Contacts of the helix formed by residues 131 - 144 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87C ALA* 3.0 17.0 + - - -
89C PHE* 3.8 10.4 - - - -
130C LEU* 1.3 76.5 - - - +
132C LEU* 1.3 66.4 + - - +
133C SER 3.3 2.7 - - - -
134C LYS* 2.9 20.8 + - - +
135C PHE* 3.9 0.9 + - - -
822C 8DG 3.4 32.3 - - - -
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Residues in contact with LEU 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B GLN* 5.3 0.7 - - + -
150B GLU* 4.1 6.5 - - - +
177B HIS* 3.4 44.0 - - + +
180B MET* 3.7 21.2 - - + +
192B THR* 3.6 23.8 - - + +
97C VAL* 4.7 2.9 - - + -
99C VAL* 3.9 27.4 - - + +
130C LEU 3.2 3.5 + - - +
131C GLY* 1.3 69.2 - - - -
133C SER* 1.3 63.2 + - - +
135C PHE* 3.2 29.5 + - + +
136C ALA 4.1 1.4 + - - -
822C 8DG 3.1 40.0 + - + +
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Residues in contact with SER 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B CYS 5.4 0.4 - - - -
180B MET* 3.8 28.8 - - - -
185B VAL* 3.6 12.9 - - - +
132C LEU* 1.3 78.4 - - - +
134C LYS* 1.3 61.9 + - - +
136C ALA* 3.0 15.8 + - - +
137C ARG* 3.1 14.3 + - - +
822C 8DG 2.6 63.0 + - - +
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Residues in contact with LYS 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C VAL* 3.6 12.9 + - - +
84C VAL* 3.5 32.3 + - + +
85C GLY* 5.5 1.2 - - - -
87C ALA* 3.5 12.8 - - + -
130C LEU* 3.7 19.7 - - + -
131C GLY 2.9 13.3 + - - +
133C SER* 1.3 74.8 + - - +
135C PHE* 1.3 59.1 + - - +
137C ARG* 3.6 16.7 - - - +
138C ILE* 2.9 34.3 + - - +
822C 8DG 2.9 73.5 + - - +
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Residues in contact with PHE 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C VAL* 3.9 30.1 - - + -
102C VAL* 5.3 1.6 - - + -
121C ILE* 3.7 26.3 - - + +
123C TYR* 3.3 33.4 - + - -
130C LEU* 3.7 43.5 - - + -
132C LEU* 3.2 26.6 + - + +
133C SER 3.1 0.4 - - - -
134C LYS* 1.3 77.4 - - - +
136C ALA* 1.3 59.1 + - - +
138C ILE* 3.3 6.9 + - - +
139C VAL* 3.0 33.4 + - - +
160C ILE* 3.7 40.2 - - + -
164C LEU* 4.5 1.1 - - + -
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Residues in contact with ALA 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B MET* 4.7 6.5 - - + -
185B VAL* 4.0 12.1 - - + -
187B LYS* 3.7 33.2 - - + -
102C VAL* 3.9 18.5 - - + +
132C LEU 4.1 0.4 + - - -
133C SER* 3.0 12.8 + - - +
135C PHE* 1.3 76.6 - - - +
137C ARG* 1.3 60.1 + - - +
139C VAL* 3.2 3.1 + - - +
140C ASP* 2.9 34.3 + - - -
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Residues in contact with ARG 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B GLY* 3.8 21.2 - - - -
185B VAL* 3.4 22.6 - - + +
78C GLN* 5.0 2.6 + - - +
83C VAL* 3.4 40.1 - - + +
133C SER 3.1 5.0 + - - +
134C LYS* 3.2 16.9 + - - +
136C ALA* 1.3 77.7 - - - +
138C ILE* 1.3 55.8 + - - +
140C ASP* 3.5 8.2 + - - +
141C MET* 3.0 26.5 + - - +
822C 8DG 2.7 43.1 + - - -
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Residues in contact with ILE 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C LEU* 4.1 17.7 - - + -
