
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Residues in contact with GLN 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B THR* 2.8 39.9 + - + +
115B GLN* 3.9 7.9 - - - +
116B ILE 3.2 0.6 - - - -
117B ALA* 1.3 79.8 - - + +
119B THR* 1.3 59.8 + - - +
121B GLY 4.9 0.3 + - - -
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Residues in contact with THR 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B PHE* 3.6 17.9 - - + -
115B GLN 3.4 8.9 + - - -
116B ILE 3.3 1.0 + - - -
117B ALA 3.3 0.4 - - - -
118B GLN* 1.3 78.1 - - - +
120B PHE* 1.3 101.2 + - + +
121B GLY 3.6 0.4 - - - -
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Residues in contact with PHE 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B PHE* 3.9 9.2 - + - -
90B SER* 3.5 43.7 - - - -
93B ILE* 3.5 38.1 - - + -
94B LEU* 3.9 20.2 - - + -
116B ILE* 2.9 22.0 + - + +
119B THR* 1.3 103.3 - - + +
121B GLY* 1.3 53.6 + - - +
123B GLN* 2.7 25.8 - - - +
124B ALA* 3.7 19.2 - - + +
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Residues in contact with GLY 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B ALA* 2.8 24.5 + - - -
118B GLN 4.9 0.2 + - - -
119B THR 3.6 1.2 - - - -
120B PHE* 1.3 80.2 - - - +
122B SER* 1.3 65.7 + - - -
123B GLN* 3.1 14.6 - - - -
124B ALA* 3.0 15.6 + - - +
125B VAL 4.2 0.7 + - - -
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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