Contacts of the helix formed by residues 117 - 131 (chain B) in PDB entry 1VE3
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 GLU 117 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116B PHE* 1.3 77.8 - - - +
118B PRO* 1.3 77.4 - - + +
119B LEU* 3.9 28.4 - - + +
120B GLU* 3.0 40.7 + - + +
121B LEU* 3.0 15.8 + - - +
192B ASN* 3.4 19.9 - - - +
194B TRP* 3.7 0.9 - - - -
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Residues in contact with PRO 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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117B GLU* 1.3 89.0 - - + +
119B LEU* 1.3 62.7 + - - +
121B LEU 3.4 0.3 + - - -
122B ASN* 3.0 23.4 + - - +
173B GLU 5.5 4.9 - - - +
174B ARG* 3.8 32.5 - - + +
192B ASN* 5.1 1.6 - - + +
194B TRP* 3.6 24.0 - - + -
202B LEU* 3.9 11.1 - - + +
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Residues in contact with LEU 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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117B GLU* 3.4 23.5 - - - +
118B PRO* 1.3 78.9 - - - +
120B GLU* 1.3 78.6 + - + +
122B ASN* 3.5 9.2 + - - +
123B GLN* 3.2 46.5 + - - +
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Residues in contact with GLU 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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95B ARG* 3.2 39.7 + - - +
115B HIS 3.5 14.8 - - - +
116B PHE* 4.1 8.3 - - + -
117B GLU* 3.0 48.1 + - + +
119B LEU* 1.3 87.2 - - + +
121B LEU* 1.3 65.1 + - - +
122B ASN 3.1 1.6 - - - -
123B GLN* 3.1 12.1 + - - +
124B VAL* 3.1 24.4 + - - +
192B ASN* 4.9 0.5 + - - -
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Residues in contact with LEU 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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109B PHE* 3.9 31.9 - - + -
113B ILE* 3.9 26.2 - - + -
116B PHE* 3.8 13.3 - - + +
117B GLU 3.0 16.3 + - - +
118B PRO 3.9 1.6 - - - +
120B GLU* 1.3 76.0 - - - +
122B ASN* 1.3 62.9 + - - +
124B VAL* 3.2 8.0 + - + +
125B PHE* 3.0 55.2 + - + -
194B TRP* 3.7 34.8 - - + -
199B VAL* 4.7 3.6 - - + -
202B LEU* 4.7 2.7 - - + -
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Residues in contact with ASN 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 PRO 3.0 17.5 + - - +
119B LEU* 3.5 10.1 + - - +
120B GLU 3.1 0.2 - - - -
121B LEU* 1.3 78.0 - - - +
123B GLN* 1.3 62.2 + - - +
125B PHE* 3.3 7.5 + - - +
126B LYS* 3.1 38.2 + - - +
202B LEU* 4.4 15.7 - - + +
205B LEU* 4.2 8.7 - - - +
206B TYR* 2.7 36.0 + - - -
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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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95B ARG* 3.8 34.2 + - + +
119B LEU* 3.2 39.3 + - - +
120B GLU* 3.1 13.3 + - - +
122B ASN* 1.3 78.4 - - - +
124B VAL* 1.3 65.8 + - - +
126B LYS* 3.4 18.5 + - - +
127B GLU* 3.1 27.4 + - - +
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Residues in contact with VAL 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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45B LEU* 3.9 26.9 - - + -
94B ALA* 3.5 24.5 - - + +
95B ARG* 3.9 2.5 - - + -
109B PHE* 4.6 15.9 - - + -
116B PHE* 3.5 31.6 - - + -
120B GLU 3.1 15.1 + - - +
121B LEU* 3.2 11.9 + - + +
123B GLN* 1.3 77.4 - - - +
125B PHE* 1.3 63.9 + - + +
127B GLU* 3.0 3.8 + - - +
