Contacts of the helix formed by residues 115 - 125 (chain A) in PDB entry 2VWK
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 115 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A ASP 3.3 11.2 - - - +
114A ILE* 1.3 87.1 - - + +
116A PHE* 1.3 55.4 + - - +
117A ALA* 3.3 2.5 - - + +
118A LYS* 3.1 34.8 + - + +
119A ARG* 2.8 31.4 + - - +
355A TRP* 6.2 1.3 - - - +
1777A SO4 3.4 23.3 - - - +
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Residues in contact with PHE 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A TYR* 3.6 28.7 - + + -
14A PRO* 4.0 25.8 - - + -
16A ILE* 3.5 29.6 - - + -
34A PHE* 3.3 47.3 - + + -
36A PRO* 3.8 30.1 - - + -
90A PRO* 3.8 23.1 - - + -
93A GLN* 5.7 0.4 - - - -
114A ILE 3.4 2.6 + - - -
115A PRO* 1.3 72.0 - - - +
117A ALA* 1.3 62.4 + - - +
119A ARG* 3.3 10.2 + - + +
120A TYR* 3.0 23.6 + - - +
1777A SO4 2.7 20.0 + - - +
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Residues in contact with ALA 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A THR* 3.0 29.4 + - - +
6A ASP* 3.6 35.2 - - - +
7A TYR* 4.5 5.8 - - + +
16A ILE* 4.0 11.0 - - - -
115A PRO* 3.3 2.3 - - + +
116A PHE* 1.3 79.3 - - - +
118A LYS* 1.3 62.8 + - + +
120A TYR* 3.5 11.8 - - - +
121A LEU* 3.6 6.5 + - - +
1777A SO4 5.1 1.2 + - - +
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Residues in contact with LYS 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A ILE* 5.1 5.4 - - + -
115A PRO* 3.1 32.1 + - + +
117A ALA* 1.3 78.5 - - + +
119A ARG* 1.3 65.3 + - - +
120A TYR 2.9 1.6 - - - -
121A LEU* 3.0 14.2 + - + +
122A ILE* 3.1 21.7 + - + +
339A GLN* 3.3 29.0 + - - +
343A ASP* 2.8 43.2 + - - +
355A TRP* 3.7 36.6 - - + +
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Residues in contact with ARG 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A PHE* 4.1 9.2 - - + -
36A PRO* 6.5 0.7 - - + -
37A TYR* 3.3 37.2 + - - +
111A GLU* 2.8 34.3 + - - +
114A ILE* 3.8 43.3 - - + +
115A PRO 2.8 12.8 + - - +
116A PHE* 3.3 17.3 - - + +
118A LYS* 1.3 71.9 - - - +
120A TYR* 1.3 56.8 + - - +
122A ILE* 3.5 26.9 + - - +
123A ASP* 2.7 68.1 + - - +
358A LEU* 4.9 6.1 + - - +
362A TYR* 4.0 8.7 - - - +
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Residues in contact with TYR 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A THR* 4.6 9.9 - - + -
16A ILE* 3.8 35.2 - - + -
18A ILE* 3.6 18.9 - - + +
31A ASP* 2.7 35.0 + - - +
34A PHE* 3.5 34.1 - + + -
116A PHE 3.0 13.1 + - - +
117A ALA 3.5 10.3 - - - +
118A LYS 2.9 0.6 - - - -
119A ARG* 1.3 75.7 - - - +
121A LEU* 1.3 67.3 + - - +
124A LYS* 3.1 52.0 + - + +
126A LEU* 3.6 27.6 - - + +
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Residues in contact with LEU 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ILE* 4.4 13.9 - - + -
4A ASP* 5.8 0.9 - - - +
5A THR* 3.7 42.8 - - + +
117A ALA 3.6 3.3 + - - +
118A LYS* 3.0 7.6 + - + +
120A TYR* 1.3 78.7 - - + +
122A ILE* 1.3 63.9 + - - +
125A GLY 3.2 1.2 + - - -
126A LEU* 3.0 53.5 + - + +
128A PRO* 4.1 15.5 - - + -
338A GLY 3.9 9.2 - - - +
339A GLN* 3.7 23.1 - - - +
340A SER* 4.4 6.1 - - - +
359A ARG* 3.1 17.6 + - - +
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Residues in contact with ILE 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A ILE* 4.9 6.3 - - + -
118A LYS* 3.1 17.7 + - + +
119A ARG* 3.5 33.0 - - - +
121A LEU* 1.3 75.5 - - - +
123A ASP* 1.3 64.5 + - - +
125A GLY* 3.0 15.2 + - - -
339A GLN* 3.9 19.3 - - - +
355A TRP* 4.9 3.4 - - + +
358A LEU* 3.8 32.5 - - + +
359A ARG* 3.7 33.0 + - + +
362A TYR* 3.5 29.4 - - + -
363A GLU* 6.0 1.2 - - - +
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Residues in contact with ASP 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A PHE* 3.9 19.7 - - + -
37A TYR* 2.5 35.5 + - - -
119A ARG* 2.7 51.2 + - - +
122A ILE* 1.3 72.7 - - - +
124A LYS* 1.3 63.1 + - + +
125A GLY 3.2 0.7 + - - -
362A TYR* 3.4 41.1 + - + +
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Residues in contact with LYS 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ASP* 3.9 10.7 + - - -
33A ASN 5.7 2.6 + - - -
34A PHE* 4.2 17.3 - - + -
120A TYR* 3.1 56.3 + - + +
123A ASP* 1.3 79.0 - - + +
125A GLY* 1.3 62.0 + - - +
126A LEU* 3.2 24.6 + - + +
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Residues in contact with GLY 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A ILE 3.0 10.4 + - - -
123A ASP 3.2 1.8 + - - -
124A LYS* 1.3 77.8 - - - +
126A LEU* 1.3 63.0 + - - +
127A ILE* 3.5 17.2 - - - +
359A ARG* 3.3 15.9 - - - -
363A GLU* 6.1 0.2 - - - -
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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