Contacts of the strand formed by residues 114 - 124 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A TYR* 5.9 4.5 - - + -
106A SER 3.1 13.7 - - - +
107A MET* 3.7 22.7 - - + -
112A LEU 4.6 0.2 - - - +
113A LEU* 1.3 95.0 - - + +
115A PHE* 1.3 59.3 + - - +
116A PHE* 4.6 9.0 - - + -
178A LEU* 3.1 51.9 + - + +
179A CYS 4.6 0.3 + - - -
182A MET* 6.0 0.2 - - - -
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Residues in contact with PHE 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A PHE* 3.7 24.7 - + - -
105A TYR* 3.8 0.2 - - - -
106A SER* 2.8 55.3 + - - +
107A MET 3.7 13.5 - - - -
108A CYS* 3.5 29.6 - - + -
113A LEU 4.9 0.9 - - - +
114A PRO* 1.3 74.1 - - - +
116A PHE* 1.3 62.3 + - - +
147A GLN* 3.9 14.6 - - + -
149A GLN* 3.8 39.7 - - + -
152A LEU* 4.2 4.7 - - + -
175A GLY* 5.6 0.4 - - - -
176A VAL 3.2 14.8 - - - +
177A HIS* 3.4 33.4 - + + +
821A 8DG 4.8 1.3 - - - -
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Residues in contact with PHE 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A PHE* 3.2 27.6 - - - +
105A TYR* 3.4 36.3 - + + -
114A PRO* 4.6 7.0 - - + -
115A PHE* 1.3 83.8 - - - +
117A GLY* 1.3 62.9 + - - +
175A GLY* 3.1 0.4 - - - -
176A VAL* 2.8 57.1 + - + +
178A LEU* 4.3 28.0 - - + -
181A MET* 6.1 1.1 - - + -
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Residues in contact with GLY 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A GLU* 3.2 8.7 - - - +
104A PHE* 2.9 31.1 + - - +
116A PHE* 1.3 83.7 - - - +
118A LYS* 1.3 66.0 + - - +
174A GLU 3.3 10.3 - - - -
175A GLY* 4.1 0.9 - - - -
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Residues in contact with LYS 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A GLY* 3.8 21.0 - - - +
102A VAL 3.4 6.5 - - - +
103A GLU* 4.2 11.7 - - + -
104A PHE* 3.5 1.7 - - - -
117A GLY* 1.3 80.0 - - - +
119A VAL* 1.3 64.0 + - - +
120A HIS* 4.0 26.6 + - + +
172A VAL 3.9 0.7 - - - +
173A VAL* 3.5 1.9 - - - -
174A GLU* 2.9 39.7 + - + +
189E HIS* 4.3 16.9 + - + +
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Residues in contact with VAL 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A GLY 3.5 2.3 + - - -
102A VAL* 2.8 40.5 + - + +
104A PHE* 3.6 20.6 - - + -
118A LYS* 1.3 77.7 - - - +
120A HIS* 1.3 64.0 + - - +
121A ILE* 4.0 14.8 - - + -
139A VAL* 3.8 35.0 - - + -
152A LEU* 5.4 0.4 - - + -
156A ILE* 4.1 9.2 - - + -
171A VAL* 3.8 26.5 - - + -
172A VAL 3.3 4.7 - - - +
173A VAL* 4.2 12.3 - - + -
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Residues in contact with HIS 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A VAL 3.6 4.0 - - - -
100A LYS* 3.4 9.1 - - + +
101A GLY* 3.0 36.4 + - - -
118A LYS* 4.0 31.2 + - + +
119A VAL* 1.3 72.8 - - - +
121A ILE* 1.3 61.4 + - - +
171A VAL* 3.4 4.7 - - - +
172A VAL* 2.8 50.4 + - + +
174A GLU* 4.7 15.6 + - + +
211A PHE* 3.8 3.5 - - + -
215A LEU* 3.7 47.0 - - + +
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Residues in contact with ILE 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A VAL 3.8 0.5 - - - +
98A VAL* 3.2 4.7 - - - +
99A VAL* 2.7 49.0 + - + +
102A VAL* 5.1 5.2 - - + -
119A VAL* 4.0 10.3 - - + -
120A HIS* 1.3 79.9 - - - +
122A GLY* 1.3 67.6 + - - +
123A TYR* 5.0 2.2 - - + -
135A PHE* 3.7 47.6 - - + +
139A VAL* 4.2 22.2 - - + -
156A ILE* 4.2 4.0 - - + -
160A ILE* 3.5 27.8 - - + -
169A VAL* 4.5 3.4 - - + -
170A GLY 3.5 6.5 - - - +
171A VAL* 4.3 9.0 - - + -
211A PHE* 3.7 4.2 - - - -
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Residues in contact with GLY 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A VAL 3.3 9.2 - - - -
98A VAL* 4.3 1.6 - - - -
121A ILE* 1.3 76.6 - - - +
123A TYR* 1.3 63.3 + - - +
169A VAL* 3.3 1.7 - - - +
170A GLY 2.7 38.5 + - - +
201A PHE* 3.5 7.8 - - - -
211A PHE* 3.5 22.2 - - - -
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Residues in contact with TYR 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A MET* 3.3 3.0 - - - +
97A VAL* 2.9 64.5 + - + +
99A VAL* 6.1 0.7 - - + -
121A ILE* 5.0 2.0 - - + -
122A GLY* 1.3 77.1 - - - +
124A ILE* 1.3 66.3 + - - +
125A PRO* 3.8 24.0 - - + +
128A LYS 4.0 7.2 - - - -
129A ILE* 3.2 14.0 - - - +
130A LEU 3.1 23.9 + - - -
132A LEU* 6.1 0.2 - - - +
135A PHE* 3.3 29.2 - + - -
160A ILE* 5.0 1.8 - - + -
164A LEU* 3.6 26.2 - - + -
166A PRO* 4.0 9.2 - - + -
168A GLY 3.2 15.5 - - - +
169A VAL* 4.0 11.4 - - + -
201A PHE* 3.6 5.4 - - - -
150E GLU* 4.6 2.3 + - - -
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Residues in contact with ILE 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A SER 3.6 20.6 - - - +
96A MET* 3.9 22.2 - - + +
123A TYR* 1.3 79.9 - - - +
125A PRO* 1.3 72.0 - - - +
166A PRO* 3.2 4.7 - - - +
167A GLN* 2.8 53.3 + - + +
168A GLY 3.2 4.6 + - - +
200A VAL* 3.9 11.0 - - + -
201A PHE* 3.8 6.3 - - + -
207A THR* 3.7 33.0 - - + +
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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