Contacts of the strand formed by residues 36 - 44 (chain R) 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 ILE 36 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34R THR 3.7 14.4 - - - +
35R ASP* 1.3 71.7 - - - +
37R LEU* 1.3 67.6 + - - +
102R ALA* 3.5 1.4 - - - -
103R TYR* 2.8 38.1 + - + -
105R ILE* 4.1 8.7 - - - -
108R PHE* 3.7 39.7 - - + -
116R MET* 4.9 3.1 - - - -
120R ILE* 3.8 28.9 - - + -
138R LEU* 4.6 4.0 - - + -
139R ARG 3.5 9.4 - - - +
140R ILE* 4.9 7.9 - - + -
141R PRO* 3.8 18.8 - - + -
144R TYR* 4.2 23.6 - - + -
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Residues in contact with LEU 37 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31R VAL* 4.0 21.3 - - + -
35R ASP* 3.8 13.5 - - + -
36R ILE* 1.3 80.6 - - - +
38R ALA* 1.3 59.4 + - - +
85R TYR* 3.7 15.7 - - - +
101R VAL 3.3 4.3 - - - +
102R ALA* 3.8 24.5 - - + -
138R LEU* 3.1 11.8 - - - +
139R ARG* 2.8 76.3 + - + +
364R PHE* 3.8 21.5 - - + -
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Residues in contact with ALA 38 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37R LEU* 1.3 75.1 - - - +
39R ALA* 1.3 60.3 + - - +
40R PHE* 3.6 26.2 - - + -
99R ALA 3.5 1.4 - - - +
100R TYR* 3.3 6.1 - - - +
101R VAL* 2.8 31.8 + - + +
103R TYR* 3.7 16.8 - - + -
120R ILE* 4.2 1.6 - - + -
135R LEU* 3.9 4.0 - - + -
137R ASP 3.5 4.3 - - - -
138R LEU* 3.7 16.8 - - + -
364R PHE* 3.7 4.9 - - - -
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Residues in contact with ALA 39 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38R ALA* 1.3 71.8 - - - +
40R PHE* 1.3 61.2 + - - +
98R ILE* 4.1 4.7 - - + -
99R ALA 3.7 3.4 - - - -
100R TYR* 3.8 9.9 - - + -
135R LEU* 3.7 2.7 - - - +
136R GLU* 2.8 30.5 + - + +
137R ASP 3.0 13.4 + - - +
363R TYR* 3.8 30.5 - - + -
364R PHE* 3.7 22.1 - - + -
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Residues in contact with PHE 40 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38R ALA* 3.6 17.0 - - + -
39R ALA* 1.3 71.7 - - - +
41R ARG* 1.3 58.8 + - - +
42R MET* 3.5 1.3 + - + -
57R VAL* 3.7 22.4 - - + -
97R TYR 3.3 1.6 - - - +
98R ILE* 3.2 7.5 - - - -
99R ALA* 2.7 50.1 + - + +
101R VAL* 3.9 15.7 - - + -
103R TYR* 3.5 19.3 - - - -
120R ILE* 3.5 37.5 - - + -
124R VAL* 4.6 0.2 - - + -
125R PHE* 4.1 9.2 - + - -
133R LEU* 3.8 43.3 - - + -
134R ARG 3.4 1.6 - - - -
135R LEU* 4.1 20.0 - - + -
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Residues in contact with ARG 41 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39R ALA 4.0 1.2 + - - -
40R PHE* 1.3 68.9 - - - +
42R MET* 1.3 60.7 + - - +
43R THR* 5.2 0.6 + - - +
90R VAL* 3.8 13.9 - - + +
96R GLN* 3.0 41.9 + - + +
97R TYR 3.4 4.9 - - - +
98R ILE* 3.9 16.5 - - + +
132R ALA 4.1 0.2 - - - +
133R LEU* 3.3 5.8 + - - +
134R ARG* 2.7 46.1 + - + +
136R GLU* 2.8 34.7 + - + +
305R ARG* 3.3 50.5 + - - +
306R ASN* 4.3 7.6 - - - +
363R TYR* 3.6 15.7 + - - -
474R LYS 5.0 0.2 + - - -
475R LEU* 3.2 24.5 + - - -
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Residues in contact with MET 42 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40R PHE 4.2 4.9 - - - +
41R ARG* 1.3 74.0 - - - +
43R THR* 1.3 62.9 + - - +
44R PRO* 3.6 6.1 - - + +
50R PRO* 3.4 32.3 - - + +
53R CYS* 3.7 24.9 - - + +
54R GLY* 3.4 26.9 - - - +
57R VAL* 4.7 5.4 - - + -
87R ILE* 4.6 3.1 - - + -
96R GLN* 3.4 5.7 - - - -
97R TYR* 2.7 58.9 + - + +
99R ALA* 4.0 18.6 - - + -
130R LEU* 5.3 0.7 - - + -
132R ALA 5.0 0.7 - - - +
133R LEU* 3.9 19.7 - - + -
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Residues in contact with THR 43 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41R ARG* 5.2 0.5 + - - +
42R MET* 1.3 74.0 - - - +
44R PRO* 1.3 57.9 - - - +
95R ASN* 3.4 27.8 - - + +
96R GLN* 3.6 22.1 + - + +
130R LEU* 3.6 3.1 - - - -
131R ARG* 2.7 46.7 + - + +
132R ALA* 2.9 34.1 + - + +
306R ASN* 4.8 3.8 + - - +
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Residues in contact with PRO 44 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42R MET* 3.6 10.3 - - + +
43R THR* 1.3 85.9 - - - +
45R GLN* 1.3 62.2 + - - +
48R VAL* 3.6 25.1 - - + +
50R PRO* 4.5 5.8 - - + -
53R CYS* 3.8 33.4 - - + -
95R ASN* 2.8 47.3 + - - +
97R TYR* 3.9 20.6 - - + -
129R ALA 4.0 0.9 - - - +
131R ARG* 4.0 4.5 - - - -
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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