Contacts of the strand formed by residues 116 - 124 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156K GLN* 4.1 26.7 - - + +
159K ARG* 4.4 10.8 - - + -
160K ASP* 3.9 20.6 - - - +
165K TYR* 4.0 8.1 - - + -
110P PHE* 4.3 6.0 - - - +
111P ASP* 2.9 29.0 + - - +
114P LYS* 3.8 34.1 - - + +
115P GLN* 1.3 76.7 - - - +
117P GLN* 1.3 77.6 + - - +
118P ILE* 3.5 6.4 + - + -
184R ASN* 6.0 0.7 - - - +
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Residues in contact with GLN 117 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159K ARG* 4.8 3.3 - - - -
160K ASP* 5.0 1.0 + - - -
163K ASN* 5.4 0.3 + - - -
165K TYR* 3.1 66.2 - - + +
166K GLY 5.3 0.2 + - - -
43P GLU* 4.7 2.3 - - - +
106P ARG* 5.7 2.8 + - - +
108P VAL* 3.3 31.9 - - + +
109P ALA 3.4 11.4 - - - +
110P PHE* 3.7 22.6 - - + -
116P VAL* 1.3 83.0 - - - +
118P ILE* 1.3 57.9 + - - +
119P MET 3.1 27.1 + - - +
120P GLY* 4.0 4.0 - - - -
183R LYS* 5.0 1.2 + - - -
187R ARG* 4.4 9.4 + - - -
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Residues in contact with ILE 118 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166K GLY* 3.5 16.8 + - - +
396K ASP* 4.3 8.1 - - - +
32P TYR* 6.1 0.2 - - - -
38P TRP* 3.4 62.9 - - + -
109P ALA* 2.8 20.7 + - + +
111P ASP* 4.0 25.6 - - + +
114P LYS* 4.0 31.6 - - + +
116P VAL* 3.5 4.2 + - + +
117P GLN* 1.3 73.1 - - - +
119P MET* 1.3 63.9 + - - +
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Residues in contact with MET 119 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165K TYR* 4.5 2.9 - - - -
166K GLY* 3.8 12.8 - - - +
432K ASN* 5.3 3.1 - - - +
15P PHE* 5.6 0.9 - - + -
29P GLN* 4.1 20.4 - - - +
32P TYR* 5.2 7.6 - - + -
33P ILE* 3.6 37.2 - - + -
38P TRP* 4.7 9.0 - - + -
107P LEU 4.4 2.9 - - - +
108P VAL* 4.0 4.5 - - - -
109P ALA* 3.2 40.1 + - + -
117P GLN* 3.1 20.4 + - - +
118P ILE* 1.3 86.5 - - + +
120P GLY* 1.3 61.5 + - - +
121P PHE* 3.5 29.8 - - + -
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Residues in contact with GLY 120 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165K TYR 4.4 4.7 + - - +
166K GLY* 4.7 1.0 - - - -
14P THR* 3.3 26.4 + - - +
15P PHE* 5.2 0.4 - - - -
106P ARG* 6.4 0.4 - - - -
107P LEU 3.1 14.4 - - - -
108P VAL* 4.1 1.8 - - - -
117P GLN* 4.0 10.8 - - - -
119P MET* 1.3 82.0 - - - +
121P PHE* 1.3 68.1 + - - +
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Residues in contact with PHE 121 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12P PHE 5.3 2.9 - - - -
14P THR 3.4 18.8 - - - +
15P PHE* 3.8 21.1 - + + -
21P LEU* 3.8 21.1 - - + -
26P ILE* 4.2 14.6 - - + -
29P GLN* 3.6 26.0 - - + -
106P ARG* 3.4 7.9 - - - +
107P LEU* 2.9 49.3 + - + -
119P MET* 3.5 30.1 - - + -
120P GLY* 1.3 79.5 - - - +
122P LEU* 1.3 75.2 + - - +
123P VAL* 3.6 19.3 - - + -
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Residues in contact with LEU 122 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12P PHE* 3.8 60.3 + - + +
14P THR 4.9 1.4 + - - -
21P LEU* 5.5 1.4 - - - +
26P ILE* 5.9 0.7 - - - +
73P TRP* 4.0 6.5 - - + -
104P TYR* 3.9 7.2 - - + -
105P VAL 3.4 20.4 - - - +
106P ARG* 4.1 4.0 - - + +
121P PHE* 1.3 83.9 - - - +
123P VAL* 1.3 59.2 + - - +
124P GLN 3.5 20.9 - - - +
125P ARG* 4.0 34.8 - - + +
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Residues in contact with VAL 123 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26P ILE* 4.8 18.3 - - + +
42P LEU* 4.5 3.8 - - + -
93P ILE* 4.2 32.5 - - + +
97P THR* 5.0 1.7 - - + +
105P VAL* 2.8 38.0 + - + +
106P ARG 4.4 0.4 - - - -
107P LEU* 4.0 20.6 - - + +
121P PHE* 3.6 31.4 + - + -
122P LEU* 1.3 72.4 - - - +
124P GLN* 1.3 64.2 + - + +
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Residues in contact with GLN 124 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97P THR* 3.1 39.4 - - + +
100P PHE 2.9 27.9 + - - -
101P PRO* 3.5 16.6 + - - +
103P ALA 2.9 18.8 + - - +
104P TYR* 3.3 3.8 - - - -
105P VAL* 2.9 37.3 + - + +
122P LEU* 3.5 12.4 - - - +
123P VAL* 1.3 80.8 - - - +
125P ARG* 1.3 71.3 + - - +
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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