Contacts of the strand formed by residues 114 - 124 (chain B) 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 PRO 114 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105B TYR* 6.0 3.6 - - + -
106B SER 3.1 14.1 - - - +
107B MET* 3.8 21.8 - - + -
112B LEU 4.6 0.2 - - - +
113B LEU* 1.3 95.3 - - + +
115B PHE* 1.3 60.1 + - - +
116B PHE* 4.4 10.8 - - + -
177B HIS* 5.0 0.2 - - - +
178B LEU* 3.1 48.7 + - + +
179B CYS 4.5 0.2 + - - -
182B MET* 5.9 0.4 - - - -
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Residues in contact with PHE 115 (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 PHE* 3.7 26.5 - + - -
106B SER* 2.9 53.9 + - - +
107B MET 3.7 13.5 - - - -
108B CYS* 3.5 26.2 - - + -
113B LEU 4.8 0.4 - - - +
114B PRO* 1.3 75.5 - - - +
116B PHE* 1.3 62.1 + - - +
147B GLN* 3.8 19.3 - - + -
149B GLN* 3.9 38.6 - - + -
152B LEU* 4.2 4.5 - - + -
175B GLY* 5.6 0.4 - - - -
176B VAL 3.1 14.8 - - - +
177B HIS* 3.4 33.4 - + + +
822C 8DG 4.7 0.2 - - - -
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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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104B PHE* 3.2 26.7 - - - +
105B TYR* 3.5 33.2 - + + -
114B PRO* 4.4 6.3 - - + -
115B PHE* 1.3 84.1 - - - +
117B GLY* 1.3 61.6 + - - +
175B GLY* 3.1 0.3 - - - -
176B VAL* 2.8 59.5 + - + +
178B LEU* 4.0 35.4 - - + -
181B MET* 6.0 0.2 - - - -
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Residues in contact with GLY 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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103B GLU* 3.2 9.2 - - - +
104B PHE* 2.9 29.7 + - - +
116B PHE* 1.3 84.1 - - - +
118B LYS* 1.3 68.5 + - - +
174B GLU 3.2 10.3 - - - -
175B GLY* 4.1 0.9 - - - -
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Residues in contact with LYS 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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189A HIS* 3.8 42.1 + - - -
101B GLY* 4.0 17.9 - - - -
102B VAL 3.4 5.6 - - - +
103B GLU* 4.2 7.6 - - - +
104B PHE* 3.4 2.5 - - - -
117B GLY* 1.3 80.9 + - - +
119B VAL* 1.3 63.7 + - - +
120B HIS* 4.0 22.2 + - + +
172B VAL 3.9 0.9 - - - +
173B VAL* 3.6 1.7 - - - -
174B GLU* 2.9 36.7 + - + +
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Residues in contact with VAL 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B VAL 4.1 0.2 - - - +
101B GLY 3.6 1.7 + - - -
102B VAL* 2.8 40.7 + - + +
104B PHE* 3.6 24.7 - - + -
118B LYS* 1.3 74.3 - - - +
120B HIS* 1.3 64.0 + - - +
121B ILE* 4.0 9.9 - - + -
139B VAL* 4.0 38.1 - - + -
152B LEU* 5.3 1.3 - - + -
156B ILE* 4.1 9.4 - - + -
171B VAL* 3.8 27.1 - - + -
172B VAL 3.4 4.7 - - - +
173B VAL* 4.1 13.7 - - + -
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Residues in contact with HIS 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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99B VAL 3.6 4.0 - - - -
100B LYS* 3.4 9.3 - - + +
101B GLY* 3.0 34.9 + - - -
118B LYS* 4.0 24.4 + - + +
119B VAL* 1.3 73.5 - - - +
121B ILE* 1.3 62.7 + - - +
171B VAL* 3.4 4.9 - - - +
172B VAL* 2.8 57.3 + - + +
174B GLU* 4.6 15.7 + - + +
211B PHE* 3.8 3.5 - - + -
215B LEU* 3.6 40.0 - - + +
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Residues in contact with ILE 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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97B VAL 3.8 0.7 - - - +
98B VAL* 3.2 4.3 - - - +
99B VAL* 2.7 48.4 + - + +
102B VAL* 5.2 4.5 - - + -
119B VAL* 4.0 10.8 - - + -
120B HIS* 1.3 79.9 - - - +
122B GLY* 1.3 70.0 + - - +
123B TYR* 5.1 1.3 - - + -
135B PHE* 3.7 46.7 - - + +
139B VAL* 4.2 22.7 - - + -
156B ILE* 4.2 4.5 - - + -
160B ILE* 3.5 28.3 - - + -
169B VAL* 4.4 1.8 - - + -
170B GLY 3.5 6.7 - - - +
171B VAL* 4.3 8.3 - - + -
211B PHE* 3.7 4.0 - - - -
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Residues in contact with GLY 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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97B VAL 3.3 7.9 - - - -
98B VAL* 4.3 2.2 - - - -
121B ILE* 1.3 75.8 - - - +
123B TYR* 1.3 64.3 + - - +
169B VAL* 3.2 2.8 - - - +
170B GLY 2.7 38.1 + - - +
201B PHE* 3.4 8.3 - - - -
211B PHE* 3.4 23.1 - - - -
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Residues in contact with TYR 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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150A GLU* 4.5 2.1 + - - -
96B MET* 3.3 3.0 - - - +
97B VAL* 2.9 65.4 + - + +
99B VAL* 6.1 0.4 - - + -
121B ILE* 5.1 2.0 - - + -
122B GLY* 1.3 76.8 - - - +
124B ILE* 1.3 66.3 + - - +
125B PRO* 3.6 25.3 - - + +
128B LYS 4.0 6.5 - - - -
129B ILE* 3.2 28.2 - - - +
130B LEU 3.2 11.3 + - - -
132B LEU* 6.2 0.2 - - - +
135B PHE* 3.4 29.6 - + - -
160B ILE* 5.0 1.1 - - + -
164B LEU* 3.6 26.5 - - + -
166B PRO* 4.1 8.7 - - + -
168B GLY 3.3 14.8 - - - +
169B VAL* 4.0 11.9 - - + -
201B PHE* 3.4 6.4 - - - -
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Residues in contact with ILE 124 (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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94B SER 3.4 22.4 - - - +
95B GLU* 6.0 0.2 - - - -
96B MET* 3.9 23.6 - - + +
123B TYR* 1.3 80.1 - - - +
125B PRO* 1.3 56.4 - - - +
166B PRO* 3.2 5.0 - - - +
167B GLN* 2.8 63.0 + - + +
168B GLY 3.1 6.9 + - - -
200B VAL* 4.0 10.1 - - + -
201B PHE* 3.9 6.7 - - + -
207B THR* 3.6 33.7 - - + +
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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