Contacts of the strand formed by residues 238 - 245 (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 GLY 238 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1091 LYS* 3.7 4.9 + - - +
1101 ILE* 3.0 25.2 + - - +
1601 VAL 3.5 6.7 - - - -
1621 PRO* 3.4 19.6 - - - +
2351 ASN* 3.1 23.1 + - - -
2371 PHE* 1.3 80.7 - - - +
2391 ILE* 1.3 67.3 + - - +
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Residues in contact with ILE 239 (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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1071 VAL* 3.7 24.2 - - + -
1081 TRP 3.1 16.4 - - - +
1091 LYS* 3.7 17.5 - - + +
1101 ILE* 4.1 6.9 - - - +
1591 TYR* 3.4 5.4 - - - -
1601 VAL* 2.8 61.1 + - + +
1661 VAL* 4.2 20.2 - - + -
2351 ASN* 4.8 5.4 - - - +
2371 PHE 4.1 0.2 + - - -
2381 GLY* 1.3 81.4 - - - +
2401 LEU* 1.3 74.2 + - - +
2411 ALA* 3.8 11.9 - - + +
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Residues in contact with LEU 240 (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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01 SPH 4.0 36.3 - - + -
901 MET* 3.5 17.0 - - + +
1071 VAL* 3.4 2.9 - - - -
1081 TRP* 2.8 60.1 + - + -
1101 ILE* 4.0 14.1 - - + +
1341 LEU* 5.1 3.8 - - + -
1361 PHE* 3.9 28.3 - - + -
1571 ILE* 4.3 12.6 - - + -
1581 MET 3.4 3.1 - - - +
1591 TYR* 4.1 8.5 - - - -
2391 ILE* 1.3 78.9 - - - +
2411 ALA* 1.3 59.7 + - - +
2421 VAL* 4.8 0.2 - - + -
2591 VAL* 4.5 8.7 - - + -
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Residues in contact with ALA 241 (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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1061 ALA 3.1 8.3 - - - +
1071 VAL* 4.4 3.6 - - + -
1561 GLN 3.4 2.1 - - - +
1571 ILE* 3.6 0.7 - - - -
1581 MET* 2.8 40.7 + - + +
1601 VAL* 4.4 3.4 - - + -
1671 PRO* 3.7 20.6 - - + -
1751 TRP* 3.5 22.9 - - + -
2391 ILE* 3.8 13.6 - - + +
2401 LEU* 1.3 73.5 - - - +
2421 VAL* 1.3 60.9 + - - +
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Residues in contact with VAL 242 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901 MET* 3.6 31.9 - - + -
921 VAL* 3.3 12.2 - - + +
1051 PHE* 3.3 4.9 - - - +
1061 ALA* 2.8 34.6 + - + -
1551 TYR* 4.8 4.9 - - + -
1561 GLN 3.2 8.3 - - - +
1571 ILE* 4.0 29.6 - - + -
1751 TRP* 3.9 1.1 - - - -
2401 LEU* 4.8 0.2 - - + -
2411 ALA* 1.3 80.7 - - - +
2431 ARG* 1.3 70.3 + - - +
2571 ILE* 3.7 33.9 - - + -
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Residues in contact with ARG 243 (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* 4.4 3.8 - - - -
1031 LYS* 5.8 0.2 - - - -
1051 PHE* 4.1 10.8 - - + +
1551 TYR* 3.3 8.2 - - - +
1561 GLN* 2.9 64.5 + - + -
1701 TRP* 2.8 58.3 + - + +
1711 ASP* 3.9 10.5 - - - +
1751 TRP* 3.5 45.4 + - + +
1841 PHE* 4.9 2.8 - - - -
2421 VAL* 1.3 78.3 - - - +
2441 VAL* 1.3 67.1 + - - +
2451 VAL* 4.0 23.7 - - - +
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Residues in contact with VAL 244 (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* 3.9 14.6 - - + +
931 ASP 3.9 23.9 + - - +
941 ASN* 4.0 10.8 - - + +
1031 LYS* 3.0 28.1 + - - +
1041 LEU 5.5 0.8 + - - -
1531 GLN* 3.6 29.4 - - + +
1541 VAL 3.7 4.7 - - - +
1551 TYR* 3.9 24.0 - - + -
1701 TRP* 3.5 8.0 - - - -
2431 ARG* 1.3 73.5 - - - +
2451 VAL* 1.3 59.3 + - - +
2461 ASN* 3.8 25.6 - - + +
2551 SER* 4.7 2.0 - - - +
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Residues in contact with VAL 245 (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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1541 VAL* 2.8 30.6 + - + +
1551 TYR 4.0 2.0 - - - -
1561 GLN* 3.7 33.7 - - + +
1701 TRP* 3.5 14.7 - - - -
1841 PHE* 4.1 16.6 - - + -
2431 ARG* 4.0 22.8 + - - +
2441 VAL* 1.3 71.2 - - - +
2461 ASN* 1.3 66.3 + - - +
2471 ASP* 3.6 2.8 + - - +
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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