Contacts of the strand formed by residues 42 - 48 (chain R) in PDB entry 1G3I
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 42 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36R ARG* 3.8 4.2 - - - +
37R LEU* 2.9 58.5 + - + +
38R TYR* 4.3 3.4 - - + -
40R GLY 5.0 1.0 - - - -
41R LYS* 1.3 87.8 + - + +
43R LEU* 1.3 68.8 + - - +
44R ALA* 5.9 0.7 - - + -
60R PHE* 5.3 2.0 - - + -
64R LEU* 3.4 24.9 - - + -
69R GLY* 5.0 6.3 - - - +
71R LEU* 4.0 24.0 - - + -
98R ALA 3.7 4.7 - - - +
99R ASP* 3.6 19.3 - - + +
172R LEU* 4.6 0.4 - - - -
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Residues in contact with LEU 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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12R VAL* 3.7 24.5 - - + +
14R VAL* 4.4 18.8 - - + +
34R VAL* 5.1 0.4 - - + -
35R ARG 4.0 2.5 - - - +
36R ARG* 3.6 30.3 - - + +
42R VAL* 1.3 73.9 - - - +
44R ALA* 1.3 62.2 + - - +
96R ILE 3.6 1.7 - - - +
97R VAL* 3.1 7.8 - - - +
98R ALA 2.7 36.4 + - - +
170R GLU* 3.4 48.9 - - + +
172R LEU* 3.6 28.5 - - + -
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Residues in contact with ALA 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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14R VAL* 4.7 0.2 - - - -
33R LYS 3.9 0.5 - - - +
34R VAL* 3.1 7.8 - - - +
35R ARG* 2.8 40.4 + - - +
37R LEU* 4.8 9.9 - - + -
42R VAL* 4.1 1.1 + - + -
43R LEU* 1.3 76.4 - - - +
45R GLY* 1.3 59.0 + - - +
46R PHE* 4.7 2.2 - - - -
57R PHE* 3.4 34.1 - - + -
60R PHE* 5.6 0.2 - - + -
95R LEU* 5.1 1.8 - - + -
96R ILE 3.3 3.8 - - - -
97R VAL* 4.1 15.0 - - + -
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Residues in contact with GLY 45 (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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3R ILE* 4.0 21.1 - - - -
14R VAL* 4.3 3.4 - - - +
33R LYS 3.3 9.2 - - - -
34R VAL* 4.1 5.4 - - - -
44R ALA* 1.3 74.5 - - - +
46R PHE* 1.3 61.5 + - - -
95R LEU* 3.4 4.2 - - - -
96R ILE* 2.8 42.3 + - - +
123R ILE* 3.8 4.2 - - - +
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Residues in contact with PHE 46 (chain R).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1R THR* 3.9 3.5 - - - +
3R ILE* 3.4 16.6 - - - +
32R ARG 3.1 23.8 - - - -
33R LYS* 3.0 35.1 + - + +
35R ARG* 4.1 16.6 - - + -
44R ALA 4.7 3.1 - - - -
45R GLY* 1.3 77.0 - - - -
47R ALA* 1.3 64.8 + - - +
48R GLY 5.5 0.2 - - - -
50R THR* 6.3 0.9 - - - -
53R ALA* 3.6 30.5 - - + +
54R PHE* 3.4 33.4 - + - -
57R PHE* 4.8 13.2 - + + -
93R ALA* 6.0 0.2 - - + -
94R MET 3.5 4.9 - - - +
95R LEU* 3.4 20.4 - - + -
444S LEU* 5.8 2.9 - - + -
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Residues in contact with ALA 47 (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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1R THR* 3.7 21.5 - - + -
3R ILE* 3.8 4.7 - - + -
46R PHE* 1.3 80.0 - - - +
48R GLY* 1.3 58.3 + - - +
53R ALA* 5.1 0.4 - - - -
93R ALA* 3.2 3.3 - - - -
94R MET* 2.8 35.6 + - + +
123R ILE* 3.6 20.6 - - + -
124R GLY* 3.9 21.1 - - - +
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Residues in contact with GLY 48 (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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1R THR* 4.7 10.5 + - - -
46R PHE* 5.5 0.2 - - - -
47R ALA* 1.3 75.7 - - - +
49R GLY* 1.3 63.9 + - - -
50R THR* 3.4 4.2 + - - +
53R ALA* 4.6 4.9 - - - +
92R GLU 3.4 11.9 - - - -
93R ALA* 3.6 4.0 - - - -
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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