Contacts of the strand formed by residues 91 - 99 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52M ASP* 3.2 11.7 - - - +
55M THR* 3.4 24.9 - - - +
56M LEU* 3.3 34.8 - - + +
59M LEU* 4.6 4.7 - - + -
82M TRP* 4.0 18.8 - - + -
88M LEU* 4.2 10.3 - - + +
89M ARG* 3.5 22.2 - - - +
90M LYS* 1.3 89.2 - - - +
92M GLU* 1.3 58.5 + - - +
93M ALA 2.8 16.1 + - - +
108M GLY* 2.9 34.5 + - - -
109M ILE* 4.4 5.3 + - - +
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Residues in contact with GLU 92 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48M GLY* 3.5 2.1 - - - -
49M GLY* 2.9 23.4 + - - +
52M ASP* 3.3 20.4 + - + +
90M LYS* 5.5 7.4 - - - +
91M LEU* 1.3 68.4 - - - +
93M ALA* 1.3 65.9 + - - +
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Residues in contact with ALA 93 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46M PHE* 6.0 0.2 - - + -
47M ALA 3.2 15.7 - - - +
48M GLY* 3.6 7.2 - - - -
52M ASP 3.6 21.3 - - - +
53M ALA* 3.8 12.6 - - - +
56M LEU* 4.4 6.1 - - + +
91M LEU* 2.8 7.7 + - + +
92M GLU* 1.3 77.7 - - - +
94M MET* 1.3 71.0 + - - +
107M THR* 4.5 0.2 - - - -
108M GLY* 3.0 25.8 + - - -
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Residues in contact with MET 94 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46M PHE* 3.5 2.9 - - - +
47M ALA 2.8 32.7 + - - +
56M LEU* 4.5 1.3 - - - -
93M ALA* 1.3 81.6 - - - +
95M LEU* 1.3 64.1 + - - +
105M ILE* 4.5 8.5 - - + -
106M ILE 3.4 7.9 - - - +
107M THR* 3.9 27.8 - - + -
123M ILE* 3.2 47.2 - - + +
124M GLY* 4.0 11.4 - - - +
22R LEU* 5.0 18.8 - - + -
27R MET* 5.7 0.9 - - - +
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Residues in contact with LEU 95 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44M ALA* 5.1 1.1 - - + -
45M GLY 3.4 2.7 - - - +
46M PHE* 3.4 34.5 - - + +
53M ALA* 4.4 1.3 - - - +
56M LEU* 3.2 45.1 - - + +
57M PHE* 3.8 24.9 - - + -
60M PHE* 4.0 18.6 - - + -
93M ALA* 6.2 0.2 - - + -
94M MET* 1.3 75.0 - - - +
96M ILE* 1.3 63.5 + - - +
97M VAL* 3.9 18.8 + - + -
105M ILE* 2.9 8.1 - - - +
106M ILE* 2.7 48.2 + - + +
123M ILE* 4.2 0.7 - - - -
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Residues in contact with ILE 96 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3M ILE* 3.9 10.8 - - + +
5M SER* 4.2 8.5 - - - -
14M VAL* 4.1 28.9 - - + +
43M LEU 3.6 1.2 - - - +
44M ALA* 3.3 2.9 - - - -
45M GLY 2.8 40.4 + - - +
95M LEU* 1.3 76.9 - - - +
97M VAL* 1.3 65.2 + - - +
98M ALA* 5.6 0.9 - - + -
103M SER* 6.4 0.4 - - - -
104M LEU 3.2 12.1 - - - +
105M ILE* 4.2 2.2 - - + -
121M LEU* 3.5 45.8 - - + +
122M ALA* 3.7 4.3 - - - +
123M ILE* 3.8 30.5 - - + -
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Residues in contact with VAL 97 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42M VAL* 5.7 1.3 - - + -
43M LEU 3.1 9.2 - - - +
44M ALA* 4.1 12.1 - - + -
60M PHE* 3.2 48.2 - - + -
71M LEU* 3.9 12.9 - - + +
75M ALA* 5.5 0.7 - - + -
95M LEU* 4.3 13.0 - - + -
96M ILE* 1.3 79.7 - - - +
98M ALA* 1.3 58.9 + - - +
103M SER* 3.2 0.5 - - - -
104M LEU* 2.4 58.5 + - + +
106M ILE* 4.0 12.3 - - + -
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Residues in contact with ALA 98 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5M SER* 4.9 0.9 - - - +
12M VAL* 3.8 20.2 - - + -
14M VAL* 4.7 12.1 - - + +
42M VAL* 3.7 1.5 - - - +
43M LEU* 2.7 44.1 + - - +
71M LEU* 3.8 6.1 - - - +
96M ILE* 4.4 1.8 + - + -
97M VAL* 1.3 74.5 - - - +
99M ASP* 1.3 57.8 + - - +
102M GLU 3.2 5.6 - - - +
103M SER* 3.2 29.6 - - - -
172M LEU* 4.0 0.8 - - - +
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Residues in contact with ASP 99 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7M ARG* 3.3 10.0 + - - -
12M VAL* 4.0 4.5 - - - +
41M LYS 3.2 18.4 - - - +
42M VAL* 3.5 11.8 - - + +
69M GLY 4.5 6.6 - - - +
71M LEU* 3.5 25.8 + - - +
98M ALA* 1.3 74.5 - - - +
100M GLU* 1.3 61.5 + - - +
101M LYS* 2.7 16.1 + - - +
102M GLU 2.7 39.9 + - - +
172M LEU* 3.6 12.1 - - - -
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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