Contacts of the strand formed by residues 96 - 101 (chain V) in PDB entry 5A0Q
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 ALA 96 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46V SER 3.4 6.7 - - - -
47V GLY* 4.1 0.4 - - - -
52V THR* 4.2 12.1 - - + +
55V VAL* 5.5 3.6 - - + -
87V CYS* 4.2 18.5 - - - -
94V LEU* 4.1 16.7 - - + +
95V MET* 1.3 77.0 - - - +
97V GLY* 1.3 59.1 + - - +
98V ILE* 3.7 12.3 - - + -
114V VAL* 3.4 5.7 - - - +
115V PRO 4.3 0.2 - - - +
116V MET* 2.9 38.1 + - - +
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Residues in contact with GLY 97 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3V ILE* 5.2 0.2 - - - +
45V ARG* 3.3 1.6 - - - -
46V SER* 2.4 57.7 + - - -
47V GLY 3.9 0.4 - - - +
96V ALA* 1.3 72.8 - - - +
98V ILE* 1.3 62.6 + - - -
99V ILE* 5.1 2.3 - - - +
114V VAL 3.7 7.0 - - - -
115V PRO* 5.3 0.9 - - - -
116V MET* 4.0 6.9 - - - +
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Residues in contact with ILE 98 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43V CYS* 3.1 26.9 - - - -
44V CYS 3.3 9.9 - - - +
45V ARG* 4.3 1.8 - - + -
52V THR* 3.6 25.4 - - + -
55V VAL* 5.0 1.6 - - + -
83V PHE* 3.9 20.0 - - + -
87V CYS* 5.3 1.6 - - - -
96V ALA* 3.7 13.4 - - + -
97V GLY* 1.3 77.2 - - - +
99V ILE* 1.3 82.4 + - - +
100V ILE* 2.9 43.5 - - + +
113V SER* 3.9 1.7 + - - -
114V VAL* 3.2 34.8 + - + +
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Residues in contact with ILE 99 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3V ILE* 3.2 35.0 - - + +
5V ALA* 3.5 27.1 - - + -
14V LEU* 6.0 0.2 - - + -
44V CYS* 3.1 33.0 + - + +
97V GLY 5.1 1.8 - - - +
98V ILE* 1.3 84.0 - - - +
100V ILE* 1.3 60.8 + - - +
101V ALA* 3.7 1.3 + - + +
111V VAL* 4.1 7.6 - - + -
112V TYR 3.3 16.6 - - - +
113V SER* 4.2 6.5 - - - +
126V ALA* 3.9 18.2 - - + +
127V ILE* 3.8 10.3 - - - +
128V GLY* 3.8 23.3 - - - +
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Residues in contact with ILE 100 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37V ILE* 4.5 2.2 - - + -
41V ILE* 3.6 19.3 - - + -
42V PHE 4.5 4.5 - - - +
43V CYS* 4.5 3.4 - - - +
76V VAL* 4.5 9.4 - - + +
79V ALA* 4.6 5.4 - - + -
80V ALA* 3.9 11.2 - - + +
83V PHE* 2.8 52.9 - - + -
98V ILE* 2.9 26.9 - - + +
99V ILE* 1.3 71.7 - - - +
101V ALA* 1.3 73.0 + - - +
110V GLN 3.7 0.5 - - - +
112V TYR* 2.8 44.1 + - + +
113V SER 4.9 1.3 - - - +
114V VAL* 3.7 13.9 - - + -
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Residues in contact with ALA 101 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12V VAL* 3.8 20.4 - - + -
14V LEU* 3.4 33.7 - - + -
41V ILE* 3.2 25.8 - - - +
42V PHE 3.6 15.1 + - - +
76V VAL* 3.6 5.1 - - - +
99V ILE* 3.7 1.7 + - + +
100V ILE* 1.3 75.6 - - - +
102V GLY* 1.3 59.4 + - - +
110V GLN 3.6 7.6 - - - +
111V VAL* 4.7 5.4 - - + -
179V ILE* 4.9 1.8 - - + -
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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