Contacts of the strand formed by residues 101 - 112 (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 LEU 101 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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492 PRO* 3.6 32.5 - - + -
992 HIS* 3.5 6.4 - - - +
1002 TYR* 1.3 121.8 - - + +
1022 GLY* 1.3 58.0 + - - +
2182 ILE* 4.0 17.7 - - + +
2192 ASP* 3.4 30.1 - - - +
2202 SER 3.9 1.3 - - - +
2212 MET* 5.2 0.7 - - - -
2602 PHE* 3.3 8.6 - - - +
2612 ASN* 2.9 35.6 + - + +
2622 GLY 5.2 0.2 - - - +
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Residues in contact with GLY 102 (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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1012 LEU* 1.3 76.1 - - - +
1032 ARG* 1.3 60.2 + - - +
2122 TYR* 4.2 3.6 + - - -
2182 ILE* 3.6 8.1 - - - +
2192 ASP* 2.9 21.8 + - - +
2212 MET* 3.4 23.5 - - - +
2592 GLU 3.3 11.7 - - - -
2602 PHE* 3.6 14.1 - - - -
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Residues in contact with ARG 103 (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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402 GLU* 2.9 40.8 + - - +
412 TYR* 3.8 2.4 - - - +
422 LEU* 3.7 47.4 - - - +
462 GLU* 5.6 1.6 + - - -
1022 GLY* 1.3 73.8 - - - +
1042 SER* 1.3 63.2 + - - +
2122 TYR* 3.6 48.9 + - + +
2172 SER* 3.0 27.7 + - - +
2182 ILE* 3.9 9.2 - - + -
2212 MET* 3.8 3.9 - - - +
2572 CYS 4.7 3.3 + - - +
2582 CYS* 3.1 5.1 - - - +
2592 GLU* 2.9 52.3 + - + +
2602 PHE* 4.9 0.7 - - - -
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Residues in contact with SER 104 (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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922 PHE* 4.3 3.8 - - - -
1032 ARG* 1.3 79.1 - - - +
1052 GLY* 1.3 77.2 + - - +
1062 TYR* 3.6 21.9 + - - -
2122 TYR* 3.3 30.4 - - - +
2212 MET* 3.8 17.7 - - - +
2272 TRP* 5.3 0.3 - - - -
2552 PRO* 3.5 12.6 - - - +
2562 MET 3.6 4.8 + - - -
2572 CYS 4.4 1.6 - - - -
2582 CYS* 3.4 20.1 - - - +
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Residues in contact with GLY 105 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392 PRO* 4.2 8.7 - - - +
1042 SER* 1.3 79.6 + - - +
1062 TYR* 1.3 71.4 + - - -
2102 LEU 3.2 12.8 - - - -
2112 PRO 4.1 0.2 - - - -
2122 TYR* 3.9 11.3 - - - +
2562 MET* 2.8 36.7 + - - -
2572 CYS* 4.8 0.6 + - - +
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Residues in contact with TYR 106 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
822 LEU* 3.8 31.4 - - + -
832 PRO* 3.3 30.4 - - + +
862 LEU* 3.9 17.5 - - + -
922 PHE* 4.3 4.0 - + - -
1042 SER* 3.6 35.6 + - - -
1052 GLY* 1.3 80.3 - - - -
1072 THR* 1.3 60.3 + - - +
1082 VAL* 3.9 10.1 - - + -
2082 LEU 3.6 0.5 - - - +
2092 VAL* 3.5 2.3 - - - -
2102 LEU* 2.8 45.9 + - + +
2212 MET* 4.0 2.8 - - - +
2262 ASN* 4.6 4.1 + - - -
2272 TRP* 4.3 19.5 - + - -
2532 ILE* 4.0 23.6 - - + -
2542 ALA 3.1 7.2 - - - +
2552 PRO* 3.9 13.0 - - + -
2562 MET* 3.8 8.8 - - - +
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Residues in contact with THR 107 (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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162 LEU* 4.0 17.7 - - + -
