Contacts of the helix formed by residues 103 - 113 (chain B) in PDB entry 3Q72
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 103 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101B GLY 3.1 0.6 - - - -
102B VAL* 1.3 80.2 - - - +
104B LYS* 1.3 65.7 + - - +
105B SER 3.4 2.7 - - - -
106B ALA* 3.3 2.9 + - - +
107B LEU* 3.1 30.8 + - - +
168B VAL* 4.9 0.2 - - - -
203B ASN* 3.6 9.6 - - - -
256B GNP 3.0 33.2 + - - -
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Residues in contact with LYS 104 (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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188A ARG* 3.6 6.4 - - - +
96B LEU* 3.2 35.1 - - + +
97B LEU 3.6 27.4 - - - -
98B GLY* 3.4 12.2 + - - +
99B ALA 2.7 29.1 + - - -
102B VAL* 3.4 12.5 - - + +
103B GLY* 1.3 76.3 - - - +
105B SER* 1.3 62.1 + - - +
107B LEU* 3.5 2.8 + - - +
108B ALA 3.2 16.8 + - - -
144B ASP* 4.5 9.2 - - - +
146B TRP* 4.2 14.4 - - - -
168B VAL* 3.9 17.5 - - + -
256B GNP 3.0 36.4 + - - +
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Residues in contact with SER 105 (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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104B LYS* 1.3 73.0 - - - +
106B ALA* 1.3 67.2 + - - +
108B ALA* 3.2 2.8 + - - +
109B ARG* 2.8 51.8 + - - +
125B HIS* 4.7 3.1 - - - -
127B TYR* 5.4 0.7 - - - -
144B ASP* 2.5 27.7 + - - -
147B GLU* 3.5 5.1 + - - +
256B GNP 3.0 7.3 + - - -
257B MG 2.4 28.8 - - - -
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Residues in contact with ALA 106 (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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103B GLY 3.3 7.2 + - - +
105B SER* 1.3 76.1 - - - +
107B LEU* 1.3 57.2 + - - +
109B ARG* 3.6 17.3 + - - +
110B ILE* 2.9 38.9 + - + +
234B ALA* 3.7 19.7 - - + -
256B GNP 3.0 34.7 + - + +
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Residues in contact with LEU 107 (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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96B LEU* 5.2 2.9 - - + -
103B GLY 3.1 16.3 + - - +
104B LYS 3.6 4.7 - - - +
105B SER 3.2 0.2 - - - -
106B ALA* 1.3 80.0 - - - +
108B ALA* 1.3 56.0 + - - +
110B ILE* 3.5 0.6 + - - -
111B PHE* 3.0 29.1 + - - +
168B VAL* 4.0 33.7 - - + -
201B VAL* 4.5 2.2 - - + -
203B ASN* 4.2 6.7 - - + +
232B THR* 3.8 33.9 - - + +
234B ALA* 3.9 17.7 - - + -
240B VAL* 3.6 26.5 - - + +
243B LEU* 4.4 13.9 - - + -
244B PHE* 4.0 10.7 - - + -
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Residues in contact with ALA 108 (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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96B LEU* 3.6 25.8 - - + +
104B LYS 3.2 7.0 + - - +
105B SER* 3.8 6.1 - - - +
107B LEU* 1.3 78.4 - - - +
109B ARG* 1.3 56.0 + - - +
111B PHE* 3.4 5.4 + - - +
112B GLY 3.0 25.5 + - - -
127B TYR* 3.5 35.2 - - + +
142B VAL* 4.2 8.3 - - + -
144B ASP* 5.0 3.4 - - + +
244B PHE* 4.7 4.5 - - - -
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Residues in contact with ARG 109 (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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105B SER* 2.8 43.7 + - - +
106B ALA* 3.6 19.6 - - - +
108B ALA* 1.3 74.9 - - - +
110B ILE* 1.3 61.8 + - + +
113B GLY* 2.7 30.7 + - - -
114B VAL* 2.8 25.5 + - - +
123B ALA 6.5 0.7 - - - -
125B HIS* 6.0 2.0 + - - -
127B TYR* 3.0 32.2 + - + +
256B GNP 4.0 12.1 + - - -
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Residues in contact with ILE 110 (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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106B ALA* 2.9 20.0 + - + +
107B LEU* 3.9 4.0 - - - +
109B ARG* 1.3 76.2 - - + +
111B PHE* 1.3 70.6 + - - +
112B GLY 3.5 0.2 + - - -
113B GLY* 3.8 3.8 + - - -
114B VAL* 5.0 4.9 - - - +
129B ARG* 5.2 0.2 + - - -
234B ALA* 2.9 46.7 - - + +
237B HIS* 3.3 39.7 - - + +
240B VAL* 4.2 20.4 - - + -
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Residues in contact with PHE 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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107B LEU 3.0 18.5 + - - +
108B ALA* 3.7 4.5 - - - +
110B ILE* 1.3 79.4 - - - +
112B GLY* 1.3 63.1 + - - +
113B GLY 3.8 0.5 + - - -
127B TYR* 5.4 1.6 - - + -
128B ASP 5.0 1.1 - - - -
129B ARG* 3.0 76.5 + - + +
131B ILE* 4.1 13.0 - - + -
140B LEU* 4.0 27.6 - - + -
142B VAL* 4.1 22.4 - - + -
240B VAL* 4.1 7.3 - - + +
241B GLN* 3.8 12.8 - - - -
244B PHE* 3.4 48.2 - + + -
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Residues in contact with GLY 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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108B ALA 3.0 12.2 + - - -
111B PHE* 1.3 82.2 - - - +
113B GLY* 1.3 67.2 + - - +
127B TYR* 3.7 11.2 - - - +
128B ASP* 3.9 27.3 - - - +
129B ARG* 4.4 3.8 - - - -
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Residues in contact with GLY 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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109B ARG 2.7 10.9 + - - -
110B ILE 3.8 2.9 + - - -
111B PHE 3.5 3.4 + - - -
112B GLY* 1.3 85.0 - - - +
114B VAL* 1.3 64.2 + - - -
127B TYR* 2.9 24.8 - - - -
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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