Contacts of the strand formed by residues 116 - 124 (chain W) in PDB entry 1UW9
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 VAL 116 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184H ASN* 6.0 0.7 - - - +
155V ILE* 6.6 0.7 - - + -
156V GLN* 4.2 25.1 - - + +
159V ARG* 4.4 11.0 - - + -
160V ASP* 3.8 20.0 - - - +
165V TYR* 3.9 8.7 - - + -
110W PHE* 4.3 6.8 - - - +
111W ASP* 2.9 27.9 + - + +
114W LYS* 3.8 35.0 - - + +
115W GLN* 1.3 76.4 - - - +
117W GLN* 1.3 79.1 + - - +
118W ILE* 3.4 6.4 + - + +
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Residues in contact with GLN 117 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183H LYS* 4.9 1.0 + - - -
187H ARG* 4.4 9.5 + - - -
159V ARG* 4.8 3.1 - - - -
160V ASP* 5.0 1.0 + - - -
165V TYR* 3.2 64.4 - - + +
166V GLY 5.3 0.2 + - - -
43W GLU* 4.7 2.6 - - - +
106W ARG* 5.7 1.7 + - - +
108W VAL* 3.3 32.0 - - + +
109W ALA 3.4 10.8 - - - +
110W PHE* 3.8 22.6 - - + -
116W VAL* 1.3 83.5 - - - +
118W ILE* 1.3 58.0 + - - +
119W MET 3.1 27.5 + - - +
120W GLY* 3.9 4.2 - - - -
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Residues in contact with ILE 118 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166V GLY* 3.5 17.1 + - - -
396V ASP* 4.4 8.3 - - + +
38W TRP* 3.3 60.9 - - + -
109W ALA* 2.8 20.9 + - + +
111W ASP* 3.9 31.6 - - + +
114W LYS* 4.0 28.7 - - + +
116W VAL* 3.4 3.8 + - + -
117W GLN* 1.3 73.5 - - - +
119W MET* 1.3 63.1 + - - +
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Residues in contact with MET 119 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165V TYR* 4.5 2.0 - - - -
166V GLY* 3.8 14.6 - - - +
432V ASN* 5.3 5.2 - - - +
15W PHE* 5.6 1.1 - - + -
29W GLN* 4.1 21.1 - - - +
32W TYR* 5.3 5.6 - - + -
33W ILE* 3.6 36.8 - - + -
38W TRP* 4.7 9.0 - - + -
107W LEU 4.3 3.6 - - - +
108W VAL* 3.4 4.0 - - - -
109W ALA* 3.2 39.2 + - + -
117W GLN* 3.1 20.0 + - - +
118W ILE* 1.3 82.8 - - + +
120W GLY* 1.3 63.8 + - - +
121W PHE* 3.5 29.4 - - + -
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Residues in contact with GLY 120 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165V TYR* 4.3 5.2 + - - +
166V GLY* 4.6 1.0 - - - -
14W THR* 3.3 26.0 + - - +
15W PHE* 4.9 0.5 - - - -
106W ARG* 6.4 0.2 - - - -
107W LEU 3.1 14.1 - - - -
108W VAL* 4.4 1.6 - - - -
117W GLN* 3.9 10.5 - - - -
119W MET* 1.3 82.9 - - - +
121W PHE* 1.3 69.2 + - - +
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Residues in contact with PHE 121 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12W PHE 5.3 2.5 - - - -
14W THR 3.4 19.7 - - - +
15W PHE* 3.8 22.2 - + + -
21W LEU* 3.8 21.5 - - + -
26W ILE* 4.2 13.9 - - + -
29W GLN* 3.6 26.9 - - + -
106W ARG* 3.4 7.7 - - - +
107W LEU* 3.0 48.5 + - + -
119W MET* 3.5 30.5 - - + -
120W GLY* 1.3 77.7 - - - +
122W LEU* 1.3 74.0 + - - +
123W VAL* 3.6 18.8 - - + +
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Residues in contact with LEU 122 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12W PHE* 3.8 60.7 + - + -
14W THR 4.9 1.2 + - - -
21W LEU* 5.5 1.6 - - - +
26W ILE* 5.8 0.7 - - - +
73W TRP* 4.1 7.0 - - + -
104W TYR* 4.0 7.4 - - + -
105W VAL 3.4 19.7 - - - +
106W ARG* 4.1 3.5 - - + +
121W PHE* 1.3 83.4 - - - +
123W VAL* 1.3 57.8 + - - +
124W GLN 3.5 21.8 - - - +
125W ARG* 4.0 34.3 - - + +
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Residues in contact with VAL 123 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26W ILE* 4.8 19.0 - - + +
42W LEU* 4.4 4.0 - - + -
93W ILE* 4.3 31.4 - - + +
97W THR* 5.1 1.3 - - + +
105W VAL* 2.8 42.6 + - + +
106W ARG 4.3 0.4 - - - -
107W LEU* 4.0 21.3 - - + +
121W PHE* 3.5 30.7 + - + -
122W LEU* 1.3 71.8 - - - +
124W GLN* 1.3 58.2 + - + +
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Residues in contact with GLN 124 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97W THR* 3.1 37.2 - - + +
100W PHE 2.9 27.9 + - - -
101W PRO* 3.4 17.2 + - - +
103W ALA 3.0 17.6 + - - +
104W TYR* 3.3 3.8 - - - -
105W VAL* 2.9 37.7 + - + +
122W LEU* 3.5 12.2 - - - +
123W VAL* 1.3 81.2 - - - +
125W ARG* 1.3 71.7 + - - +
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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