Contacts of the strand formed by residues 91 - 99 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52P ASP* 3.2 11.9 - - - +
55P THR* 3.4 25.8 - - - +
56P LEU* 3.3 34.1 - - + +
59P LEU* 4.6 4.5 - - + -
82P TRP* 4.0 18.4 - - + -
88P LEU* 4.2 10.1 - - + +
89P ARG* 3.5 25.8 - - - +
90P LYS* 1.3 88.7 - - - +
92P GLU* 1.3 57.5 + - - +
93P ALA 2.7 16.3 + - - +
108P GLY* 2.9 34.9 + - - -
109P ILE* 5.0 4.9 - - - +
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Residues in contact with GLU 92 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48P GLY* 3.5 1.5 - - - -
49P GLY* 2.9 23.4 + - - +
52P ASP* 3.2 20.9 + - + +
90P LYS* 5.5 7.8 - - - +
91P LEU* 1.3 68.4 - - - +
93P ALA* 1.3 66.0 + - - +
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Residues in contact with ALA 93 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46P PHE* 6.0 0.4 - - + -
47P ALA 3.2 16.4 - - - +
48P GLY* 3.6 7.6 - - - -
52P ASP 3.6 21.8 - - - +
53P ALA* 3.8 11.7 - - - +
56P LEU* 4.5 6.0 - - + +
91P LEU* 2.7 9.8 + - + +
92P GLU* 1.3 78.1 - - - +
94P MET* 1.3 70.9 + - - +
108P GLY* 3.0 26.0 + - - -
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Residues in contact with MET 94 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22O LEU* 5.0 18.4 - - + -
27O MET* 5.7 1.8 - - - +
46P PHE* 3.5 3.1 - - - +
47P ALA 2.8 31.9 + - - +
56P LEU* 4.5 2.0 - - - -
93P ALA* 1.3 82.1 - - - +
95P LEU* 1.3 64.0 + - - +
105P ILE* 4.4 8.7 - - + -
106P ILE 3.4 7.0 - - - +
107P THR* 4.0 26.7 - - + -
123P ILE* 3.2 45.5 - - + +
124P GLY* 3.9 11.4 - - - +
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Residues in contact with LEU 95 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44P ALA* 5.1 1.6 - - + -
45P GLY 3.4 3.4 - - - +
46P PHE* 3.3 34.5 - - + +
53P ALA* 4.4 0.9 - - - +
56P LEU* 3.2 45.5 - - + +
57P PHE* 3.7 25.4 - - + -
60P PHE* 4.0 24.5 - - + -
93P ALA* 6.2 0.2 - - + -
94P MET* 1.3 74.5 - - - +
96P ILE* 1.3 64.1 + - - +
97P VAL* 4.0 10.5 - - + -
105P ILE* 2.9 8.0 - - - +
106P ILE* 2.7 47.7 + - + +
123P ILE* 4.3 0.9 - - - -
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Residues in contact with ILE 96 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3P ILE* 3.9 10.1 - - + +
5P SER* 4.2 8.7 - - - -
14P VAL* 4.1 28.3 - - + +
43P LEU 3.6 1.2 - - - +
44P ALA* 3.3 3.3 - - - -
45P GLY 2.8 42.1 + - - +
95P LEU* 1.3 75.2 - - - +
97P VAL* 1.3 63.4 + - - +
98P ALA* 5.5 1.1 - - + -
103P SER* 6.3 0.2 - - - -
104P LEU 3.2 12.8 - - - +
105P ILE* 4.2 1.8 - - + -
121P LEU* 3.5 35.9 - - + +
122P ALA* 3.6 15.3 - - - +
123P ILE* 3.8 30.5 - - + -
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Residues in contact with VAL 97 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42P VAL* 5.7 1.6 - - + -
43P LEU 3.1 9.6 - - - +
44P ALA* 4.0 12.1 - - + -
60P PHE* 3.2 48.5 - - + -
71P LEU* 3.9 13.1 - - + +
75P ALA* 5.5 0.2 - - + -
95P LEU* 4.4 13.0 - - + -
96P ILE* 1.3 78.1 - - - +
98P ALA* 1.3 59.3 + - - +
103P SER* 3.2 0.3 - - - -
104P LEU* 2.4 58.6 + - + +
106P ILE* 4.1 11.9 - - + -
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Residues in contact with ALA 98 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5P SER* 4.9 0.7 - - - +
12P VAL* 3.8 20.0 - - + -
14P VAL* 4.7 12.3 - - + +
42P VAL* 4.5 1.1 - - - +
43P LEU* 2.7 45.1 + - - +
71P LEU* 3.8 5.1 - - - +
96P ILE* 5.5 1.6 - - + -
97P VAL* 1.3 75.3 - - - +
99P ASP* 1.3 58.5 + - - +
102P GLU 3.2 5.8 - - - +
103P SER* 3.2 28.7 - - - +
172P LEU* 4.0 0.6 - - - +
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Residues in contact with ASP 99 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7P ARG* 3.3 9.7 + - - -
12P VAL* 3.9 4.2 - - - +
41P LYS 3.2 18.4 - - - +
42P VAL* 3.5 12.6 - - + +
69P GLY 4.5 6.4 - - - +
71P LEU* 3.5 25.3 + - - +
98P ALA* 1.3 74.4 - - - +
100P GLU* 1.3 61.8 + - - +
101P LYS* 2.7 17.1 + - - +
102P GLU* 2.7 39.1 + - - +
172P LEU* 3.6 12.6 - - - -
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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