Contacts of the helix formed by residues 131 - 144 (chain E) in PDB entry 1WUR
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 GLY 131 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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824D 8DG 3.4 32.8 - - - -
87E ALA* 3.0 16.5 + - - -
89E PHE* 3.8 10.2 - - - -
130E LEU* 1.3 75.2 - - - +
132E LEU* 1.3 67.9 + - - +
133E SER 3.3 2.7 - - - -
134E LYS* 2.9 19.4 + - - +
135E PHE* 3.9 0.9 + - - -
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Residues in contact with LEU 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D GLN* 5.3 1.3 - - + -
150D GLU* 4.0 9.0 - - - +
177D HIS* 3.4 44.4 - - + +
180D MET* 3.7 21.1 - - + +
192D THR* 3.5 24.0 - - + +
824D 8DG 3.2 39.1 + - + +
97E VAL* 4.6 3.6 - - + -
99E VAL* 3.9 25.2 - - + +
130E LEU 3.2 4.6 + - - +
131E GLY* 1.3 69.4 - - - -
133E SER* 1.3 62.0 + - - +
135E PHE* 3.1 28.3 + - + +
136E ALA 4.1 1.0 + - - -
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Residues in contact with SER 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179D CYS 5.4 0.2 - - - -
180D MET* 3.8 29.5 - - - -
185D VAL* 3.6 12.5 - - - +
824D 8DG 2.6 62.0 + - - +
132E LEU* 1.3 78.2 - - - +
134E LYS* 1.3 62.1 + - - +
135E PHE 3.1 0.2 - - - -
136E ALA* 3.1 14.7 + - - +
137E ARG* 3.1 14.4 + - - +
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Residues in contact with LYS 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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824D 8DG 2.9 77.7 + - - +
83E VAL* 3.6 17.5 + - - +
84E VAL* 3.4 28.2 + - + +
85E GLY* 5.3 1.4 - - - -
87E ALA* 3.6 10.8 - - + -
130E LEU* 3.7 22.0 - - + -
131E GLY 2.9 13.3 + - - +
133E SER* 1.3 73.9 + - - +
135E PHE* 1.3 60.1 + - - +
136E ALA 3.2 0.2 - - - -
137E ARG* 3.3 15.6 + - - +
138E ILE* 2.9 32.9 + - - +
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Residues in contact with PHE 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E VAL* 3.9 30.1 - - + -
102E VAL* 5.3 1.3 - - + -
121E ILE* 3.8 26.1 - - + +
123E TYR* 3.3 35.2 - + - -
130E LEU* 3.7 42.6 - - + -
132E LEU* 3.1 26.6 + - + +
133E SER 3.1 0.4 - - - -
134E LYS* 1.3 78.6 - - - +
136E ALA* 1.3 56.6 + - - +
138E ILE* 3.3 6.7 + - - +
139E VAL* 3.0 33.7 + - - +
160E ILE* 3.6 41.3 - - + -
164E LEU* 4.5 1.6 - - + -
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Residues in contact with ALA 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180D MET* 4.6 8.5 - - + +
185D VAL* 3.9 12.1 - - + -
187D LYS* 3.7 32.3 - - + -
102E VAL* 4.0 19.2 - - + +
132E LEU 4.1 0.8 + - - -
133E SER 3.1 11.0 + - - +
135E PHE* 1.3 78.0 - - - +
137E ARG* 1.3 59.5 + - - +
139E VAL* 3.3 2.3 + - - +
140E ASP* 3.0 34.8 + - - +
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Residues in contact with ARG 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184D GLY* 3.8 22.6 - - - -
185D VAL* 3.3 21.4 - - + +
824D 8DG 2.9 42.4 + - - -
78E GLN* 5.1 3.1 + - - +
83E VAL* 3.4 39.3 - - + +
133E SER 3.1 6.3 + - - +
134E LYS* 3.3 16.2 + - - +
136E ALA* 1.3 76.9 - - - +
138E ILE* 1.3 56.9 + - - +
140E ASP* 3.5 7.9 + - - +
141E MET* 3.0 26.9 + - - +
