Contacts of the strand formed by residues 179 - 183 (chain A) in PDB entry 3L6B
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 179 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A VAL* 3.3 6.7 - - - +
178A ASP* 1.3 79.4 - - - +
180A LEU* 1.3 64.7 + - - +
204A VAL* 3.8 1.1 - - - +
205A LYS* 3.2 20.2 - - + +
207A TYR* 3.8 14.8 - - + -
305A VAL* 3.6 22.2 - - + -
307A ASN 3.2 2.6 + - - -
308A ILE* 3.4 12.3 - - + -
309A CYS 2.8 25.6 + - - -
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Residues in contact with LEU 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ILE* 5.5 0.2 - - + -
167A ALA* 4.3 8.1 - - + +
170A VAL* 4.0 33.9 - - + -
171A LEU* 5.0 2.5 - - + -
177A VAL* 4.0 14.4 - - + -
179A ALA* 1.3 80.6 - - - +
181A VAL* 1.3 62.9 + - - +
182A VAL* 4.4 9.5 - - + +
193A ILE* 3.8 33.0 - - + -
197A VAL* 4.2 13.7 - - + -
204A VAL* 3.9 19.3 - - + -
205A LYS 2.8 9.1 + - - +
206A VAL* 3.7 4.0 - - + -
207A TYR* 2.8 29.8 + - - +
309A CYS* 3.2 9.2 - - + +
311A VAL* 5.1 5.4 - - + -
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Residues in contact with VAL 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A LEU* 1.3 73.9 - - - +
182A VAL* 1.3 64.2 + - - +
183A PRO* 4.2 1.1 - - - +
207A TYR* 3.3 25.6 - - + +
208A ALA 5.1 0.4 - - - -
209A ALA* 4.1 12.1 - - + -
260A PHE* 6.2 0.4 - - + -
289A GLY* 3.7 33.7 - - - +
292A ALA* 4.4 4.5 - - + -
293A VAL* 3.8 13.2 - - + -
298A PHE* 4.2 4.5 - - + -
308A ILE* 3.6 25.1 - - + -
309A CYS 2.8 9.7 + - - +
310A ILE* 3.6 11.8 - - + +
311A VAL* 3.1 27.7 + - - +
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Residues in contact with VAL 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A LEU* 4.4 5.8 - - + +
181A VAL* 1.3 85.1 - - - +
183A PRO* 1.4 76.8 - - + +
184A VAL* 3.6 0.5 + - - +
189A MET* 3.7 31.9 - - + -
190A LEU* 3.9 26.5 - - + -
193A ILE* 3.8 30.7 - - + -
206A VAL* 4.7 1.8 - - + -
207A TYR 2.9 14.3 + - - +
208A ALA* 3.3 5.9 - - - +
209A ALA* 2.9 24.4 + - - -
311A VAL* 4.4 5.2 - - + -
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Residues in contact with PRO 183 (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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181A VAL 4.2 2.0 - - - +
182A VAL* 1.4 92.4 - - + +
184A VAL* 1.3 58.9 + - - +
189A MET* 3.4 26.7 - - + +
190A LEU* 5.1 0.9 - - - +
209A ALA* 3.3 14.1 - - + +
240A VAL* 4.8 4.0 - - + -
285A THR 3.9 18.4 - - - +
286A ALA* 5.1 1.1 - - - -
288A VAL* 4.4 9.0 - - + -
289A GLY* 4.7 8.7 - - - +
311A VAL* 3.8 19.5 - - + +
313A SER* 3.5 24.2 - - - +
350A PLP 3.9 13.7 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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