Contacts of the strand formed by residues 267 - 270 (chain 1) in PDB entry 1AR9
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 ARG 267 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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771 ILE* 5.1 1.1 - - - -
1281 SER* 3.2 4.7 - - - -
1291 ARG* 2.8 39.9 + - + +
2651 HIS 5.1 2.9 - - - +
2661 ILE* 1.3 79.1 - - - +
2681 VAL* 1.3 65.0 + - - +
2691 TRP* 3.5 33.8 - - + +
333 PRO* 3.6 32.9 - - - +
343 ILE 5.0 4.6 + - - -
353 ASP* 5.9 2.0 + - - +
393 GLU* 3.0 40.6 + - - +
403 VAL 5.8 0.4 - - - -
413 LYS* 5.2 2.8 - - - +
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Residues in contact with VAL 268 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
771 ILE* 3.7 34.3 - - + +
811 PHE* 4.4 2.5 - - + -
1221 LEU* 5.7 0.2 - - + -
1251 PHE* 3.6 45.8 - - + -
1271 TYR 3.4 5.2 - - - +
1281 SER* 3.9 15.3 - - - -
2071 HIS* 5.3 1.1 - - + -
2661 ILE* 4.0 16.8 - - + -
2671 ARG* 1.3 80.9 - - - +
2691 TRP* 1.3 64.9 - - - +
393 GLU* 3.3 9.4 + - - +
403 VAL* 3.0 29.4 + - + +
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Residues in contact with TRP 269 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1251 PHE* 3.7 4.7 - - - +
1261 THR 3.0 16.3 + - - -
1271 TYR* 3.0 37.2 + - + +
1281 SER 4.0 2.0 - - - -
1291 ARG* 3.8 33.7 - - + -
2031 ASN 5.3 0.2 - - - -
2041 ALA* 4.2 6.1 - - + -
2671 ARG* 3.5 58.7 - - + +
2681 VAL* 1.3 78.4 - - - +
2701 CYS* 1.3 71.5 + - - +
2711 PRO 4.1 0.2 - - - -
333 PRO* 5.3 1.1 - - + -
343 ILE 4.5 7.6 - - - -
353 ASP* 5.6 0.2 - - - +
363 ILE* 3.0 61.2 + - + +
373 PRO 3.8 5.4 - - - +
383 GLY 3.4 4.0 - - - -
393 GLU* 3.5 33.4 + - + +
403 VAL* 4.6 0.4 - - - +
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Residues in contact with CYS 270 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1251 PHE* 3.5 0.8 - - - -
1261 THR* 2.9 43.4 + - - +
1271 TYR* 4.2 5.8 - - - -
2691 TRP* 1.3 73.7 - - - +
2711 PRO* 1.3 72.0 - - - +
352 TYR* 3.8 30.1 - - - +
1282 PRO* 4.1 5.4 - - + -
2132 VAL* 4.0 20.4 - - - -
373 PRO 3.3 22.9 - - - -
383 GLY 2.8 13.5 + - - -
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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