Contacts of the strand formed by residues 42 - 48 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36O ARG* 3.8 4.3 - - - +
37O LEU* 2.9 60.0 + - + +
38O TYR* 4.3 2.5 - - + -
40O GLY 5.0 1.4 - - - -
41O LYS* 1.3 86.1 + - + +
43O LEU* 1.3 68.7 + - - +
44O ALA* 5.9 0.4 - - + -
60O PHE* 5.3 1.6 - - + -
64O LEU* 3.4 24.0 - - + -
69O GLY* 5.1 6.1 - - - +
71O LEU* 4.0 24.9 - - + -
97O VAL* 6.1 0.4 - - + -
98O ALA 3.7 4.9 - - - +
99O ASP* 3.6 21.8 - - + +
172O LEU* 4.6 0.9 - - - -
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Residues in contact with LEU 43 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12O VAL* 3.7 24.0 - - + +
14O VAL* 4.3 18.4 - - + -
34O VAL* 5.1 0.7 - - + -
35O ARG 4.0 2.9 - - - +
36O ARG* 3.6 30.3 - - + +
42O VAL* 1.3 75.1 - - - +
44O ALA* 1.3 60.7 + - - +
96O ILE 3.6 1.2 - - - +
97O VAL* 3.1 8.0 - - - +
98O ALA 2.8 36.8 + - - +
170O GLU* 3.4 49.8 - - + +
172O LEU* 3.6 27.4 - - + -
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Residues in contact with ALA 44 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14O VAL* 4.7 0.4 - - - -
33O LYS 3.9 0.7 - - - +
34O VAL* 3.1 7.2 - - - +
35O ARG* 2.8 41.3 + - - +
37O LEU* 4.8 9.2 - - + -
42O VAL* 5.9 0.7 - - + -
43O LEU* 1.3 76.0 - - - +
45O GLY* 1.3 59.1 + - - +
46O PHE* 4.2 2.4 + - - -
57O PHE* 3.4 34.3 - - + -
60O PHE* 5.8 0.2 - - + -
95O LEU* 5.1 2.2 - - + -
96O ILE 3.3 4.3 - - - -
97O VAL* 4.1 15.5 - - + -
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Residues in contact with GLY 45 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3O ILE* 4.0 20.6 - - - -
14O VAL* 4.3 5.0 - - - +
33O LYS 3.3 9.0 - - - -
34O VAL* 4.1 3.4 - - - -
44O ALA* 1.3 74.7 - - - +
46O PHE* 1.3 60.5 + - - -
95O LEU* 3.4 4.8 - - - -
96O ILE* 2.8 42.2 + - - +
123O ILE* 3.8 4.5 - - - +
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Residues in contact with PHE 46 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1O THR* 3.9 3.5 - - - +
3O ILE* 3.4 16.7 - - - +
32O ARG 3.1 22.9 - - - -
33O LYS* 3.0 35.2 + - + +
34O VAL* 4.8 0.2 - - - -
35O ARG* 4.1 16.8 - - + -
44O ALA 4.7 3.1 - - - -
45O GLY* 1.3 75.3 - - - -
47O ALA* 1.3 64.7 + - - +
50O THR* 5.8 0.7 - - - -
53O ALA* 3.6 31.2 - - + +
54O PHE* 3.4 33.0 - + - -
57O PHE* 4.8 14.1 - + + -
93O ALA* 5.9 0.2 - - + -
94O MET 3.5 4.7 - - - +
95O LEU* 3.4 19.5 - - + -
444V LEU* 4.8 11.2 - - + -
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Residues in contact with ALA 47 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1O THR* 3.6 22.7 - - + -
3O ILE* 3.9 3.1 - - + -
46O PHE* 1.3 80.2 - - - +
48O GLY* 1.3 58.8 + - - +
53O ALA* 5.1 0.4 - - - -
93O ALA* 3.1 3.9 - - - +
94O MET* 2.8 36.6 + - + +
123O ILE* 3.6 19.7 - - + -
124O GLY* 3.9 22.7 - - - +
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Residues in contact with GLY 48 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1O THR* 4.7 11.1 + - - -
46O PHE* 5.6 0.2 - - - -
47O ALA* 1.3 75.4 - - - +
49O GLY* 1.3 63.6 + - - -
50O THR* 3.4 4.3 + - - +
53O ALA* 4.6 4.7 - - - +
92O GLU 3.5 11.0 - - - -
93O 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