Contacts of the strand formed by residues 258 - 263 (chain A) in PDB entry 6PAI
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 ILE 258 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A SER* 4.5 4.5 + - - -
218A MET* 3.1 29.7 - - + +
232A ILE* 4.1 22.8 - - + +
233A GLY 5.2 1.3 - - - +
234A GLN* 5.8 1.7 + - - +
237A ILE* 4.7 1.8 - - + -
253A ILE* 4.0 36.6 - - + -
256A SER 4.7 5.6 - - - +
257A THR* 1.3 83.0 - - - +
259A VAL* 1.3 61.1 + - - +
260A CYS 3.8 11.7 - - - +
273A LEU* 4.0 36.1 - - + -
274A GLY 3.3 12.6 - - - +
275A ASP* 4.0 11.2 - - + +
281A PHE* 4.9 5.6 - - + -
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Residues in contact with VAL 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A MET* 3.8 13.4 - - - +
257A THR* 3.5 21.1 - - + +
258A ILE* 1.3 78.0 - - - +
260A CYS* 1.3 63.7 + - + +
274A GLY 2.8 14.7 + - - +
275A ASP 4.6 6.1 - - - +
276A MET* 3.8 28.3 - - + +
310A ILE* 5.5 2.9 - - + -
311A ALA 3.3 26.2 - - - +
312A GLU* 4.6 6.5 - - - +
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Residues in contact with CYS 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A MET* 4.2 3.8 - - - -
258A ILE* 3.8 6.0 - - - +
259A VAL* 1.3 81.3 - - - +
261A HIS* 1.3 64.9 + - - +
273A LEU* 3.4 2.9 - - - -
274A GLY* 2.9 32.5 + - - +
311A ALA* 3.6 39.9 - - - -
312A GLU 3.4 20.6 - - - +
313A CYS* 4.0 5.6 - - - -
314A LEU* 3.9 18.4 - - - +
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Residues in contact with HIS 261 (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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166A ASP* 5.1 1.0 + - - -
168A LYS* 4.3 18.9 + - - -
218A MET* 3.7 33.5 - - + +
219A VAL 4.1 8.1 + - - -
220A ILE* 3.6 37.8 - - + +
232A ILE* 5.1 0.4 - - + -
260A CYS* 1.3 75.5 - - - +
262A ASN* 1.3 71.9 + - - +
271A TYR* 5.3 2.7 - - + -
272A LEU 3.1 7.6 - - - -
273A LEU* 3.5 24.2 - - + -
314A LEU* 4.5 8.2 + - - +
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Residues in contact with ASN 262 (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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18A CYS 5.3 0.2 + - - -
20A THR* 5.5 3.6 - - - +
261A HIS* 1.3 78.7 - - - +
263A ARG* 1.3 72.6 + - - +
264A VAL* 5.2 0.4 - - - -
271A TYR* 3.3 10.6 - - - -
272A LEU* 2.9 36.5 + - + +
314A LEU* 2.6 35.1 + - + +
315A THR* 2.9 30.5 - - - +
316A TYR 4.1 2.6 - - - +
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Residues in contact with ARG 263 (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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171A TYR* 3.1 30.5 + - - -
221A ALA 4.9 1.2 + - - -
223A PRO* 3.6 26.2 - - - +
262A ASN* 1.3 83.3 + - - +
264A VAL* 1.3 63.8 + - - +
265A ASP 3.2 23.2 + - - +
266A PRO* 3.6 23.2 + - - +
268A GLY* 4.0 3.6 - - - -
270A ARG 4.2 0.4 - - - +
271A TYR* 3.5 38.9 - - + -
316A TYR* 4.4 9.2 + - - +
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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