Contacts of the strand formed by residues 112 - 117 (chain V) in PDB entry 3ALQ
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 CYS 112 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82V GLN* 3.2 16.9 + - - +
96V CYS* 2.9 26.0 + - - +
97V THR* 4.3 6.3 - - + -
98V CYS* 3.5 17.7 - - - +
104V CYS* 2.0 50.0 - - + -
108V LYS* 4.2 12.5 + - - -
110V GLU 4.1 0.6 + - - -
111V GLY* 1.3 74.4 - - - -
113V ARG* 1.3 59.2 + - - +
114V LEU 3.1 20.2 - - - -
115V CYS* 3.6 4.0 - - - -
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Residues in contact with ARG 113 (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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63E LEU* 4.0 2.4 - - - +
115E TYR* 3.9 13.5 + - - +
143E ASP* 3.0 26.9 + - - -
145E ALA* 3.4 16.4 - - + +
146E GLU* 2.9 37.1 + - - +
149E GLN* 2.7 36.8 + - - +
97F ILE* 2.9 31.6 - - - +
79V SER* 5.2 5.5 - - - -
82V GLN* 3.5 13.9 + - - +
106V LEU* 3.0 30.6 + - + +
107V SER 4.5 0.7 - - - -
108V LYS* 4.0 23.3 - - + +
112V CYS* 1.3 74.7 - - - +
114V LEU* 1.3 60.5 + - - +
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Residues in contact with LEU 114 (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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67E GLN* 4.4 17.0 - - - +
113E PRO* 3.5 36.1 - - + -
115E TYR* 4.0 15.5 - - - +
73F HIS* 5.6 3.8 - - + -
75F LEU* 3.4 28.3 - - + -
82V GLN* 4.4 0.7 - - - +
105V ALA* 3.0 33.8 + - + -
106V LEU* 3.4 16.4 + - + -
112V CYS* 3.1 9.9 - - - -
113V ARG* 1.3 82.6 - - + +
115V CYS* 1.3 77.9 + - - +
116V ALA* 5.7 1.3 - - + -
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Residues in contact with CYS 115 (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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67E GLN* 4.8 5.9 + - - -
80V SER 5.5 0.7 - - - +
81V ASP* 4.1 13.3 - - + +
82V GLN* 3.8 22.0 - - + +
98V CYS* 2.0 62.6 - - + -
102V TRP* 3.6 20.3 - - + -
112V CYS* 3.6 9.9 - - - -
114V LEU* 1.3 88.4 - - - +
116V ALA* 1.3 59.4 + - - +
117V PRO* 4.4 0.3 - - - +
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Residues in contact with ALA 116 (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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73F HIS* 3.7 23.1 - - + +
102V TRP* 3.3 6.4 - - - -
103V TYR* 2.9 65.4 + - + +
105V ALA* 4.0 7.4 - - + +
114V LEU* 4.1 2.6 + - + -
115V CYS* 1.3 73.4 - - - +
117V PRO* 1.3 68.3 - - + +
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Residues in contact with PRO 117 (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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73F HIS* 5.6 3.1 - - + -
101V GLY 4.3 0.7 - - - +
102V TRP* 3.3 42.6 - - + -
103V TYR* 3.4 9.4 - - - -
115V CYS 4.4 0.2 - - - +
116V ALA* 1.3 89.5 - - + +
118V LEU* 1.3 68.5 + - - +
119V ARG 3.5 1.4 + - - -
136V ASP* 4.1 1.6 - - - +
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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