Contacts of the strand formed by residues 247 - 256 (chain 2) 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 ILE 247 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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712 TRP* 2.8 59.8 + - + +
1122 CYS* 3.4 25.8 - - - -
1132 ASN 3.9 14.4 - - - +
1142 ALA* 3.8 17.9 - - + -
1182 HIS* 4.2 16.2 - - + +
2002 LEU* 3.8 19.1 - - + -
2372 LEU* 3.9 11.2 - - + +
2462 GLU* 1.3 84.8 - - - +
2482 PRO* 1.3 70.7 - - + +
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Residues in contact with PRO 248 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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682 THR* 3.6 22.4 - - + -
692 VAL 3.4 6.5 - - - +
1112 GLN 4.0 0.2 - - - +
1122 CYS* 3.4 24.4 - - - +
1132 ASN 4.9 3.2 + - - +
2462 GLU* 3.6 16.2 - - - +
2472 ILE* 1.3 94.3 - - + +
2492 ILE* 1.3 60.7 + - - +
2502 THR* 4.2 1.8 - - - +
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Residues in contact with ILE 249 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672 ASP 4.8 0.3 - - - +
682 THR* 3.4 1.8 - - - +
692 VAL* 2.9 44.4 + - + +
712 TRP* 3.9 12.8 - - + -
782 TRP* 3.6 42.4 - - + -
802 TRP* 5.7 0.2 - - + -
1102 VAL* 3.9 24.2 - - + -
1112 GLN 3.4 9.2 - - - +
1122 CYS* 4.0 13.9 - - + -
1222 LEU* 3.6 19.5 - - + -
2312 ILE* 4.6 6.5 - - + -
2482 PRO* 1.3 79.3 - - - +
2502 THR* 1.3 62.7 + - - +
2512 LEU* 4.2 13.8 + - + +
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Residues in contact with THR 250 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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652 THR* 3.5 31.0 - - + -
662 LEU 4.6 1.3 - - - +
682 THR* 2.9 30.9 + - - +
1102 VAL* 3.7 1.4 - - - -
1112 GLN* 2.8 68.2 + - - +
2482 PRO* 4.2 2.1 - - - +
2492 ILE* 1.3 72.3 - - - +
2512 LEU* 1.3 62.8 + - - +
2522 THR* 4.2 0.4 - - - +
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Residues in contact with LEU 251 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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652 THR* 3.5 3.1 - - - +
662 LEU* 2.9 51.5 + - + +
672 ASP 5.3 2.8 + - - +
692 VAL* 5.9 0.2 - - + -
802 TRP* 3.6 57.7 - - + -
1082 VAL* 5.3 1.3 - - + -
1092 HIS 3.9 2.5 - - - +
1102 VAL* 4.4 14.6 - - + +
2292 ILE* 4.7 9.6 - - + -
2312 ILE* 3.8 16.4 - - + -
2492 ILE* 4.2 9.6 + - + +
2502 THR* 1.3 77.6 - - - +
2522 THR* 1.3 61.3 + - - +
2532 ILE* 4.2 18.8 - - + -
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Residues in contact with THR 252 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232 ILE* 4.0 13.9 - - + -
632 PHE* 3.5 37.5 - - + -
642 TYR 3.3 7.6 - - - +
652 THR* 2.9 29.0 + - - +
1072 THR 3.9 0.7 - - - +
1092 HIS* 2.8 39.6 + - - +
1112 GLN* 2.9 24.1 + - - +
2512 LEU* 1.3 72.8 - - - +
2532 ILE* 1.3 62.8 + - - +
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Residues in contact with ILE 253 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622 ARG 3.7 1.0 - - - +
632 PHE* 4.1 1.3 - - - -
642 TYR* 2.9 40.5 + - - +
662 LEU* 4.7 13.7 - - + -
802 TRP* 5.9 0.7 - - + -
822 LEU* 3.9 26.5 - - + -
852 ALA* 5.0 1.8 - - + -
862 LEU* 4.0 24.4 - - + +
1062 TYR* 4.0 22.0 - - + -
1072 THR 3.3 9.2 - - - +
1082 VAL* 4.0 20.6 - - + -
2292 ILE* 5.0 3.8 - - + -
2512 LEU* 4.2 23.6 - - + -
2522 THR* 1.3 82.7 - - - +
2542 ALA* 1.3 63.4 + - - +
2552 PRO* 3.8 0.9 - - - +
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Residues in contact with ALA 254 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182 LEU* 3.6 19.3 - - + -
622 ARG 3.2 20.6 - - - +
632 PHE* 3.4 26.8 - - + -
1062 TYR* 3.1 3.7 - - - -
1072 THR* 2.8 37.0 + - - +
2532 ILE* 1.3 75.2 - - - +
2552 PRO* 1.3 69.1 - - - +
2562 MET* 3.7 0.7 - - - +
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Residues in contact with PRO 255 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182 LEU* 4.8 0.3 - - - +
602 ALA 3.1 26.5 - - - +
612 CYS* 3.0 26.4 - - - +
622 ARG 3.6 6.1 - - - +
642 TYR* 3.8 8.5 - - + -
862 LEU* 3.8 11.9 - - + -
922 PHE* 3.5 35.0 - - + -
1042 SER* 3.5 13.7 - - - +
1052 GLY 3.4 7.6 - - - +
1062 TYR* 3.9 4.7 - - + -
2532 ILE 3.8 6.1 - - - +
2542 ALA* 1.3 88.5 - - - +
2562 MET* 1.3 62.0 + - - +
2582 CYS* 4.6 4.0 - - - -
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Residues in contact with MET 256 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182 LEU* 4.4 25.8 - - + -
382 TRP* 3.9 35.4 - - + +
392 PRO* 3.6 26.9 - - + +
612 CYS* 3.9 4.0 - - - -
1042 SER* 3.6 0.2 + - - -
1052 GLY* 2.8 31.6 + - - +
1062 TYR 3.8 2.7 - - - +
1072 THR* 3.0 34.1 - - - +
2092 VAL* 4.2 2.7 - - - -
2542 ALA 3.7 8.1 - - - +
2552 PRO* 1.3 80.4 - - - +
2572 CYS* 1.3 73.2 + - - +
2582 CYS 3.1 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