Contacts of the strand formed by residues 82 - 85 (chain B) in PDB entry 1M1B
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 ILE 82 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B LYS* 5.7 0.9 - - + +
11B LEU* 4.9 0.2 - - - -
43B ILE* 3.3 32.8 - - + +
45B GLY* 4.2 9.9 - - - +
71B LEU* 4.4 19.1 - - + +
74B MET* 3.8 21.1 - - + +
75B SER* 3.6 39.5 - - - +
78B SER* 3.9 6.7 - - - +
80B VAL 4.3 1.3 - - - +
81B PRO* 1.3 81.5 - - - +
83B LEU* 1.3 69.6 + - - +
84B LEU 4.3 1.6 - - - +
108B VAL* 3.2 16.3 - - + +
109B ALA* 3.2 25.5 + - - +
110B GLY 3.5 3.3 + - - -
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Residues in contact with LEU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B LEU* 4.5 23.0 - - + +
15B LEU* 5.4 0.7 - - + -
23B ILE* 4.3 15.7 - - + -
43B ILE 2.9 11.2 + - - +
44B TRP* 3.7 28.3 - - + -
45B GLY 2.7 30.3 + - - -
81B PRO 4.2 0.2 - - - -
82B ILE* 1.3 72.3 - - - +
84B LEU* 1.3 55.3 + - - +
85B ASP 3.6 0.5 + - - -
110B GLY* 3.4 29.2 - - - +
111B ALA 3.5 7.2 - - - +
112B CYS* 3.6 17.0 - - + +
157B VAL* 4.0 27.8 - - + -
188B LEU* 6.0 0.4 - - + -
213B VAL* 5.6 2.7 - - + -
234B MET* 5.0 5.8 - - - -
236B ILE* 5.0 2.9 - - + -
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Residues in contact with LEU 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B GLY* 4.0 7.2 - - - +
47B GLY* 5.9 1.1 - - - +
50B VAL* 5.9 0.9 - - + -
67B VAL* 4.0 21.5 - - + -
68B VAL* 5.6 2.2 - - + -
71B LEU* 3.0 37.0 - - + -
82B ILE* 3.7 2.8 + - - +
83B LEU* 1.3 73.5 - - - +
85B ASP* 1.3 74.0 + - - +
86B ALA* 3.0 22.6 + - + +
90B TYR* 4.4 5.2 - - - +
99B LEU* 4.5 6.3 - - + -
103B LEU* 3.5 35.9 - - + -
108B VAL* 4.3 5.4 - - + -
110B GLY 3.0 14.9 + - - +
111B ALA* 3.6 1.2 - - - -
112B CYS* 3.0 25.8 + - - +
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Residues in contact with ASP 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B TRP* 3.5 23.9 - - + -
45B GLY 2.7 23.4 + - - +
47B GLY* 2.9 25.2 + - - +
67B VAL* 5.5 0.5 - - - +
83B LEU 3.6 1.0 + - - -
84B LEU* 1.3 79.3 - - - +
86B ALA* 1.3 56.7 + - - +
87B ASP* 3.2 21.8 + - - +
90B TYR* 3.9 3.8 + - - -
112B CYS* 4.2 6.1 - - - +
114B GLU* 4.8 0.5 - - - +
159B ARG* 3.6 11.3 + - - -
997B SPV 3.0 7.4 - - - +
999B MG 2.3 30.9 - - - -
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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