Contacts of the strand formed by residues 42 - 48 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36J ARG* 3.4 7.1 - - - +
37J LEU* 3.0 64.5 + - + +
38J TYR* 4.0 7.0 - - + -
40J GLY 3.7 0.4 - - - -
41J LYS* 1.3 85.7 - - + +
43J LEU* 1.3 70.6 + - - +
60J PHE* 5.4 0.9 - - + -
64J LEU* 3.5 24.5 - - + -
69J GLY 4.9 4.9 - - - +
71J LEU* 4.0 19.3 - - + -
98J ALA 3.6 4.9 - - - +
99J ASP* 3.6 17.9 - - + +
172J LEU* 5.0 0.2 - - - +
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Residues in contact with LEU 43 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12J VAL* 4.0 9.4 - - + +
14J VAL* 3.6 24.0 - - + -
34J VAL* 5.1 0.9 - - + -
35J ARG 3.9 2.2 - - - +
36J ARG* 3.6 34.5 - - + +
42J VAL* 1.3 81.6 - - - +
44J ALA* 1.3 60.0 + - - +
96J ILE 3.4 2.2 - - - +
97J VAL* 2.9 6.6 - - - +
98J ALA 2.6 46.2 + - - +
170J GLU* 3.1 39.5 - - + +
171J GLU* 3.9 13.2 - - - -
172J LEU* 3.8 16.6 - - + -
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Residues in contact with ALA 44 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14J VAL* 4.5 0.2 - - - -
34J VAL* 3.1 6.9 - - - +
35J ARG 2.9 37.6 + - - +
37J LEU* 3.7 19.1 - - + -
42J VAL 4.0 0.2 + - - -
43J LEU* 1.3 76.6 - - - +
45J GLY* 1.3 59.4 + - - +
46J PHE* 4.3 0.9 + - - -
57J PHE* 3.6 32.0 - - + -
60J PHE* 5.2 0.2 - - + -
95J LEU* 5.0 2.5 - - + -
96J ILE 3.1 4.7 - - - -
97J VAL* 4.1 13.2 - - + -
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Residues in contact with GLY 45 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3J ILE* 3.6 9.9 - - - -
14J VAL* 4.1 6.4 - - - +
33J LYS 3.4 9.0 - - - -
34J VAL* 3.6 14.1 - - - -
44J ALA* 1.3 76.7 - - - +
46J PHE* 1.3 60.2 + - - -
95J LEU* 3.1 5.9 - - - +
96J ILE 2.7 41.3 + - - -
123J ILE* 3.8 2.9 - - - +
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Residues in contact with PHE 46 (chain J).
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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444C LEU* 5.2 5.4 - - + -
1J THR* 4.7 1.0 - - - +
3J ILE* 2.8 18.4 - - - +
32J ARG 3.6 17.9 - - - -
33J LYS* 2.9 33.5 + - + +
35J ARG* 4.1 17.9 - - + -
44J ALA 4.8 1.3 - - - -
45J GLY* 1.3 73.4 - - - -
47J ALA* 1.3 62.0 + - - +
50J THR* 6.4 0.2 - - - -
53J ALA* 3.6 27.6 - - + -
54J PHE* 3.5 35.4 - + - -
57J PHE* 3.7 34.1 - + + -
94J MET 3.4 3.8 - - - +
95J LEU* 3.2 18.4 - - + -
123J ILE* 4.3 0.2 - - - -
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Residues in contact with ALA 47 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1J THR* 4.4 14.6 - - + -
3J ILE* 4.0 7.6 - - + -
46J PHE* 1.3 78.4 - - - +
48J GLY* 1.3 58.0 + - - +
53J ALA* 4.9 0.9 - - - +
93J ALA* 3.2 4.6 - - - +
94J MET* 2.8 40.4 + - - +
123J ILE* 3.9 21.5 - - + -
124J GLY* 4.1 21.1 - - - +
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Residues in contact with GLY 48 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1J THR* 5.0 9.2 + - - -
47J ALA* 1.3 75.9 - - - +
49J GLY* 1.3 64.2 + - - -
50J THR* 3.5 4.2 + - - +
53J ALA* 4.8 3.1 - - - +
92J GLU 3.5 11.2 - - - -
93J ALA* 3.9 2.7 - - - -
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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