Contacts of the strand formed by residues 88 - 94 (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 THR 88 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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861 CYS* 3.5 9.9 - - - -
871 VAL* 1.3 82.9 - - - +
891 ILE* 1.3 76.0 + - - +
901 MET* 3.9 11.6 - - + +
1081 TRP* 3.5 46.4 + - + -
1141 ASP* 4.6 3.4 + - - +
1151 THR* 4.8 3.4 - - - -
2581 ARG* 3.6 0.2 - - - -
2591 VAL* 3.0 50.2 + - + -
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Residues in contact with ILE 89 (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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861 CYS* 4.4 8.1 - - - -
881 THR* 1.3 86.4 + - - +
901 MET* 1.3 63.6 + - - +
911 THR* 3.9 3.4 + - - +
2561 LYS* 4.0 41.3 - - + +
2571 ILE 3.5 3.1 - - - +
2581 ARG* 3.7 42.6 - - + +
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Residues in contact with MET 90 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881 THR* 3.9 17.7 - - + +
891 ILE* 1.3 74.9 - - - +
911 THR* 1.3 61.4 + - - +
1061 ALA* 3.6 25.1 - - + +
1071 VAL 4.1 0.4 - - - +
1081 TRP* 3.6 25.4 - - + +
2401 LEU* 3.5 42.0 - - - +
2421 VAL* 3.6 28.5 - - + -
2561 LYS* 3.3 6.2 - - - -
2571 ILE* 2.8 54.9 + - + +
2591 VAL* 4.5 5.6 - - - -
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Residues in contact with THR 91 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
891 ILE* 3.9 4.5 + - - +
901 MET* 1.3 74.4 - - - +
921 VAL* 1.3 71.2 + - - +
1041 LEU* 3.6 27.7 - - + +
1061 ALA* 3.4 12.6 - - - +
2541 THR* 3.9 19.5 - - + -
2551 SER 3.5 9.4 - - - +
2561 LYS* 3.6 23.6 - - + -
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Residues in contact with VAL 92 (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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911 THR* 1.3 81.1 - - - +
931 ASP* 1.3 65.5 + - - +
1041 LEU* 3.4 13.9 - - - +
1061 ALA* 3.6 14.1 - - + +
1551 TYR* 4.2 4.7 - - + -
2421 VAL* 3.3 37.9 - - + +
2431 ARG* 4.4 0.2 - - - -
2441 VAL* 3.9 21.5 - - + +
2541 THR* 3.6 4.9 - - - +
2551 SER* 2.8 45.5 + - - +
2571 ILE* 3.7 21.8 - - + -
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Residues in contact with ASP 93 (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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921 VAL* 1.3 77.8 - - - +
941 ASN* 1.3 64.1 + - - +
951 PRO* 3.4 15.4 - - - +
1011 LYS* 5.1 8.0 + - - -
1021 ASP 5.1 0.5 - - - +
1031 LYS* 3.4 18.5 - - - +
1041 LEU* 2.8 53.2 + - + +
2441 VAL* 3.9 10.4 + - - +
2521 LYS* 3.4 25.0 + - - -
2531 VAL 3.3 14.1 - - - +
2541 THR* 4.0 12.3 + - + +
2551 SER 4.6 0.4 - - - +
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Residues in contact with ASN 94 (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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931 ASP* 1.3 78.6 - - - +
951 PRO* 1.3 62.3 - - - +
1031 LYS* 3.0 26.9 + - - +
1531 GLN* 4.0 12.3 - - - +
2441 VAL* 4.0 15.0 - - + +
2461 ASN* 3.5 16.3 + - - +
2471 ASP 2.8 23.0 + - - -
2481 HIS* 3.4 17.1 - - - +
2491 ASN* 4.1 13.0 + - - +
2511 THR 4.1 2.8 - - - +
2521 LYS* 3.5 3.5 - - - -
2531 VAL* 3.0 28.5 + - + +
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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