Contacts of the helix formed by residues 131 - 140 (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 GLU 131 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B ARG* 4.8 15.2 + - - +
129B THR* 3.0 10.0 + - - +
130B PRO* 1.3 75.4 - - + +
132B GLU* 1.3 62.7 + - + +
134B LYS* 3.2 8.3 + - - +
135B ASN* 2.8 36.5 + - - +
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Residues in contact with GLU 132 (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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127B ARG 4.2 0.3 - - - +
128B PHE* 3.4 16.9 - - + -
129B THR* 2.9 48.0 + - + +
131B GLU* 1.3 78.8 - - + +
133B ILE* 1.3 57.8 + - + +
135B ASN* 3.3 13.3 + - - +
136B MET* 2.9 33.1 + - + +
821M ARG* 3.0 38.2 + - + +
824M MET* 5.4 1.5 - - - +
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Residues in contact with ILE 133 (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* 3.9 18.2 - - + +
121B LEU* 4.0 25.8 - - + -
122B THR* 3.6 21.5 - - + -
128B PHE* 3.3 25.8 - - + +
129B THR 2.9 17.1 + - - +
130B PRO* 4.3 7.2 - - + -
131B GLU 3.4 0.2 - - - -
132B GLU* 1.3 72.5 - - + +
134B LYS* 1.3 63.1 + - + +
136B MET* 3.1 11.8 - - + +
137B TRP* 3.0 58.2 + - + +
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Residues in contact with LYS 134 (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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130B PRO* 3.4 24.1 + - - +
131B GLU* 3.2 9.1 + - - +
133B ILE* 1.3 76.1 - - + +
135B ASN* 1.3 63.9 + - - +
137B TRP* 3.2 18.0 + - + +
138B ALA* 3.1 22.9 + - - +
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Residues in contact with ASN 135 (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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131B GLU* 2.8 29.8 + - - +
132B GLU* 3.3 10.9 - - - +
134B LYS* 1.3 75.2 - - - +
136B MET* 1.3 57.3 + - - +
138B ALA* 3.3 7.0 + - - +
139B ALA* 2.8 35.0 + - + +
824M MET* 4.5 16.1 - - - -
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Residues in contact with MET 136 (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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121B LEU* 5.3 14.1 - - + -
132B GLU* 2.9 20.9 + - + +
133B ILE* 3.1 21.3 - - + +
135B ASN* 1.3 72.9 - - - +
137B TRP* 1.3 60.6 + - + +
139B ALA* 4.9 0.2 - - - -
140B PHE* 2.7 67.2 + - + +
144B VAL* 5.4 4.0 - - + -
153B ILE* 5.7 6.3 - - + -
820M VAL* 2.9 50.7 - - + -
824M MET* 4.6 7.6 - - - +
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Residues in contact with TRP 137 (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* 3.7 29.9 + - + +
117B LEU* 5.0 7.2 - - + -
118B GLU* 3.2 52.3 + - + -
121B LEU* 5.7 4.7 - - + -
133B ILE* 3.0 47.5 + - + +
134B LYS* 3.2 18.5 + - + +
136B MET* 1.3 72.9 - - + +
138B ALA* 1.3 56.2 + - - +
140B PHE 3.0 18.4 - - - +
141B PRO* 3.2 16.8 - - - +
142B PRO* 5.0 0.7 - - - +
144B VAL* 3.1 47.1 - - + +
148B VAL* 4.9 3.8 - - + -
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Residues in contact with ALA 138 (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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134B LYS 3.1 12.6 + - - +
135B ASN* 3.7 9.4 - - - +
137B TRP* 1.3 79.2 - - - +
139B ALA* 1.3 57.1 + - + +
141B PRO* 3.2 13.0 - - - +
142B PRO* 5.8 0.5 - - - +
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Residues in contact with ALA 139 (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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135B ASN* 2.8 19.5 + - + +
138B ALA* 1.3 70.3 - - - +
140B PHE* 1.3 71.1 + - + +
141B PRO* 3.2 10.8 - - - +
156B VAL* 4.9 5.9 - - - +
161B GLU* 5.1 3.4 - - - +
823M PHE* 4.8 3.6 - - + -
824M MET* 3.6 26.2 - - + -
827M LYS* 3.9 18.8 - - - +
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Residues in contact with PHE 140 (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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136B MET* 2.7 49.0 + - + +
137B TRP 3.0 1.8 - - - +
139B ALA* 1.3 75.7 - - + +
141B PRO* 1.3 55.6 - - - +
143B ASP* 3.5 20.0 - - - +
144B VAL* 2.9 34.7 - - + +
153B ILE* 3.7 38.1 - - + -
156B VAL* 4.0 13.5 - - + -
157B ILE* 3.3 27.1 - - + -
820M VAL* 4.8 5.4 - - + -
823M PHE* 3.3 39.0 - + - -
824M MET* 3.8 10.5 - - + -
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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