Contacts of the strand formed by residues 114 - 124 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105D TYR* 6.1 3.8 - - + -
106D SER 3.1 13.9 - - - +
107D MET* 3.7 20.9 - - + -
112D LEU 4.6 0.2 - - - +
113D LEU* 1.3 95.9 - - + +
115D PHE* 1.3 59.8 + - - +
116D PHE* 4.6 9.0 - - + -
178D LEU* 3.1 51.8 + - + +
179D CYS 4.5 0.3 + - - -
182D MET* 5.9 0.4 - - - -
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Residues in contact with PHE 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D PHE* 3.6 26.8 - + - -
106D SER* 2.9 54.3 + - - -
107D MET 3.6 13.2 - - - -
108D CYS* 3.6 26.0 - - + -
113D LEU 4.9 0.4 - - - +
114D PRO* 1.3 74.4 - - - +
116D PHE* 1.3 62.7 + - - +
147D GLN* 3.9 18.8 - - + -
149D GLN* 3.9 33.2 - - + -
152D LEU* 4.2 5.6 - - + -
175D GLY* 5.6 0.4 - - - -
176D VAL 3.1 15.3 - - - +
177D HIS* 3.5 33.9 - + + +
824D 8DG 4.7 1.8 - - - -
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Residues in contact with PHE 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D PHE* 3.2 26.2 - - - +
105D TYR* 3.4 34.5 - + + -
114D PRO* 4.6 6.3 - - + -
115D PHE* 1.3 84.1 - - - +
117D GLY* 1.3 63.3 + - - +
175D GLY* 3.1 0.2 - - - -
176D VAL* 2.8 54.2 + - + +
178D LEU* 4.2 30.5 - - + -
181D MET* 6.1 0.2 - - - -
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Residues in contact with GLY 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D GLU* 3.2 9.0 - - - +
104D PHE* 2.9 29.6 + - - +
116D PHE* 1.3 84.4 - - - +
118D LYS* 1.3 66.0 + - - +
174D GLU 3.3 10.3 - - - -
175D GLY* 4.1 0.7 - - - -
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Residues in contact with LYS 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C HIS* 3.3 42.1 + - + +
101D GLY* 4.0 23.8 - - - -
102D VAL 3.3 7.2 - - - +
103D GLU* 4.5 3.3 - - + +
104D PHE* 3.5 3.2 - - - -
117D GLY* 1.3 80.2 - - - +
119D VAL* 1.3 64.6 + - - +
120D HIS* 4.0 22.9 + - + +
172D VAL 4.0 0.3 - - - +
173D VAL* 3.6 2.1 - - - -
174D GLU* 2.9 36.2 + - + +
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Residues in contact with VAL 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D VAL 4.1 0.2 - - - +
101D GLY 3.6 1.7 + - - -
102D VAL* 2.7 41.3 + - + +
104D PHE* 3.6 20.9 - - + -
118D LYS* 1.3 78.9 - - - +
120D HIS* 1.3 64.3 + - - +
121D ILE* 4.1 9.7 + - + +
139D VAL* 3.9 33.7 - - + -
152D LEU* 5.4 0.7 - - + -
156D ILE* 4.0 15.0 - - + -
171D VAL* 3.8 27.1 - - + -
172D VAL 3.4 4.7 - - - +
173D VAL* 4.2 12.3 - - + -
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Residues in contact with HIS 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D VAL 3.6 3.4 - - - -
100D LYS* 3.3 9.9 - - + +
101D GLY* 3.0 36.3 + - - -
118D LYS* 4.0 25.4 + - + +
119D VAL* 1.3 74.1 - - - +
121D ILE* 1.3 62.9 + - - +
170D GLY 3.8 0.5 - - - +
171D VAL* 3.3 4.9 - - - +
172D VAL* 2.8 50.2 + - + +
174D GLU* 4.7 15.0 + - + +
211D PHE* 3.9 3.1 - - + -
215D LEU* 3.6 46.8 - - + +
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Residues in contact with ILE 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D VAL 3.8 0.7 - - - +
98D VAL* 3.3 4.0 - - - +
99D VAL* 2.7 49.6 + - + +
102D VAL* 5.5 4.3 - - + -
119D VAL* 4.1 10.8 - - + -
120D HIS* 1.3 80.1 - - - +
122D GLY* 1.3 67.2 + - - +
123D TYR* 5.0 2.4 - - + -
135D PHE* 3.6 46.0 - - + +
139D VAL* 4.3 15.0 - - + -
156D ILE* 4.1 11.2 - - + -
160D ILE* 3.5 28.7 - - + -
169D VAL* 4.6 2.7 - - + -
170D GLY 3.4 7.6 - - - +
171D VAL* 4.1 7.9 - - + -
211D PHE* 3.8 4.0 - - - -
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Residues in contact with GLY 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D VAL 3.3 8.3 - - - -
98D VAL* 4.3 2.7 - - - -
121D ILE* 1.3 76.7 - - - +
123D TYR* 1.3 63.4 + - - +
169D VAL* 3.4 2.4 - - - +
170D GLY 2.7 38.7 + - - +
201D PHE* 3.5 8.0 - - - -
211D PHE* 3.4 23.2 - - - -
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Residues in contact with TYR 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C GLU* 4.4 2.8 + - - -
96D MET* 3.1 2.9 - - - +
97D VAL* 2.8 68.0 + - + +
99D VAL* 6.0 0.7 - - + -
121D ILE* 5.0 2.0 - - + -
122D GLY* 1.3 77.1 - - - +
124D ILE* 1.3 66.6 + - - +
125D PRO* 3.8 29.8 - - + +
128D LYS 3.9 1.8 - - - -
129D ILE* 3.2 14.6 - - - +
130D LEU 3.2 23.9 + - - -
135D PHE* 3.3 33.6 - + - -
160D ILE* 5.1 1.6 - - + -
164D LEU* 3.6 27.1 - - + -
166D PRO* 4.1 7.4 - - + -
168D GLY 3.3 14.1 - - - +
169D VAL* 4.2 13.5 - - + -
201D PHE* 3.6 5.3 - - - -
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Residues in contact with ILE 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D SER 3.4 21.8 - - - +
95D GLU* 6.0 0.2 - - - -
96D MET* 3.6 28.0 - - + +
123D TYR* 1.3 74.4 - - - +
125D PRO* 1.3 62.8 - - - +
166D PRO* 3.2 5.0 - - - +
167D GLN* 2.8 60.6 + - + +
168D GLY 3.2 5.2 + - - +
200D VAL* 3.9 11.9 - - + -
201D PHE* 3.8 7.2 - - + -
207D THR* 3.8 30.3 - - + +
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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