Contacts of the helix formed by residues 105 - 118 (chain B) in PDB entry 2QTV
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 ARG 105 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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719A SER* 4.9 3.4 + - - -
31B LEU* 3.7 21.4 - - + +
32B ASP* 2.5 53.6 + - - -
33B ASN* 4.3 4.6 - - - +
102B ASP* 3.0 31.7 + - + +
104B GLU* 1.3 85.2 - - + +
106B PHE* 1.3 57.5 + - - +
107B ASP 3.0 2.5 - - - -
108B GLU* 2.7 64.6 + - + +
109B ALA* 2.9 10.1 + - - +
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Residues in contact with PHE 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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98B VAL* 4.0 11.9 - - + -
99B ASP 3.3 23.6 - - - -
100B ALA* 4.0 17.3 - - - -
102B ASP 3.7 11.0 - - - -
103B PRO* 3.5 34.3 + - + +
105B ARG* 1.3 77.8 - - - +
107B ASP* 1.3 52.1 + - - +
109B ALA* 3.1 6.4 + - + +
110B ARG* 2.6 38.9 + - - +
140B VAL* 4.3 12.1 - - + -
144B GLU* 5.1 1.6 - - + -
145B LEU* 3.8 34.1 - - + -
148B ALA* 3.3 35.4 - - + +
149B LEU* 4.1 4.1 - - + +
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Residues in contact with ASP 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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103B PRO 5.0 0.8 + - - -
104B GLU 5.1 4.5 + - - +
105B ARG 3.0 1.3 - - - -
106B PHE* 1.3 79.1 - - - +
108B GLU* 1.3 58.8 + - - +
110B ARG* 3.7 16.3 - - - +
111B VAL* 3.0 36.4 + - - +
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Residues in contact with GLU 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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31B LEU* 3.4 13.3 - - + +
78B ILE* 5.0 5.5 - - - +
81B ARG* 3.4 25.8 + - - +
105B ARG* 2.7 61.3 + - + +
107B ASP* 1.3 73.0 - - - +
109B ALA* 1.3 67.8 + - - +
111B VAL* 3.6 7.1 + - - +
112B GLU* 3.4 20.3 + - + +
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Residues in contact with ALA 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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31B LEU* 3.5 23.5 - - + +
96B PHE* 4.5 14.4 - - + -
98B VAL* 4.6 11.9 - - + -
105B ARG 2.9 10.2 + - - +
106B PHE* 3.4 12.1 - - - +
108B GLU* 1.3 74.6 - - - +
110B ARG* 1.3 67.4 + - - +
112B GLU* 2.7 18.1 + - - +
113B LEU* 2.9 15.0 + - - +
149B LEU* 4.3 10.5 - - + -
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Residues in contact with ARG 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 PHE 2.6 21.1 + - - +
107B ASP* 3.7 18.8 - - - +
109B ALA* 1.3 71.3 - - - +
111B VAL* 1.3 65.2 + - + +
113B LEU* 3.4 5.0 + - - +
114B ASP* 2.9 45.8 + - - +
147B SER 5.0 2.5 - - - -
148B ALA 3.2 19.0 + - - +
149B LEU* 3.0 47.1 + - + +
150B GLY* 3.0 12.1 - - - +
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Residues in contact with VAL 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 ASP* 3.0 22.8 + - - +
108B GLU* 3.6 10.3 - - - +
109B ALA 2.9 1.4 + - - -
110B ARG* 1.3 80.7 - - + +
112B GLU* 1.3 63.7 + - - +
114B ASP* 3.5 4.9 + - - +
115B ALA* 3.1 21.5 + - - +
907D VAL* 4.4 5.6 - - - -
908D SER* 3.7 33.7 - - - +
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Residues in contact with GLU 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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31B LEU* 3.9 18.8 - - + -
81B ARG* 3.6 23.4 + - - +
84B TRP* 4.1 9.7 - - + -
96B PHE* 4.5 7.9 - - + -
108B GLU* 3.4 15.1 - - - +
109B ALA* 2.7 11.9 + - - +
111B VAL* 1.3 75.0 - - - +
113B LEU* 1.3 64.6 + - - +
115B ALA* 3.2 2.2 + - - -
116B LEU* 3.1 12.8 + - - +
907D VAL 4.6 0.5 - - - +
908D SER* 2.9 24.9 + - - -
909D GLY 2.7 24.3 + - - -
910D GLN* 3.1 41.0 + - - +
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Residues in contact with LEU 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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96B PHE* 4.0 29.3 - - + -
109B ALA 2.9 10.3 + - - +
110B ARG* 3.9 8.5 - - - +
112B GLU* 1.3 76.0 - - - +
114B ASP* 1.3 66.0 + - - +
116B LEU* 3.0 9.6 + - + +
117B PHE* 2.9 47.9 + - + -
127B PHE* 4.2 13.0 - - + -
129B ILE* 3.9 20.6 - - + -
149B LEU* 4.5 19.1 - - + +
151B LEU* 3.8 30.7 - - + -
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Residues in contact with ASP 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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110B ARG* 2.9 41.8 + - - +
111B VAL* 3.9 4.4 - - - +
113B LEU* 1.3 76.7 - - - +
115B ALA* 1.3 59.5 + - - +
117B PHE* 3.1 28.2 + - - +
118B ASN* 2.8 32.2 + - - +
149B LEU 4.2 12.0 - - - +
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Residues in contact with ALA 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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111B VAL 3.1 14.3 + - - +
112B GLU 3.3 10.1 - - - +
114B ASP* 1.3 78.1 - - - +
116B LEU* 1.3 59.9 + - - +
118B ASN* 3.5 13.8 + - - +
119B ILE* 3.4 18.6 - - - +
908D SER* 3.8 19.3 - - - +
910D GLN* 3.5 17.3 - - + +
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Residues in contact with LEU 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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29B LEU* 4.0 17.0 - - + -
84B TRP* 4.0 9.4 - - + -
88B PHE* 3.7 23.1 - - + -
94B ILE* 5.1 0.4 - - + -
96B PHE* 3.8 34.8 - - + -
112B GLU 3.3 11.4 - - - +
113B LEU* 3.0 8.6 + - - +
115B ALA* 1.3 72.0 - - - +
117B PHE* 1.3 66.1 + - - +
118B ASN 2.9 5.7 + - - -
119B ILE* 3.0 22.3 + - - +
122B LEU* 4.3 10.3 - - + +
127B PHE* 4.0 26.2 - - + -
164B ARG* 4.6 0.3 + - - -
910D GLN* 3.0 31.0 - - - +
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Residues in contact with PHE 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 LEU* 2.9 46.7 + - + -
114B ASP* 3.1 24.0 + - - +
116B LEU* 1.3 74.8 - - - +
118B ASN* 1.3 64.4 + - - +
119B ILE 3.4 3.3 + - - +
123B LYS* 5.5 1.2 - - - -
127B PHE* 3.5 33.2 - + + -
129B ILE* 5.2 1.3 - - + -
149B LEU 5.7 0.7 - - - -
151B LEU* 4.0 14.4 - - + -
164B ARG* 2.9 36.2 + - - +
166B VAL* 3.8 35.4 - - + -
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Residues in contact with ASN 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 ASP* 2.8 29.7 + - - +
115B ALA* 3.5 9.6 + - - +
116B LEU 2.9 1.4 + - - -
117B PHE* 1.3 85.8 - - - +
119B ILE* 1.3 59.9 + - - +
120B ALA 3.7 2.6 + - - -
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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