Contacts of the strand formed by residues 202 - 211 (chain A) 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 LEU 202 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A GLY* 3.3 9.1 - - - -
179A PHE* 3.3 19.1 - - + +
180A ASP 3.5 24.2 - - - +
181A VAL 3.5 12.8 - - - +
182A ALA* 4.1 6.3 - - + -
198A CYS 2.9 20.2 + - - +
199A LEU* 3.8 11.4 - - + +
200A GLN 3.3 0.6 - - - -
201A LEU* 1.3 78.9 - - + +
203A ARG* 1.3 63.0 + - - +
206A GLY* 4.2 3.8 - - - -
207A ILE 3.7 17.0 - - - +
208A LEU* 3.6 37.2 - - + -
261A LYS* 2.7 35.1 + - + -
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Residues in contact with ARG 203 (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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101A ILE* 3.4 48.3 + - - +
177A GLY 3.2 23.1 - - - +
178A THR* 4.8 2.5 - - - -
179A PHE 2.9 20.9 + - - +
180A ASP* 2.7 24.2 + - - +
202A LEU* 1.3 76.6 - - - +
204A PRO* 1.4 103.2 + - + +
205A GLY* 3.3 18.8 + - - -
206A GLY* 2.9 19.4 + - - +
261A LYS* 3.5 8.7 - - - +
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Residues in contact with PRO 204 (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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177A GLY* 4.8 4.9 - - - +
202A LEU 4.5 1.6 - - - +
203A ARG* 1.4 108.9 + - + +
205A GLY* 1.3 57.3 + - - +
261A LYS* 4.0 12.7 - - + +
262A ILE 3.5 26.7 - - - +
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Residues in contact with GLY 205 (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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101A ILE* 4.1 6.1 - - - +
203A ARG* 3.4 17.6 + - - -
204A PRO* 1.3 70.1 - - - +
206A GLY* 1.3 61.6 + - - +
246A TYR* 5.1 4.5 - - - -
261A LYS 2.8 20.2 + - - -
262A ILE 4.5 0.6 + - - -
100B LEU* 3.1 35.1 - - - +
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Residues in contact with GLY 206 (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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180A ASP* 3.2 17.7 - - - -
202A LEU* 4.2 11.2 - - - +
203A ARG* 2.9 23.5 + - - +
204A PRO 3.2 1.2 + - - -
205A GLY* 1.3 82.2 - - - +
207A ILE* 1.3 61.5 + - - +
208A LEU 4.2 0.2 - - - -
259A ALA 3.9 0.2 - - - +
260A PHE* 3.6 3.6 - - - +
261A LYS* 2.9 26.2 + - - +
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Residues in contact with ILE 207 (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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94A LEU* 5.4 2.5 - - + -
97A LEU* 3.6 35.7 - - + +
101A ILE* 4.0 20.2 - - + -
180A ASP 3.0 8.8 + - - +
181A VAL* 3.3 15.3 - - + +
182A ALA 2.9 26.7 + - - +
202A LEU* 3.7 4.4 - - - +
206A GLY* 1.3 76.9 - - - -
208A LEU* 1.3 68.3 + - - +
209A ALA* 4.6 2.9 - - + +
258A LEU* 4.4 17.5 - - + -
259A ALA 3.7 4.0 - - - +
260A PHE* 4.0 26.5 - - + -
100B LEU* 4.0 21.8 - - + -
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Residues in contact with LEU 208 (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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182A ALA* 3.4 4.5 - - + -
184A VAL* 3.9 18.4 - - + -
195A TYR* 3.6 46.2 - - + +
198A CYS* 3.9 9.4 - - + -
199A LEU* 3.6 28.5 - - + +
202A LEU* 3.6 13.2 - - + +
207A ILE* 1.3 73.7 - - - +
209A ALA* 1.3 62.7 + - - +
210A VAL* 3.7 25.5 + - + +
257A THR 3.7 1.6 - - - +
258A LEU 3.7 0.2 - - - -
259A ALA* 2.8 49.6 + - + +
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Residues in contact with ALA 209 (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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94A LEU* 3.7 38.8 - - + -
181A VAL* 5.8 0.7 - - + -
182A ALA 2.8 15.0 + - - +
183A VAL* 4.4 5.6 - - + -
184A VAL* 2.8 36.0 + - - +
207A ILE* 4.0 3.7 - - + -
208A LEU* 1.3 72.6 - - - +
210A VAL* 1.3 58.8 + - - +
211A LEU* 4.8 1.8 - - + -
256A LEU* 4.3 4.3 - - + -
257A THR 3.3 5.6 - - - +
258A LEU* 4.0 9.0 - - + -
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Residues in contact with VAL 210 (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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184A VAL* 3.8 19.7 - - + +
188A LYS* 4.2 8.3 - - - +
191A CYS* 5.6 0.7 - - + -
195A TYR* 4.4 4.3 - - + -
208A LEU* 3.7 22.0 - - + +
209A ALA* 1.3 75.7 - - - +
211A LEU* 1.3 70.8 + - - +
213A VAL* 3.4 23.5 - - + +
235A LEU* 4.3 18.8 - - + -
239A ILE* 4.1 21.5 - - + -
256A LEU* 3.6 3.6 - - - +
257A THR* 2.8 39.9 + - + +
259A ALA* 6.2 0.2 - - + -
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Residues in contact with LEU 211 (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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86A MET* 3.2 29.2 - - + -
90A GLN* 3.2 32.3 - - - +
94A LEU* 4.3 2.7 - - + -
183A VAL* 3.4 32.5 - - + -
184A VAL 3.1 10.4 + - - +
185A ASP* 3.6 18.1 - - + +
188A LYS* 2.7 32.2 + - - -
209A ALA* 4.7 2.5 - - + +
210A VAL* 1.3 77.4 - - - +
212A ARG* 1.3 84.6 + - - +
213A VAL 3.3 1.5 + - - -
255A GLY 4.1 1.6 - - - -
256A LEU* 3.9 9.6 - - + -
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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