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Residues in contact with ILE 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80E LEU* 4.0 18.6 - - + -
83E VAL* 4.2 7.9 - - + -
84E VAL* 4.2 14.8 - - + -
130E LEU* 4.1 21.1 - - + -
134E LYS 2.9 20.4 + - - +
135E PHE* 3.6 6.1 - - - +
136E ALA 3.2 0.2 - - - -
137E ARG* 1.3 74.5 - - - +
139E VAL* 1.3 67.6 + - - +
141E MET* 3.1 15.0 + - - +
142E PHE* 3.3 24.6 + - + -
156E ILE* 4.2 18.2 - - + +
159E ALA* 3.8 24.9 - - + -
160E ILE* 4.2 18.4 - - + +
163E VAL* 4.9 1.8 - - + -
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Residues in contact with VAL 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102E VAL* 4.0 22.0 - - + -
103E GLU 4.6 0.2 - - - +
104E PHE* 3.7 29.8 - - + -
119E VAL* 3.8 24.5 - - + -
121E ILE* 4.1 10.3 - - + -
135E PHE 3.0 19.8 + - - +
136E ALA 3.5 7.6 - - - +
138E ILE* 1.3 76.9 - - - +
140E ASP* 1.3 62.2 + - - +
142E PHE* 3.2 2.3 + - - +
143E ALA* 2.9 30.2 + - + +
152E LEU* 4.6 1.6 - - + +
156E ILE* 4.0 23.3 - - + -
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Residues in contact with ASP 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185D VAL* 5.2 6.9 - - - +
187D LYS* 2.9 35.0 + - - -
78E GLN* 4.4 4.4 - - - +
103E GLU 4.6 0.3 - - - +
104E PHE* 5.1 2.1 - - - -
105E TYR 5.7 0.7 + - - -
136E ALA 3.0 19.8 + - - +
137E ARG* 3.8 7.2 - - - +
138E ILE 3.3 0.2 - - - -
139E VAL* 1.3 81.4 - - - +
141E MET* 1.3 61.7 + - - +
143E ALA* 4.3 6.2 - - - +
144E ARG* 3.0 66.5 + - - +
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Residues in contact with MET 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75E GLY* 3.1 23.6 - - - +
78E GLN* 3.4 43.0 + - + +
80E LEU* 3.7 31.2 - - + +
83E VAL* 3.9 21.3 - - + -
137E ARG 3.0 14.7 + - - +
138E ILE* 3.1 11.2 + - - +
140E ASP* 1.3 76.4 - - - +
142E PHE* 1.3 82.4 + - + +
145E ARG* 3.0 37.1 + - - +
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Residues in contact with PHE 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80E LEU* 4.9 3.1 - - + -
138E ILE* 3.3 30.0 + - + +
139E VAL 3.2 3.3 + - - +
141E MET* 1.3 103.4 - - + +
143E ALA* 1.3 63.2 + - - +
144E ARG 3.4 0.4 - - - -
145E ARG* 3.6 34.8 - - - +
147E GLN* 2.9 29.7 + - - +
152E LEU* 3.6 17.5 - - + -
155E GLN* 3.6 46.0 - - + +
156E ILE* 4.4 5.4 - - + -
159E ALA* 3.7 26.2 - - + -
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Residues in contact with ALA 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104E PHE* 4.2 24.7 - - + -
105E TYR 3.4 18.6 - - - +
106E SER* 2.7 32.3 + - - -
139E VAL* 2.9 19.2 + - + +
140E ASP* 4.2 6.5 - - - +
142E PHE* 1.3 75.4 - - - +
144E ARG* 1.3 57.8 + - + +
145E ARG 2.8 12.2 + - - +
152E LEU* 3.7 11.2 - - + +
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Residues in contact with ARG 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187D LYS* 5.2 3.2 - - - +
71E PHE* 3.4 41.1 - - + +
72E LEU* 3.0 28.7 - - + +
73E THR 3.3 4.3 - - - -
74E ARG* 3.9 31.4 - - - +
75E GLY* 2.9 29.8 + - - +
78E GLN* 5.6 0.9 + - - -
105E TYR 4.7 8.0 + - - +
140E ASP* 3.0 55.6 + - - +
142E PHE 3.4 0.2 - - - -
143E ALA* 1.3 73.4 - - + +
145E ARG* 1.3 62.5 + - - +
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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