Contacts of the strand formed by residues 130 - 141 (chain B) in PDB entry 2AVN
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 LEU 130 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101B GLY* 3.5 8.8 - - - -
103B PHE 3.4 13.7 - - - +
104B GLU 3.9 4.5 - - - +
105B ALA* 3.7 10.8 - - - +
106B VAL* 3.7 18.2 - - + -
126B ILE* 3.3 33.6 + - + +
127B ARG* 3.5 5.3 - - - +
128B ARG 3.3 0.6 - - - +
129B VAL* 1.3 79.6 - - - +
131B VAL* 1.3 64.6 + - - +
132B PRO* 4.6 0.2 - - - +
134B GLY 3.9 13.5 - - - +
135B LEU 3.4 33.0 - - - +
193B PHE* 4.1 15.9 - - + -
244B LYS* 2.7 34.4 + - + -
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Residues in contact with VAL 131 (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 ARG* 4.0 18.4 - - - +
101B GLY* 3.3 26.0 - - - +
103B PHE 2.9 24.0 + - - +
104B GLU* 4.0 19.7 - - + +
130B LEU* 1.3 75.8 - - - +
132B PRO* 1.4 80.7 - - + +
133B ASP 3.3 0.6 + - - -
134B GLY* 2.7 30.8 + - - +
244B LYS* 3.6 6.9 - - - +
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Residues in contact with PRO 132 (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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101B GLY* 5.7 1.8 - - - -
130B LEU 4.6 0.9 - - - +
131B VAL* 1.4 97.1 - - + +
133B ASP* 1.3 71.2 + - - +
134B GLY 3.2 0.2 + - - -
244B LYS* 4.4 15.9 - - + +
245B LYS 5.5 0.9 - - - +
246B ARG* 4.4 25.4 - - + +
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Residues in contact with ASP 133 (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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131B VAL* 3.3 0.9 + - - -
132B PRO* 1.3 74.5 - - - +
134B GLY* 1.3 64.8 + - - +
135B LEU* 3.8 6.2 + - - +
243B LYS* 3.6 32.8 - - + +
244B LYS 2.9 23.5 + - - +
245B LYS* 5.2 1.0 - - - -
246B ARG* 2.5 46.4 + - - +
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Residues in contact with GLY 134 (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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104B GLU 3.2 14.4 - - - -
130B LEU* 3.9 12.6 - - - +
131B VAL* 2.7 32.4 + - - +
132B PRO 3.2 1.4 + - - -
133B ASP* 1.3 72.9 - - - +
135B LEU* 1.3 61.4 + - - -
243B LYS* 3.4 2.3 - - - -
244B LYS* 2.9 27.8 + - - +
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Residues in contact with LEU 135 (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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39B TYR* 3.9 33.9 - - + +
40B LEU* 4.8 5.2 - - + -
104B GLU 3.0 11.4 + - - +
105B ALA* 3.2 7.2 - - + +
106B VAL 2.9 25.3 + - - +
130B LEU* 3.4 7.0 - - - +
133B ASP 4.2 4.7 - - - +
134B GLY* 1.3 75.1 - - - -
136B LEU* 1.3 58.9 + - - +
137B ILE* 4.1 15.7 - - + -
196B VAL* 4.6 4.9 - - + -
241B VAL* 4.0 19.5 - - + -
242B LEU 3.2 12.3 - - - +
243B LYS* 4.0 25.4 - - + -
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Residues in contact with LEU 136 (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 VAL* 3.5 33.2 - - + +
108B ALA* 4.2 16.6 - - + -
113B LEU* 4.2 3.8 - - + -
123B PHE* 3.7 29.6 - - + -
126B ILE* 4.1 31.0 - - + -
130B LEU* 4.2 1.4 - - - +
134B GLY 4.2 0.2 + - - -
135B LEU* 1.3 73.3 - - - +
137B ILE* 1.3 62.9 + - - +
138B ALA* 4.4 5.4 - - + -
193B PHE* 4.5 5.8 - - + -
240B PHE* 3.8 10.2 - - + +
241B VAL* 3.2 5.5 - - - +
242B LEU* 2.8 53.5 + - + +
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Residues in contact with ILE 137 (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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36B LEU* 3.9 21.8 - - + -
39B TYR* 4.0 24.9 - - + -
40B LEU* 4.1 26.7 - - + -
105B ALA* 5.0 1.8 - - + -
106B VAL 3.0 7.5 + - - +
107B LEU* 3.4 14.3 - - + -
108B ALA 2.9 23.9 + - - -
109B LEU* 4.1 5.8 - - + +
135B LEU* 4.3 14.8 - - + +
136B LEU* 1.3 78.7 - - - +
138B ALA* 1.3 63.5 + - - +
239B PHE* 3.6 33.2 - - + -
240B PHE 3.5 3.4 - - - +
241B VAL* 4.3 7.9 - - + -
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Residues in contact with ALA 138 (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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108B ALA* 3.2 25.1 - - + +
109B LEU* 4.2 2.7 - - - -
113B LEU* 4.2 7.0 - - + -
136B LEU* 4.4 3.1 - - + -
137B ILE* 1.3 79.1 - - - +
139B THR* 1.3 65.3 + - - +
238B ILE 3.8 0.2 - - - +
239B PHE* 3.2 6.9 - - - -
240B PHE* 2.8 63.8 + - + -
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Residues in contact with THR 139 (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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32B ILE* 4.0 12.1 - - + -
108B ALA 3.1 8.4 + - - +
109B LEU* 3.5 16.0 - - + +
110B GLY* 2.8 31.0 + - - -
111B ASP* 3.1 26.4 + - - -
113B LEU 4.7 0.7 + - - -
138B ALA* 1.3 79.2 - - - +
140B VAL* 1.3 69.0 + - - +
201B ILE* 3.6 29.2 - - + -
237B HIS* 5.1 3.6 - - - -
238B ILE 3.0 7.6 - - - +
239B PHE* 4.1 4.9 - - + -
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Residues in contact with VAL 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B ASP* 3.0 11.5 - - - +
113B LEU* 4.0 18.4 - - + -
114B SER* 3.6 10.1 - - - +
139B THR* 1.3 81.2 - - - +
141B ASP* 1.3 61.7 + - - +
182B PHE* 3.7 45.1 - - + -
187B LEU* 5.3 0.4 - - + -
237B HIS* 3.7 3.3 - - - +
238B ILE* 2.9 49.9 + - + +
240B PHE* 3.7 29.4 - - + -
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Residues in contact with ASP 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B ASP* 3.3 8.7 + - - +
114B SER* 3.0 18.1 + - - +
115B TYR* 4.1 9.9 + - - -
140B VAL* 1.3 76.9 - - - +
142B ASN* 1.3 60.3 + - - +
146B PHE* 3.4 32.4 - - + -
170B VAL* 5.3 1.2 - - - +
179B SER* 2.7 24.2 + - - +
181B ALA* 4.1 8.7 - - - -
182B PHE* 2.8 29.2 + - - +
236B ASP 5.4 0.2 - - - +
237B HIS* 3.2 27.9 - - - -
238B ILE* 4.8 0.4 - - - +
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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