Contacts of the strand formed by residues 114 - 124 (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 PRO 114 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105E TYR* 6.0 4.5 - - + -
106E SER 3.2 13.0 - - - +
107E MET* 3.5 20.8 - - + -
112E LEU 4.6 0.2 - - - +
113E LEU* 1.3 95.3 - - + +
115E PHE* 1.3 59.8 + - - +
116E PHE* 4.5 9.2 - - + -
178E LEU* 3.1 52.1 + - + +
179E CYS 4.5 0.5 + - - -
182E MET* 5.8 0.4 - - - -
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Residues in contact with PHE 115 (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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825A 8DG 4.7 0.9 - - - -
104E PHE* 3.6 26.9 - + - -
106E SER* 2.9 52.5 + - - -
107E MET 3.8 13.2 - - - -
108E CYS* 3.6 29.4 - - + -
113E LEU 4.9 0.2 - - - +
114E PRO* 1.3 74.9 - - - +
116E PHE* 1.3 63.9 + - - +
147E GLN* 3.8 19.5 - - + -
149E GLN* 3.8 34.5 - - + -
152E LEU* 4.2 4.7 - - + -
175E GLY* 5.5 0.4 - - - -
176E VAL 3.1 14.4 - - - +
177E HIS* 3.4 31.6 - + + +
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Residues in contact with PHE 116 (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* 3.1 26.7 - - - +
105E TYR* 3.4 34.8 - + + -
114E PRO* 4.5 6.1 - - + -
115E PHE* 1.3 83.7 - - - +
117E GLY* 1.3 61.4 - - - +
175E GLY* 3.1 0.5 - - - -
176E VAL* 2.8 57.5 + - + +
178E LEU* 4.1 31.0 - - + -
181E MET* 6.2 0.9 - - + -
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Residues in contact with GLY 117 (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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103E GLU* 3.2 8.8 - - - +
104E PHE* 3.0 29.4 + - - +
116E PHE* 1.3 84.6 - - - +
118E LYS* 1.3 67.0 + - - +
174E GLU 3.3 10.8 - - - -
175E GLY* 4.1 0.9 - - - -
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Residues in contact with LYS 118 (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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189D HIS* 3.8 39.3 + - - +
191D ARG* 6.1 1.0 - - - +
101E GLY* 3.9 21.2 - - - -
102E VAL 3.4 5.8 - - - +
103E GLU* 4.3 5.6 - - + -
104E PHE* 3.5 2.5 - - - -
117E GLY* 1.3 79.9 - - - +
119E VAL* 1.3 65.6 + - - +
120E HIS* 3.9 23.0 + - + +
172E VAL 3.9 0.7 - - - +
173E VAL* 3.6 2.4 - - - -
174E GLU* 3.0 35.5 + - + +
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Residues in contact with VAL 119 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101E GLY 3.6 2.8 + - - -
102E VAL* 2.8 38.6 + - + +
104E PHE* 3.6 20.2 - - + -
118E LYS* 1.3 78.3 - - - +
120E HIS* 1.3 63.9 + - - +
121E ILE* 4.0 13.9 - - + -
139E VAL* 3.8 28.9 - - + -
152E LEU* 5.4 1.1 - - + -
156E ILE* 4.0 14.6 - - + -
171E VAL* 3.7 28.5 - - + -
172E VAL 3.3 4.9 - - - +
173E VAL* 4.2 13.2 - - + -
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Residues in contact with HIS 120 (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 3.6 4.0 - - - -
100E LYS* 3.4 9.3 - - + +
101E GLY* 3.0 36.2 + - - -
118E LYS* 3.9 26.9 + - + +
119E VAL* 1.3 73.6 - - - +
121E ILE* 1.3 63.2 + - - +
171E VAL* 3.4 5.0 - - - +
172E VAL* 2.8 49.5 + - + +
174E GLU* 4.7 15.0 + - + +
211E PHE* 3.8 3.3 - - - -
215E LEU* 3.5 45.2 - - + +
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Residues in contact with ILE 121 (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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97E VAL 3.9 0.4 - - - +
98E VAL* 3.3 5.2 - - - +
99E VAL* 2.8 48.0 + - + +
102E VAL* 5.1 5.6 - - + -
119E VAL* 4.0 10.8 - - + -
120E HIS* 1.3 79.4 - - - +
122E GLY* 1.3 68.7 + - - +
123E TYR* 5.0 1.8 - - + -
135E PHE* 3.8 45.1 - - + +
139E VAL* 4.1 23.8 - - + -
156E ILE* 4.3 2.7 - - + -
160E ILE* 3.6 29.2 - - + -
169E VAL* 4.7 2.0 - - + -
170E GLY 3.5 6.3 - - - +
171E VAL* 4.3 7.6 - - + -
211E PHE* 3.7 3.8 - - - -
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Residues in contact with GLY 122 (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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97E VAL 3.3 8.7 - - - -
98E VAL* 4.3 2.2 - - - -
121E ILE* 1.3 76.2 - - - +
123E TYR* 1.3 65.4 + - - +
169E VAL* 3.3 3.1 - - - +
170E GLY 2.7 33.9 + - - +
201E PHE* 3.5 7.9 - - - -
211E PHE* 3.4 21.1 - - - -
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Residues in contact with TYR 123 (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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150D GLU* 4.7 1.2 + - - -
96E MET* 3.2 3.5 - - - +
97E VAL* 2.8 61.9 + - + +
99E VAL* 6.2 0.4 - - + -
121E ILE* 5.0 1.3 - - + -
122E GLY* 1.3 78.3 - - - +
124E ILE* 1.3 66.8 + - - +
125E PRO* 3.5 25.1 - - + +
128E LYS 4.0 6.1 - - - -
129E ILE* 3.2 15.7 - - + +
130E LEU 3.1 25.6 + - - -
135E PHE* 3.3 33.2 - + - -
160E ILE* 5.1 1.6 - - + -
164E LEU* 3.6 21.8 - - + -
166E PRO* 4.0 10.3 - - + -
168E GLY 3.2 15.0 - - - +
169E VAL* 4.1 12.6 - - + -
201E PHE* 3.5 7.1 - - - -
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Residues in contact with ILE 124 (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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94E SER 3.4 21.5 - - - +
96E MET* 4.0 21.3 - - + +
123E TYR* 1.3 79.6 - - - +
125E PRO* 1.3 59.1 - - - +
166E PRO* 3.2 4.3 - - - +
167E GLN* 2.8 62.8 + - + +
168E GLY 3.2 4.7 + - - -
200E VAL* 3.9 13.2 - - + -
201E PHE* 3.8 7.6 - - + -
207E THR* 3.7 31.9 - - + +
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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