Contacts of the strand formed by residues 116 - 124 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156B GLN* 4.2 25.6 - - + +
159B ARG* 4.4 11.4 - - + -
160B ASP* 3.9 20.4 - - - +
165B TYR* 4.0 8.5 - - + -
110C PHE* 4.3 6.4 - - - +
111C ASP* 2.9 27.0 + - - +
114C LYS* 3.8 36.6 - - + +
115C GLN* 1.3 77.0 - - - +
117C GLN* 1.3 77.3 + - - +
118C ILE* 3.5 5.7 + - + -
184V ASN* 6.1 0.2 - - - +
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Residues in contact with GLN 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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159B ARG* 4.8 2.9 - - - -
160B ASP* 5.0 1.0 + - - -
163B ASN* 5.4 0.5 + - - -
165B TYR* 3.1 65.7 - - + +
166B GLY 5.2 0.2 + - - -
43C GLU* 4.6 2.9 - - - +
106C ARG* 5.7 2.1 + - - +
108C VAL* 3.3 31.6 - - + +
109C ALA 3.4 11.2 - - - +
110C PHE* 3.7 23.4 - - + -
116C VAL* 1.3 82.6 - - - +
118C ILE* 1.3 58.1 + - - +
119C MET 3.1 27.6 + - - +
120C GLY* 4.0 4.2 - - - -
183V LYS* 5.1 0.9 + - - -
187V ARG* 4.4 9.2 + - - -
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Residues in contact with ILE 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B GLY* 3.4 18.2 + - - -
396B ASP* 4.3 8.9 - - + +
32C TYR* 6.0 0.3 - - - -
38C TRP* 3.4 64.0 - - + -
109C ALA* 2.8 21.8 + - + +
111C ASP* 4.0 25.6 - - + +
114C LYS* 4.0 30.7 - - + +
116C VAL* 3.5 4.2 + - + -
117C GLN* 1.3 74.9 - - - +
119C MET* 1.3 62.5 + - - +
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Residues in contact with MET 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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165B TYR* 4.5 2.5 - - - -
166B GLY* 3.8 14.5 - - - +
432B ASN* 5.6 2.9 - - - +
15C PHE* 5.6 0.7 - - + -
29C GLN* 4.1 20.9 - - - +
32C TYR* 5.1 8.5 - - + -
33C ILE* 3.5 37.0 - - + -
38C TRP* 4.7 8.5 - - + -
107C LEU 4.3 3.6 - - - +
108C VAL* 4.0 4.3 - - - -
109C ALA* 3.2 40.0 + - + -
117C GLN* 3.1 20.2 + - - +
118C ILE* 1.3 86.6 - - + +
120C GLY* 1.3 62.4 + - - +
121C PHE* 3.5 31.0 - - + -
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Residues in contact with GLY 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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165B TYR 4.4 4.4 + - - +
166B GLY* 4.7 1.2 - - - -
14C THR* 3.4 25.7 + - - +
15C PHE* 4.9 0.5 - - - -
106C ARG* 6.3 0.7 - - - -
107C LEU 3.1 14.6 - - - -
108C VAL* 4.3 1.3 - - - -
117C GLN* 4.0 10.8 - - - -
119C MET* 1.3 83.1 - - - +
121C PHE* 1.3 67.6 + - - +
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Residues in contact with PHE 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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12C PHE 5.3 2.7 - - - -
14C THR 3.3 20.9 - - - +
15C PHE* 3.8 20.4 - + + -
21C LEU* 3.7 22.0 - - + -
26C ILE* 4.2 14.1 - - + -
29C GLN* 3.6 27.8 - - + -
106C ARG* 3.4 7.7 - - - +
107C LEU* 3.0 48.1 + - + -
119C MET* 3.5 30.1 - - + -
120C GLY* 1.3 79.7 - - - +
122C LEU* 1.3 75.0 + - - +
123C VAL* 3.6 18.8 - - + -
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Residues in contact with LEU 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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12C PHE* 3.8 57.9 + - + -
14C THR 4.8 1.4 + - - -
21C LEU* 5.5 1.6 - - - +
26C ILE* 5.9 0.7 - - - +
73C TRP* 4.1 5.2 - - + -
104C TYR* 3.9 6.7 - - + -
105C VAL 3.3 22.0 - - - +
106C ARG* 4.1 3.1 - - + +
121C PHE* 1.3 86.2 - - - +
123C VAL* 1.3 60.8 + - - +
124C GLN 3.4 21.3 - - - +
125C ARG* 4.0 34.5 - - + +
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Residues in contact with VAL 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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26C ILE* 4.8 18.7 - - + +
42C LEU* 4.4 3.6 - - + -
93C ILE* 4.3 31.7 - - + +
97C THR* 5.1 1.5 - - + +
105C VAL* 2.8 39.1 + - + +
106C ARG 4.4 0.2 - - - -
107C LEU* 4.0 17.7 - - + +
121C PHE* 3.5 34.9 + - + +
122C LEU* 1.3 73.2 - - - +
124C GLN* 1.3 61.5 + - + +
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Residues in contact with GLN 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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97C THR* 3.2 38.4 - - + +
100C PHE 2.9 28.5 + - - -
101C PRO* 3.5 15.6 + - - +
103C ALA 3.0 18.7 + - - +
104C TYR* 3.3 4.0 - - - -
105C VAL* 2.9 37.0 + - + +
122C LEU* 3.4 12.1 - - - +
123C VAL* 1.3 80.8 - - - +
125C ARG* 1.3 72.2 + - - +
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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