Contacts of the helix formed by residues 115 - 123 (chain B) in PDB entry 2W4G
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 SER 115 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113B LYS* 3.1 0.5 + - - +
114B LYS* 1.3 75.3 + - - +
116B PHE* 1.3 95.8 + - - +
117B LEU 3.4 0.6 - - - +
118B GLU* 3.0 24.3 + - - +
119B GLU* 2.9 41.1 + - - +
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Residues in contact with PHE 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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112B ILE* 3.9 16.6 - - + -
113B LYS* 3.4 55.2 - - + +
115B SER* 1.3 107.3 + - - +
117B LEU* 1.3 59.2 + - + +
119B GLU* 4.0 6.3 - - - +
120B LEU* 3.2 33.8 + - + +
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Residues in contact with LEU 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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101B PHE* 5.0 4.3 - - + -
104B LEU* 3.6 34.8 - - + -
112B ILE* 4.2 11.0 - - + -
113B LYS 3.5 7.1 + - - +
114B LYS* 5.9 0.2 - - - -
116B PHE* 1.3 78.3 - - + +
118B GLU* 1.3 65.5 + - - +
120B LEU* 3.7 24.0 - - + +
121B LEU* 2.9 49.1 + - + +
137B TRP* 5.0 7.9 - - + -
148B VAL* 5.6 1.6 - - + -
150B TYR* 3.0 37.2 - - + +
816M ILE* 5.1 4.7 - - + -
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Residues in contact with GLU 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 LYS* 3.4 22.1 - - - +
115B SER* 3.0 27.9 + - - +
117B LEU* 1.3 74.0 - - - +
119B GLU* 1.3 64.5 + - + +
121B LEU* 3.4 1.1 + - - -
122B THR* 3.0 23.5 + - - +
133B ILE* 3.9 17.6 - - + +
137B TRP* 3.2 40.7 + - + -
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Residues in contact with GLU 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 SER* 2.9 27.1 + - - +
116B PHE* 4.0 5.5 - - - +
118B GLU* 1.3 77.2 - - + +
120B LEU* 1.3 59.9 + - + +
122B THR* 2.9 9.9 + - - -
123B THR* 2.8 42.7 + - + +
19C ARG* 4.4 13.1 + - - +
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Residues in contact with LEU 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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104B LEU* 4.2 16.2 - - + -
116B PHE* 3.2 22.7 + - + +
117B LEU* 3.2 23.1 + - + +
119B GLU* 1.3 78.9 - - + +
121B LEU* 1.3 61.1 + - + +
123B THR* 3.6 17.9 + - - +
124B GLN* 4.8 5.2 + - - +
19C ARG* 4.3 16.8 - - - +
809M ARG* 4.3 31.9 - - - +
813M ILE* 4.0 32.7 - - + +
817M GLN* 4.5 1.9 + - - -
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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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117B LEU* 2.9 44.8 + - + +
118B GLU* 3.9 3.6 - - - +
120B LEU* 1.3 74.7 - - + +
122B THR* 1.3 61.9 + - - +
124B GLN 4.9 1.4 - - - +
127B ARG 4.2 0.3 - - - -
128B PHE* 3.1 39.4 + - + +
133B ILE* 4.0 21.8 - - + -
136B MET* 5.3 17.5 - - + -
137B TRP* 5.7 4.9 - - + -
813M ILE* 4.7 7.6 - - + -
816M ILE* 5.0 11.0 - - + -
817M GLN* 3.4 36.9 + - + +
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Residues in contact with THR 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 GLU 3.0 11.8 + - - +
119B GLU* 2.9 18.9 + - - -
121B LEU* 1.3 77.4 - - - +
123B THR* 1.3 67.0 + - - +
124B GLN 4.7 1.0 - - - +
126B ASP 4.4 12.3 - - - +
127B ARG* 4.6 5.9 - - + +
128B PHE 3.5 21.3 - - - +
130B PRO* 4.0 16.8 - - + -
133B ILE* 3.6 15.0 - - + -
19C ARG 4.4 6.6 - - - +
20C THR* 4.4 1.7 + - - -
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Residues in contact with THR 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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119B GLU* 2.8 36.9 + - + +
120B LEU* 3.6 14.2 + - - +
121B LEU 3.6 1.8 - - - -
122B THR* 1.3 79.7 - - - +
124B GLN* 1.3 74.2 + - - +
125B CYS 3.3 7.8 - - - +
19C ARG* 3.0 75.5 + - + +
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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