Contacts of the strand formed by residues 31 - 39 (chain F) in PDB entry 5GAG
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 31 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8F TYR* 5.6 0.2 - - + -
30F ARG* 1.3 79.9 - - - +
32F GLU* 1.3 64.5 + - - +
33F LYS 4.2 1.1 - - - +
34F ILE* 4.5 3.8 - - + -
96F MET* 3.5 28.8 - - + +
97F TRP* 3.9 34.9 - - + -
100F PHE* 5.1 9.0 - - + -
156F ILE* 3.5 31.9 - - + -
157F THR 3.8 6.1 - - - +
158F THR* 4.2 3.6 - - - +
169F LEU* 4.3 15.3 - - + -
170F LEU* 6.3 1.8 - - + -
173F PHE* 4.3 13.0 - - + -
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Residues in contact with GLU 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2315A G 4.8 1.9 + - - -
45B A 5.6 5.1 + - - +
30F ARG* 3.4 4.2 + - - -
31F VAL* 1.3 72.5 - - - +
33F LYS* 1.3 87.1 + - + +
92F ARG* 4.1 23.6 + - - +
93F GLY 4.7 1.2 + - - -
96F MET* 3.1 15.6 - - - +
157F THR* 3.0 25.3 + - + +
158F THR 5.5 0.5 - - - +
159F THR* 4.4 21.0 - - + +
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Residues in contact with LYS 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2314A A 3.0 42.9 + - - -
2315A G 3.1 28.5 + - - -
31F VAL* 4.2 0.3 - - - +
32F GLU* 1.3 97.5 - - + +
34F ILE* 1.3 68.3 + - - +
35F THR* 4.0 6.2 + - - +
90F THR* 3.9 15.2 - - + +
91F LEU 3.6 11.0 - - - +
92F ARG* 3.8 32.0 - - + +
96F MET* 3.8 2.2 - - - -
156F ILE* 3.7 1.2 - - - +
157F THR* 2.9 41.6 + - - +
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Residues in contact with ILE 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F VAL* 4.9 1.8 - - + -
33F LYS* 1.3 80.0 - - - +
35F THR* 1.3 62.6 + - - +
36F LEU* 3.9 9.0 - - + -
89F VAL 3.7 1.4 - - - +
90F THR* 4.7 0.2 - - - -
91F LEU* 2.8 42.8 + - + +
96F MET* 3.5 38.1 - - + +
99F PHE* 3.7 32.8 - - + -
100F PHE* 4.0 26.0 - - + -
154F ILE* 5.1 1.3 - - + -
155F THR 3.3 8.3 - - - +
156F ILE* 3.9 24.2 - - + -
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Residues in contact with THR 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2313A C 3.7 33.9 - - - +
2314A A 3.6 18.4 - - - +
33F LYS* 4.0 7.1 + - - +
34F ILE* 1.3 71.4 - - - +
36F LEU* 1.3 78.2 + - - +
88F LYS* 4.6 7.2 - - + -
89F VAL 3.4 6.1 - - - +
90F THR* 3.4 34.2 - - - +
153F ASP 3.7 0.5 - - - +
155F THR* 2.9 38.4 + - - +
157F THR* 5.5 0.3 + - - -
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Residues in contact with LEU 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34F ILE* 3.9 7.2 - - + -
35F THR* 1.3 87.7 - - - +
37F ASN* 1.3 61.8 + - - +
57F LEU* 3.8 30.7 - - + +
60F ILE* 4.1 6.7 - - + -
61F SER* 4.0 17.9 - - - -
88F LYS* 3.1 7.3 - - - +
89F VAL 2.9 39.3 + - - +
91F LEU* 4.2 8.3 - - + -
99F PHE* 3.5 47.6 - - + -
152F LEU* 4.4 4.3 - - + -
153F ASP 3.2 4.3 - - - +
154F ILE* 3.6 17.5 - - + -
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Residues in contact with ASN 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2305A U 4.2 2.9 + - - +
2312A U 2.5 50.7 + - - -
2313A C 3.3 36.7 + - - +
35F THR 4.3 0.2 - - - -
36F LEU* 1.3 76.0 - - - +
38F MET* 1.3 64.9 + - - +
39F GLY 3.5 10.9 - - - +
57F LEU* 4.9 0.4 - - - +
87F CYS 3.3 10.8 - - - +
88F LYS* 3.8 3.5 - - - +
152F LEU* 3.7 2.9 - - - +
153F ASP* 2.9 53.8 + - + +
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Residues in contact with MET 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2305A U 3.8 4.7 - - - +
2312A U 4.8 0.2 + - - -
37F ASN* 1.3 78.1 - - - +
39F GLY* 1.3 65.1 + - - +
40F VAL* 3.6 3.6 + - + +
53F ALA* 3.6 26.5 - - + +
56F ASP* 3.7 23.3 - - + -
57F LEU* 3.7 26.0 - - + +
60F ILE* 3.8 4.0 - - + -
86F GLY* 3.4 2.9 - - - -
87F CYS* 2.9 41.4 + - - +
135F GLN* 4.9 1.1 - - + -
150F ARG* 3.9 25.1 - - + -
151F GLY 3.6 16.2 - - - +
152F LEU* 3.6 29.2 - - + -
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Residues in contact with GLY 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2305A U 3.1 12.7 + - - +
2306A C 3.0 31.4 + - - +
2307A G 4.7 3.1 - - - -
2312A U 4.3 18.8 + - - -
37F ASN* 3.5 8.0 - - - +
38F MET* 1.3 73.0 - - - +
40F VAL* 1.3 63.0 + - - +
42F GLU* 4.9 0.5 - - - +
85F ILE* 4.4 4.5 - - - -
86F GLY* 4.7 1.6 - - - -
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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