Contacts of the strand formed by residues 91 - 99 (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 LEU 91 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52O ASP* 3.2 11.2 - - - +
55O THR* 3.4 25.8 - - - +
56O LEU* 3.3 34.1 - - + -
59O LEU* 4.6 4.7 - - + -
82O TRP* 4.0 18.6 - - + -
88O LEU* 4.2 10.1 - - + +
89O ARG* 3.5 26.0 - - - +
90O LYS* 1.3 87.5 - - - +
92O GLU* 1.3 58.1 + - - +
93O ALA 2.8 16.8 + - - +
108O GLY* 3.0 33.3 + - - -
109O ILE* 4.4 4.9 + - - +
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Residues in contact with GLU 92 (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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48O GLY* 3.5 2.1 - - - -
49O GLY* 2.9 23.7 + - - +
52O ASP* 3.2 21.5 + - + +
90O LYS* 5.5 7.8 - - - +
91O LEU* 1.3 67.0 - - - +
93O ALA* 1.3 64.5 + - - +
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Residues in contact with ALA 93 (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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46O PHE* 5.9 0.2 - - + -
47O ALA 3.1 15.9 - - - +
48O GLY* 3.6 7.6 - - - -
52O ASP 3.7 20.9 - - - +
53O ALA* 3.8 12.1 - - - +
56O LEU* 4.5 6.0 - - + +
91O LEU* 2.8 7.0 + - + +
92O GLU* 1.3 77.4 - - - +
94O MET* 1.3 71.2 + - - +
107O THR* 4.5 0.3 - - - -
108O GLY* 3.1 25.2 + - - -
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Residues in contact with MET 94 (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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22N LEU* 5.0 17.9 - - + -
27N MET* 5.8 1.6 - - - +
46O PHE* 3.5 2.6 - - - -
47O ALA 2.8 32.2 + - - +
56O LEU* 4.4 1.6 - - - -
93O ALA* 1.3 82.1 - - - +
95O LEU* 1.3 64.3 + - - +
105O ILE* 4.4 9.2 - - + -
106O ILE 3.3 8.1 - - - +
107O THR* 4.0 27.4 - - + -
123O ILE* 3.2 46.9 - - + +
124O GLY* 3.9 12.1 - - - +
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Residues in contact with LEU 95 (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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44O ALA* 5.1 1.3 - - + -
45O GLY 3.4 3.1 - - - +
46O PHE* 3.4 34.3 - - + +
53O ALA 4.4 0.7 - - - +
56O LEU* 3.2 45.5 - - + +
57O PHE* 3.8 24.7 - - + -
60O PHE* 4.0 17.9 - - + -
93O ALA* 6.2 0.2 - - + -
94O MET* 1.3 75.7 - - - +
96O ILE* 1.3 63.0 + - - +
97O VAL* 4.0 20.1 + - + -
105O ILE* 2.9 7.4 - - - +
106O ILE* 2.7 47.7 + - + +
123O ILE* 4.2 0.4 - - - -
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Residues in contact with ILE 96 (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* 3.9 9.4 - - + +
5O SER* 4.2 20.2 - - - -
14O VAL* 4.2 15.6 - - + +
43O LEU 3.6 1.4 - - - +
44O ALA* 3.3 2.4 - - - -
45O GLY 2.8 41.9 + - - +
95O LEU* 1.3 75.8 - - - +
97O VAL* 1.3 64.2 + - - +
98O ALA* 5.5 1.3 - - + -
103O SER* 6.3 0.7 - - - -
104O LEU 3.2 12.1 - - - +
105O ILE* 4.2 2.2 - - + -
121O LEU* 3.4 45.1 - - + +
122O ALA* 3.7 7.4 - - - +
123O ILE* 3.9 29.8 - - + -
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Residues in contact with VAL 97 (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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42O VAL* 5.7 1.3 - - + -
43O LEU 3.1 9.2 - - - +
44O ALA* 4.1 12.6 - - + -
60O PHE* 3.1 48.5 - - + -
71O LEU* 3.9 12.8 - - + +
75O ALA* 5.5 0.4 - - + -
95O LEU* 4.3 13.5 - - + -
96O ILE* 1.3 78.4 - - - +
98O ALA* 1.3 59.3 + - - +
103O SER* 3.2 0.7 - - - -
104O LEU* 2.4 56.1 + - + +
106O ILE* 4.0 12.6 - - + -
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Residues in contact with ALA 98 (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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5O SER* 4.9 1.3 - - - +
12O VAL* 3.8 19.5 - - + -
14O VAL* 4.7 12.3 - - + +
42O VAL* 4.5 0.7 - - - -
43O LEU* 2.8 45.3 + - - +
71O LEU* 3.8 5.7 - - - +
96O ILE* 4.4 2.0 + - + +
97O VAL* 1.3 73.9 - - - +
99O ASP* 1.3 58.6 + - - +
102O GLU 3.2 6.3 - - - +
103O SER* 3.2 28.5 - - - +
172O LEU* 4.0 0.2 - - - +
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Residues in contact with ASP 99 (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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7O ARG* 3.3 10.0 + - - -
12O VAL* 4.0 4.1 - - - +
41O LYS 3.3 17.7 - - - +
42O VAL* 3.6 12.8 - - + +
69O GLY 4.5 6.2 - - - +
71O LEU* 3.5 25.4 + - - +
98O ALA* 1.3 74.6 - - - +
100O GLU* 1.3 61.5 + - - +
101O LYS* 2.7 16.3 + - - +
102O GLU* 2.7 39.1 + - - +
172O LEU* 3.7 12.3 - - - -
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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