Contacts of the strand formed by residues 78 - 81 (chain A) in PDB entry 1II7
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 78 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A LEU* 5.7 0.4 - - + -
44A ILE* 3.4 17.5 - - + +
46A ILE* 3.9 33.0 - - + -
68A LEU* 4.5 6.7 - - + +
71A PRO* 3.9 25.6 - - + -
76A ILE 3.8 9.0 - - - +
77A PRO* 1.3 77.3 - - - +
79A PHE* 1.3 64.6 + - - +
80A ALA* 5.0 0.7 - - + -
103A LEU 3.8 19.2 + - - +
104A VAL* 3.4 16.6 - - + -
105A TYR* 2.8 31.3 + - - -
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Residues in contact with PHE 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A PHE* 3.8 34.5 - + + -
44A ILE 2.7 10.0 + - - +
45A LEU* 3.3 14.6 - - + -
46A ILE* 2.9 25.3 + - - +
77A PRO* 4.1 10.1 - - + -
78A VAL* 1.3 73.2 - - - +
80A ALA* 1.3 61.8 + - - +
105A TYR* 3.5 19.7 - + + -
107A ILE* 3.7 26.9 - - + -
118A TYR* 3.3 48.2 - + + -
119A LEU* 4.4 0.2 - - + -
133A GLY* 3.8 7.2 - - - -
134A VAL 3.8 12.3 - - - -
135A TYR* 4.8 2.0 - - + -
140A ILE* 3.4 26.5 - - + -
171A MET* 3.9 2.7 - - - +
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Residues in contact with ALA 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ILE* 3.3 24.7 - - + +
50A LEU* 5.7 2.0 - - + -
78A VAL* 4.0 0.9 + - + -
79A PHE* 1.3 77.6 - - - +
81A ILE* 1.3 64.6 + - - +
95A LEU* 4.2 18.4 - - + -
104A VAL* 4.7 18.4 - - + -
105A TYR 3.0 9.3 + - - +
106A VAL* 3.4 8.4 - - - +
107A ILE* 3.0 24.7 + - - +
171A MET* 4.3 3.5 - - - +
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Residues in contact with ILE 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ILE* 3.3 2.0 + - - +
47A ALA* 3.7 9.6 - - - -
48A GLY* 3.3 28.8 + - - +
49A ASP 4.6 0.2 + - - -
50A LEU* 5.6 1.2 + - - +
80A ALA* 1.3 76.5 - - - +
82A GLU* 1.3 59.6 + - - +
86A ASP* 5.1 0.7 - - - +
95A LEU* 3.4 13.3 - - - +
106A VAL* 5.0 0.9 - - - -
107A ILE* 3.5 34.1 - - + +
143A MET 3.6 31.0 - - - +
144A LYS* 4.3 2.2 - - - -
171A MET* 3.6 25.6 - - + +
172A LEU* 3.6 33.4 - - - -
173A HIS* 3.6 7.6 - - + +
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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