128B VAL* 2.8 31.7 + - + +
138B PHE* 5.9 0.2 - - + -
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Residues in contact with PHE 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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109B PHE* 4.8 2.7 - + - -
121B LEU* 3.0 56.9 + - + +
122B ASN* 3.7 5.2 - - - +
124B VAL* 1.3 81.4 - - + +
126B LYS* 1.3 57.0 + - - +
128B VAL* 3.3 2.2 + - - -
129B ARG* 3.0 26.9 + - - +
138B PHE* 3.7 33.7 - + - -
140B MSE 3.9 19.3 - - - -
199B VAL* 3.9 9.0 - - + -
202B LEU* 3.9 11.7 - - + -
203B ALA* 3.6 40.2 - - + -
206B TYR* 3.9 15.5 - + + -
207B PHE* 3.5 16.4 - + + -
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Residues in contact with LYS 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 ASN* 3.1 27.3 + - - +
123B GLN* 3.8 15.6 - - - +
124B VAL 3.2 0.2 - - - -
125B PHE* 1.3 76.1 - - - +
127B GLU* 1.3 59.7 + - + +
129B ARG* 3.9 9.4 + - - +
130B ARG* 3.1 26.7 + - - +
206B TYR* 3.3 43.1 - - + +
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Residues in contact with GLU 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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94B ALA 3.8 10.3 - - - +
95B ARG 3.4 24.2 - - - +
96B LYS* 3.6 19.3 + - - +
97B LEU* 3.0 28.4 + - + +
123B GLN 3.1 9.5 + - - +
124B VAL 3.0 8.6 + - - +
126B LYS* 1.3 77.1 - - + +
128B VAL* 1.3 61.3 + - + +
130B ARG* 2.7 48.6 + - - +
131B VAL* 3.0 35.9 + - - +
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Residues in contact with VAL 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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45B LEU* 3.6 29.8 - - + -
97B LEU* 5.6 0.4 - - + -
107B VAL* 4.0 13.5 - - + -
124B VAL* 2.8 26.6 + - + +
125B PHE* 3.7 5.4 - - - +
127B GLU* 1.3 75.8 - - - +
129B ARG* 1.3 66.9 + - - +
130B ARG 3.2 0.2 + - - -
131B VAL* 3.6 7.3 - - + +
132B LEU* 3.1 35.2 + - + +
138B PHE* 3.6 41.7 - - + -
207B PHE* 3.7 7.6 - - + -
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Residues in contact with ARG 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 PHE 3.0 16.8 + - - +
126B LYS* 3.9 7.6 + - - +
128B VAL* 1.3 77.4 - - - +
130B ARG* 1.3 66.4 + - - +
132B LEU* 3.7 15.2 + - - +
206B TYR* 3.3 43.2 + - + +
207B PHE* 3.6 18.4 - - + -
226B PRO* 4.4 14.1 - - + +
227B LYS* 3.0 37.4 + - - +
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Residues in contact with ARG 130 (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 LYS* 3.8 12.6 - - - +
97B LEU 3.1 18.4 + - - -
99B PHE 3.0 24.2 + - - -
100B GLU* 3.7 2.0 - - - +
101B ASP* 2.6 59.2 + - - +
102B LYS* 2.9 21.0 + - - +
126B LYS 3.1 18.4 + - - +
127B GLU* 2.7 43.5 + - - +
128B VAL 3.1 0.4 - - - -
129B ARG* 1.3 85.5 - - - +
131B VAL* 1.3 71.8 + - - +
132B LEU 3.2 3.2 + - - +
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Residues in contact with VAL 131 (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* 4.3 6.5 - - + -
97B LEU* 4.2 19.7 - - + -
99B PHE* 3.8 14.8 - - + -
100B GLU 3.8 16.8 - - - +
102B LYS 3.8 4.7 - - - +
103B THR 2.6 26.2 + - - -
104B PHE* 2.9 28.9 + - + -
107B VAL* 4.5 4.3 - - + -
127B GLU 3.0 18.3 + - - +
128B VAL* 3.6 9.6 - - - +
130B ARG* 1.3 97.5 - - - +
132B LEU* 1.3 57.8 + - - +
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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