Contacts of the helix formed by residues 113 - 129 (chain B) in PDB entry 2VXX
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 ASN 113 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A ARG* 3.7 29.9 - - + +
112B PHE* 1.3 76.0 - - - +
114B CYS* 1.3 59.7 + - - +
115B ARG* 3.1 13.4 - - - +
116B GLN* 2.8 59.3 + - - +
117B MET* 2.9 26.0 + - - +
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Residues in contact with CYS 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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54B VAL* 4.0 14.8 - - + -
55B GLU 4.7 11.2 - - - +
58B GLU* 4.7 12.3 - - - -
62B LEU* 3.7 31.2 - - + -
66B PHE* 5.1 0.8 - - + -
113B ASN* 1.3 76.0 - - - +
115B ARG* 1.3 61.0 + - - +
117B MET* 3.5 13.5 - - - +
118B LEU* 3.0 36.7 + - + +
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Residues in contact with ARG 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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113B ASN* 3.1 9.3 - - - +
114B CYS* 1.3 83.4 - - - +
116B GLN* 1.3 53.8 - - + +
118B LEU* 3.5 2.7 - - - +
119B SER* 2.7 37.8 - - - +
168B PHE 4.2 4.4 + - - -
169B LEU* 2.5 62.0 + - + +
170B ALA 4.8 3.8 + - - -
171B ASN* 5.2 3.4 - - - +
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Residues in contact with GLN 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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5A ALA* 3.8 25.8 - - + +
6A LEU 4.4 8.8 + - - +
8A ARG* 5.6 0.7 + - - +
112B PHE* 3.4 23.9 - - + +
113B ASN* 2.8 53.9 + - - +
115B ARG* 1.3 69.2 + - + +
117B MET* 1.3 65.1 + - - +
119B SER* 3.3 6.3 + - - -
120B ASN* 3.0 35.8 + - - +
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Residues in contact with MET 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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50B HIS* 3.2 52.5 - - + +
53B VAL* 3.7 20.0 - - + +
54B VAL* 3.8 31.2 - - + +
55B GLU 5.1 0.9 - - - +
66B PHE* 4.5 5.6 - - + -
107B GLU* 3.8 10.5 - - - +
112B PHE* 3.4 26.2 - - + +
113B ASN 2.9 10.3 + - - +
114B CYS* 3.5 24.9 - - + +
116B GLN* 1.3 77.1 - - - +
118B LEU* 1.3 62.3 + - - +
120B ASN* 3.4 0.5 + - - +
121B ASP* 3.0 29.3 + - - +
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Residues in contact with LEU 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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62B LEU* 3.8 26.9 - - + -
65B PHE* 4.1 14.1 - - + -
66B PHE* 3.9 26.7 - - + -
114B CYS* 3.0 23.8 + - - +
115B ARG* 4.8 0.9 - - - +
117B MET* 1.3 77.0 - - - +
119B SER* 1.3 56.9 + - - +
121B ASP* 3.3 4.6 + - - +
122B LEU 2.9 24.3 + - - -
165B ILE* 3.2 31.1 - - + +
168B PHE* 3.8 24.2 - - + -
169B LEU* 3.7 21.8 - - + -
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Residues in contact with SER 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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115B ARG* 2.7 26.3 - - - +
116B GLN* 3.3 7.5 + - - -
118B LEU* 1.3 75.6 - - - +
120B ASN* 1.3 59.2 + - - +
122B LEU* 3.3 5.1 + - - +
123B GLN* 3.0 45.0 + - - +
169B LEU* 4.0 18.9 - - - +
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Residues in contact with ASN 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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46B GLN* 3.6 17.9 + - - +
104B PHE* 5.3 1.4 - - - -
105B THR 5.7 2.3 - - - +
107B GLU* 2.7 43.4 + - + +
108B PRO* 5.2 2.6 - - - +
112B PHE* 5.3 3.0 - - - -
116B GLN* 3.0 25.3 + - - +
117B MET 3.6 4.5 - - - +
119B SER* 1.3 76.0 - - - +
121B ASP* 1.3 58.4 + - - +
123B GLN* 3.5 14.8 + - - +
124B ALA* 3.1 26.9 + - - +
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Residues in contact with ASP 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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43B LEU* 4.2 3.3 - - - +
46B GLN* 2.9 27.3 + - - +
47B TYR* 3.3 35.9 + - + -
50B HIS* 2.6 28.3 + - - -
