Contacts of the strand formed by residues 114 - 124 (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 PRO 114 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105C TYR* 6.0 4.7 - - + -
106C SER 3.1 12.8 - - - +
107C MET* 3.6 23.1 - - + -
112C LEU 4.6 0.4 - - - +
113C LEU* 1.3 95.5 - - + +
115C PHE* 1.3 61.1 + - - +
116C PHE* 4.6 9.4 - - + -
178C LEU* 3.2 49.4 + - + +
179C CYS 4.5 0.3 + - - -
182C MET* 6.0 0.2 - - - -
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Residues in contact with PHE 115 (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* 3.7 25.8 - + - -
105C TYR* 3.8 0.2 - - - -
106C SER* 2.9 54.0 + - - +
107C MET 3.7 14.1 - - - -
108C CYS* 3.5 28.9 - - + -
113C LEU 4.9 0.4 - - - +
114C PRO* 1.3 73.6 - - - +
116C PHE* 1.3 63.5 + - - +
147C GLN* 3.8 18.8 - - + -
149C GLN* 4.0 33.9 - - + -
152C LEU* 4.2 4.0 - - + -
175C GLY* 5.6 0.7 - - - -
176C VAL 3.2 11.7 - - - +
177C HIS* 3.4 37.0 - + + +
823D 8DG 4.7 2.2 - - - -
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Residues in contact with PHE 116 (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* 3.1 22.2 - - - +
105C TYR* 3.4 34.3 - + + -
114C PRO* 4.6 5.4 - - + -
115C PHE* 1.3 84.0 - - - +
117C GLY* 1.3 61.6 + - - +
175C GLY* 3.1 4.9 - - - -
176C VAL* 2.8 65.2 + - + +
178C LEU* 4.1 32.1 - - + -
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Residues in contact with GLY 117 (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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103C GLU* 3.2 9.0 - - - +
104C PHE* 3.0 29.4 + - - +
116C PHE* 1.3 84.1 - - - +
118C LYS* 1.3 66.5 + - - +
174C GLU 3.3 10.1 - - - -
175C GLY* 4.1 0.7 - - - -
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Residues in contact with LYS 118 (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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189B HIS* 4.3 16.2 + - + +
101C GLY* 3.7 21.8 - - - +
102C VAL 3.3 6.1 - - - +
103C GLU* 4.2 11.7 - - + -
104C PHE* 3.4 1.8 - - - -
117C GLY* 1.3 81.1 - - - +
119C VAL* 1.3 66.6 + - - +
120C HIS* 4.0 27.8 + - + +
172C VAL 3.9 0.7 - - - +
173C VAL* 3.6 1.9 - - - -
174C GLU* 2.9 38.1 + - + +
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Residues in contact with VAL 119 (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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101C GLY 3.6 2.1 + - - -
102C VAL* 2.8 40.2 + - + +
104C PHE* 3.6 20.9 - - + -
118C LYS* 1.3 77.9 - - - +
120C HIS* 1.3 64.3 + - - +
121C ILE* 4.0 10.5 - - + -
139C VAL* 3.9 39.0 - - + -
152C LEU* 5.3 0.4 - - + -
156C ILE* 4.1 9.2 - - + -
171C VAL* 3.8 27.1 - - + -
172C VAL 3.4 4.0 - - - +
173C VAL* 4.1 12.6 - - + -
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Residues in contact with HIS 120 (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 3.6 4.5 - - - -
100C LYS* 3.4 9.3 - - + +
101C GLY* 3.0 36.3 + - - -
118C LYS* 4.0 30.6 + - + +
119C VAL* 1.3 74.1 - - - +
121C ILE* 1.3 63.1 + - - +
171C VAL* 3.5 4.3 - - - +
172C VAL* 2.8 49.6 + - + +
174C GLU* 4.6 15.6 + - + +
211C PHE* 3.8 3.1 - - - -
215C LEU* 3.6 45.7 - - + +
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Residues in contact with ILE 121 (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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97C VAL 3.8 0.7 - - - +
98C VAL* 3.3 5.0 - - - +
99C VAL* 2.7 48.0 + - + +
102C VAL* 5.4 4.7 - - + -
119C VAL* 4.0 10.8 - - + -
120C HIS* 1.3 80.5 - - - +
122C GLY* 1.3 68.3 + - - +
123C TYR* 5.0 2.2 - - + -
135C PHE* 3.7 45.1 - - + +
139C VAL* 4.2 14.8 - - + -
156C ILE* 4.1 11.9 - - + -
160C ILE* 3.5 30.3 - - + -
169C VAL* 4.5 2.5 - - + -
170C GLY 3.5 6.7 - - - +
171C VAL* 4.3 6.7 - - + -
211C PHE* 3.7 4.5 - - - -
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Residues in contact with GLY 122 (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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97C VAL 3.3 8.5 - - - -
98C VAL* 4.3 2.5 - - - -
121C ILE* 1.3 76.8 - - - +
123C TYR* 1.3 63.9 + - - +
169C VAL* 3.4 2.3 - - - +
170C GLY 2.7 38.0 + - - +
201C PHE* 3.5 7.1 - - - -
211C PHE* 3.4 22.0 - - - -
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Residues in contact with TYR 123 (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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150B GLU* 4.7 1.2 + - - -
96C MET* 3.4 2.3 - - - +
97C VAL* 2.9 64.5 + - + +
99C VAL* 5.7 0.7 - - + -
121C ILE* 5.0 1.8 - - + -
122C GLY* 1.3 77.7 - - - +
124C ILE* 1.3 66.5 + - - +
125C PRO* 3.7 30.1 - - + +
128C LYS 4.1 1.8 - - - -
129C ILE* 3.3 14.6 - - - +
130C LEU* 3.1 24.6 + - - -
135C PHE* 3.3 31.4 - + - -
160C ILE* 5.1 0.9 - - + -
164C LEU* 3.6 23.1 - - + -
166C PRO* 4.0 10.5 - - + -
168C GLY 3.4 15.5 - - - +
169C VAL* 4.2 13.2 - - + -
201C PHE* 3.5 6.4 - - - -
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Residues in contact with ILE 124 (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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94C SER 3.4 22.7 - - - +
96C MET* 4.0 22.0 - - + +
123C TYR* 1.3 79.3 - - - +
125C PRO* 1.3 71.2 - - - +
166C PRO* 3.1 4.0 - - - +
167C GLN* 2.8 50.3 + - + +
168C GLY 3.2 5.3 + - - -
200C VAL* 4.0 11.0 - - + -
201C PHE* 3.8 8.5 - - + -
207C THR* 3.7 31.2 - - + +
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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