Contacts of the strand formed by residues 105 - 109 (chain B) in PDB entry 2AVD
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 LYS 105 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B ALA* 5.4 0.7 - - - -
104B LYS* 1.3 80.1 - - + +
106B ALA* 1.3 59.5 + - - +
124B LEU* 5.1 0.2 - - - -
129B ARG* 3.5 11.2 - - + +
131B VAL* 5.9 3.1 - - + -
175B GLU* 2.9 24.9 + - - +
178B THR* 2.6 51.2 + - - +
179B PHE* 3.4 33.9 - - + -
180B ASP* 2.8 36.0 + - - +
181B VAL 3.4 3.5 + - - -
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Residues in contact with ALA 106 (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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103B ALA* 5.9 0.4 - - + -
104B LYS 4.2 0.4 - - - -
105B LYS* 1.3 74.1 - - - +
107B LEU* 1.3 60.3 + - - +
120B LEU* 4.2 21.1 - - + -
124B LEU* 4.6 10.1 - - + -
129B ARG 3.0 8.0 + - - +
130B VAL* 4.2 21.3 - - + -
131B VAL 2.9 24.6 + - - -
179B PHE* 3.6 10.9 - - - -
181B VAL* 3.2 19.3 - - + +
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Residues in contact with LEU 107 (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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106B ALA* 1.3 76.0 - - - +
108B ASP* 1.3 56.3 + - - +
109B LEU* 3.9 21.5 - - + -
120B LEU* 4.8 1.4 - - - +
131B VAL* 3.4 24.0 - - + +
133B CYS* 4.4 4.0 - - - -
167B LEU* 3.7 22.9 - - + -
170B LEU* 4.0 20.9 - - + -
179B PHE* 3.9 12.8 - - + -
181B VAL 2.8 11.6 + - - +
182B ALA* 3.3 7.6 - - + -
183B VAL* 2.8 34.2 + - - +
198B CYS* 4.0 14.1 - - - -
201B LEU* 3.7 24.2 - - + -
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Residues in contact with ASP 108 (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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107B LEU* 1.3 74.3 - - - +
109B LEU* 1.3 63.3 + - - +
110B GLY 4.9 0.4 - - - -
111B THR* 4.0 8.7 - - - -
116B SER* 2.7 34.0 + - - -
117B ALA* 3.6 13.1 - - - +
120B LEU* 4.2 5.9 - - + +
130B VAL* 3.8 19.7 - - + -
131B VAL 2.8 7.9 + - - +
132B THR* 2.6 27.6 + - - +
133B CYS* 2.8 27.0 + - - +
183B VAL* 3.8 16.1 - - - +
601B SAM 4.4 2.1 + - - -
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Residues in contact with LEU 109 (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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107B LEU* 3.9 20.4 - - + -
108B ASP* 1.3 74.4 - - - +
110B GLY* 1.3 60.1 + - - +
133B CYS* 3.8 27.8 - - + -
163B ALA* 4.4 7.6 - - + -
167B LEU* 4.0 14.8 - - + -
183B VAL 2.8 20.1 + - - +
184B VAL* 4.3 6.5 - - + -
185B ASP* 3.0 36.3 + - - +
186B ALA* 3.9 12.1 - - + -
194B TYR* 3.8 32.3 - - + -
198B CYS* 3.7 24.9 - - - -
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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