66B PHE* 3.4 11.8 - - - -
117B MET 3.0 16.1 + - - +
118B LEU* 3.6 6.1 - - - +
119B SER 3.3 0.2 - - - -
120B ASN* 1.3 72.1 - - - +
122B LEU* 1.3 60.5 + - - +
124B ALA* 3.3 5.2 + - - +
125B GLU* 3.0 32.7 + - - +
165B ILE* 3.9 9.0 - - + -
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Residues in contact with LEU 122 (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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118B LEU 2.9 17.1 + - - +
119B SER* 3.6 6.5 - - - +
121B ASP* 1.3 74.3 - - - +
123B GLN* 1.3 59.9 + - + +
125B GLU* 3.3 1.8 + - - +
126B GLN* 2.8 59.5 + - - +
162B ALA* 3.4 40.8 - - + +
165B ILE* 3.8 12.9 - - + +
166B GLY* 4.7 9.2 - - - -
169B LEU* 4.3 17.7 - - + -
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Residues in contact with GLN 123 (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 PHE* 4.7 2.9 - - + +
119B SER* 3.0 33.4 + - - +
120B ASN* 3.8 14.7 + - - +
121B ASP 3.4 0.2 - - - -
122B LEU* 1.3 75.8 - - + +
124B ALA* 1.3 61.6 + - - +
126B GLN* 3.5 17.4 + - - +
127B ALA* 3.0 24.3 + - - +
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Residues in contact with ALA 124 (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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43B LEU* 3.8 15.3 - - + -
46B GLN* 4.5 0.7 - - - +
104B PHE* 3.6 46.6 - - + -
120B ASN 3.1 14.3 + - - +
121B ASP* 3.5 8.7 - - - +
122B LEU 3.2 0.4 - - - -
123B GLN* 1.3 73.2 - - - +
125B GLU* 1.3 64.8 + - - +
127B ALA* 3.2 4.5 + - - +
128B ILE* 3.0 29.1 + - - +
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Residues in contact with GLU 125 (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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43B LEU* 3.5 13.9 - - + +
47B TYR* 2.5 31.0 + - - +
121B ASP 3.0 19.6 + - - +
122B LEU 3.3 6.7 + - - +
124B ALA* 1.3 73.5 - - - +
126B GLN* 1.3 52.5 + - - +
128B ILE* 3.2 5.8 + - - +
129B ILE* 2.7 42.1 + - + +
158B THR* 3.2 13.3 - - + +
161B ARG* 2.7 46.7 + - - +
162B ALA* 4.0 20.9 - - + -
165B ILE* 4.0 9.4 - - + -
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Residues in contact with GLN 126 (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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122B LEU* 2.8 49.6 + - + +
123B GLN* 3.6 19.9 - - - +
125B GLU* 1.3 74.1 - - - +
127B ALA* 1.3 64.6 + - - +
129B ILE* 3.4 16.4 + - + +
130B GLY* 3.1 19.4 + - - -
162B ALA* 5.4 0.9 - - + -
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Residues in contact with ALA 127 (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 CYS* 3.6 27.6 - - - +
104B PHE* 3.9 10.8 - - + -
123B GLN 3.0 17.1 + - - +
124B ALA 3.2 4.7 + - - +
126B GLN* 1.3 75.4 - - - +
128B ILE* 1.3 61.7 + - - +
130B GLY* 3.4 2.8 + - - -
131B VAL* 3.2 27.0 + - - +
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Residues in contact with ILE 128 (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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36B LEU* 3.9 13.2 - - + -
39B SER* 3.8 23.6 - - - +
40B PHE* 3.5 34.8 - - + -
43B LEU* 3.7 28.5 - - + -
103B CYS* 3.8 19.7 - - - -
104B PHE* 4.2 9.4 - - + -
124B ALA 3.0 20.3 + - - +
125B GLU* 3.6 8.1 - - - +
127B ALA* 1.3 74.2 - - - +
129B ILE* 1.3 54.4 + - - +
131B VAL* 3.2 3.3 + - - +
132B LEU* 2.8 39.9 + - + +
158B THR* 4.5 4.0 - - + -
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Residues in contact with ILE 129 (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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125B GLU 2.7 30.0 + - - +
126B GLN* 3.6 13.5 - - + +
128B ILE* 1.3 73.5 - - - +
130B GLY* 1.3 63.0 + - - +
132B LEU* 3.4 2.9 + - - +
133B ARG* 3.1 61.2 + - - +
155B LEU* 4.1 11.4 - - + +
158B THR* 3.7 15.5 - - + -
159B GLU* 4.0 20.9 - - + +
162B ALA* 3.8 29.4 - - + -
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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