182 LEU* 4.1 6.3 - - - +
382 TRP* 5.6 0.2 - - - -
632 PHE* 3.8 30.2 - - + -
1062 TYR* 1.3 71.0 + - - +
1082 VAL* 1.3 61.6 + - - +
1092 HIS 4.9 0.2 - - - +
2072 THR* 4.1 14.8 - - + -
2082 LEU 3.6 4.0 - - - +
2092 VAL* 4.0 12.2 - - + +
2522 THR 3.9 0.9 - - - +
2532 ILE* 3.3 4.5 - - - +
2542 ALA 2.8 34.6 + - - -
2562 MET* 3.0 26.8 - - - +
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Residues in contact with VAL 108 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
822 LEU* 4.3 5.8 - - + -
1062 TYR* 4.3 2.5 - - + -
1072 THR* 1.3 75.2 - - - +
1092 HIS* 1.3 61.5 + - - +
1102 VAL* 4.1 20.9 - - + -
1242 VAL* 5.6 0.9 - - + -
2062 ALA 3.5 1.2 - - - +
2072 THR* 3.3 5.5 - - - +
2082 LEU* 2.8 51.6 + - + +
2102 LEU* 3.9 26.9 - - + -
2292 ILE* 4.1 24.2 - - + -
2512 LEU* 5.3 2.7 - - + -
2522 THR 4.0 1.6 - - - -
2532 ILE* 4.0 28.5 - - + -
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Residues in contact with HIS 109 (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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162 LEU* 4.8 5.6 - - + +
232 ILE* 3.5 46.3 - - + +
242 THR 4.9 1.2 + - - -
252 THR* 4.6 12.2 - - + -
632 PHE* 5.0 3.4 - - + -
1072 THR* 3.9 0.8 + - + -
1082 VAL* 1.3 75.4 - - - +
1102 VAL* 1.3 58.3 + - - +
1112 GLN* 2.9 54.3 + - + +
2052 CYS* 3.5 30.5 - - + +
2062 ALA 3.3 2.9 + - - -
2072 THR* 2.8 30.4 + - + +
2512 LEU* 4.8 0.2 - - - -
2522 THR 2.8 29.9 + - - +
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Residues in contact with VAL 110 (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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1082 VAL* 4.1 17.3 - - + -
1092 HIS* 1.3 73.0 - - - +
1112 GLN* 1.3 61.0 + - - +
1222 LEU* 5.4 0.4 - - + -
1242 VAL* 3.7 26.7 - - + -
1982 ILE* 3.7 21.8 - - + -
2052 CYS* 3.1 11.1 - - - +
2062 ALA* 2.8 39.5 + - + +
2082 LEU* 5.8 0.2 - - + -
2292 ILE* 5.2 1.3 - - + -
2312 ILE* 3.8 28.0 - - + -
2492 ILE* 3.9 17.5 - - + -
2502 THR 3.7 4.0 - - - +
2512 LEU* 4.4 9.0 - - + +
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Residues in contact with GLN 111 (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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232 ILE* 5.6 2.9 - - - +
1092 HIS* 2.9 48.2 + - + +
1102 VAL* 1.3 74.3 - - - +
1122 CYS* 1.3 63.6 + - - +
1132 ASN* 5.6 1.6 - - - +
2042 ASN 3.8 4.5 - - - +
2052 CYS* 5.0 1.3 - - + -
2482 PRO 4.0 0.5 - - - +
2492 ILE* 3.4 4.2 - - - +
2502 THR* 2.8 64.3 + - - +
2522 THR* 2.9 30.8 + - - +
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Residues in contact with CYS 112 (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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712 TRP* 3.8 20.2 - - - -
1102 VAL 4.3 0.4 + - - -
1112 GLN* 1.3 75.8 - - - +
1132 ASN* 1.3 59.3 + - - +
1222 LEU* 4.3 9.9 - - + -
1982 ILE* 4.1 9.8 - - + +
2002 LEU* 3.9 11.2 - - - +
2042 ASN* 2.9 30.2 + - - +
2472 ILE* 3.4 32.3 - - - -
2482 PRO 3.4 18.6 - - - +
2492 ILE* 4.0 10.5 - - + -
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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