83C VAL* 4.2 9.2 - - + -
84C VAL* 4.0 20.2 - - + -
130C LEU* 4.3 13.2 - - + -
134C LYS 2.9 20.5 + - - +
135C PHE* 3.6 6.3 - - - +
137C ARG* 1.3 74.9 - - - +
139C VAL* 1.3 66.9 + - - +
141C MET* 3.2 11.4 + - - +
142C PHE* 3.2 24.9 - - + -
156C ILE* 4.3 17.9 - - + +
159C ALA* 3.7 25.6 - - + -
160C ILE* 4.2 22.0 - - + +
163C VAL* 4.9 1.8 - - + -
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Residues in contact with VAL 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C VAL* 4.1 17.5 - - + -
103C GLU 4.5 0.2 - - - +
104C PHE* 3.7 29.4 - - + -
119C VAL* 3.9 36.3 - - + -
121C ILE* 4.2 10.1 - - + -
135C PHE 3.0 18.7 + - - +
136C ALA* 3.2 9.4 + - - +
138C ILE* 1.3 77.7 - - - +
140C ASP* 1.3 63.1 + - - +
142C PHE* 3.3 1.9 + - - +
143C ALA* 2.8 30.1 + - + +
152C LEU* 4.6 1.5 - - + +
156C ILE* 4.1 16.2 - - + -
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Residues in contact with ASP 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B VAL* 5.3 6.2 - - - +
187B LYS* 2.8 35.4 + - - -
78C GLN* 4.3 5.1 - - - +
104C PHE* 5.1 1.9 - - - -
105C TYR 5.7 0.5 + - - -
136C ALA 2.9 18.1 + - - +
137C ARG* 3.9 7.3 - - - +
139C VAL* 1.3 80.6 - - - +
141C MET* 1.3 61.9 + - - +
143C ALA* 4.2 6.5 - - - +
144C ARG* 3.0 68.8 + - - +
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Residues in contact with MET 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C GLY* 3.0 18.3 - - - +
78C GLN* 3.2 41.2 + - + +
79C ARG* 4.7 0.2 - - - -
80C LEU* 3.9 35.7 - - + +
83C VAL* 3.9 21.8 - - + -
137C ARG 3.0 14.8 + - - +
138C ILE* 3.2 10.7 + - - +
140C ASP* 1.3 77.7 - - - +
142C PHE* 1.3 83.1 + - + +
145C ARG* 2.9 37.1 + - - +
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Residues in contact with PHE 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C LEU* 5.0 2.7 - - + -
138C ILE* 3.2 30.6 + - + +
139C VAL 3.3 2.7 + - - +
140C ASP 3.3 0.2 - - - -
141C MET* 1.3 102.7 - - + +
143C ALA* 1.3 62.7 + - - +
144C ARG 3.4 0.7 - - - -
145C ARG* 3.6 33.6 - - - +
147C GLN* 3.0 27.4 + - - +
152C LEU* 3.7 16.4 - - + -
155C GLN* 3.5 54.7 - - + +
156C ILE* 4.5 4.7 - - + -
159C ALA* 3.7 26.9 - - + -
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Residues in contact with ALA 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C PHE* 4.3 18.8 - - + -
105C TYR 3.5 20.4 - - - +
106C SER* 2.8 33.0 + - - -
139C VAL* 2.8 21.2 + - + +
140C ASP* 4.1 6.7 - - - +
142C PHE* 1.3 75.6 - - - +
144C ARG* 1.3 57.7 + - + +
145C ARG 2.9 10.0 + - - +
152C LEU* 3.8 13.7 - - + +
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Residues in contact with ARG 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B LYS* 5.2 2.2 - - - +
71C PHE* 3.5 49.8 - - + +
72C LEU* 3.0 29.6 - - + +
73C THR* 3.3 4.5 - - - -
74C ARG* 4.0 20.7 - - - +
75C GLY 3.0 29.5 + - - +
78C GLN* 5.5 0.8 + - - +
105C TYR 4.7 6.7 + - - +
140C ASP* 3.0 57.0 + - - +
142C PHE 3.4 0.2 - - - -
143C ALA* 1.3 74.3 - - + +
145C ARG* 1.3 60.7 + - - +
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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