Contacts of the strand formed by residues 1212 - 1217 (chain B) in PDB entry 2JA7
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 ILE1212 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A PHE* 5.0 9.2 - - + -
20A GLY 3.7 11.9 - - - +
21A LEU* 3.8 12.1 - - + -
92A HIS* 5.1 0.4 - - + -
95A PHE* 4.5 3.6 - - + -
1409A LEU* 3.4 12.6 - - + +
1410A PHE* 3.3 54.1 - - + +
1413A GLY* 4.3 2.0 - - - +
1207B LEU* 3.0 35.8 + - + +
1208B MET* 3.3 21.9 + - - +
1210B MET* 3.2 6.7 - - + +
1211B ASN* 1.3 80.2 - - - +
1213B THR* 1.3 68.4 + - - +
1214B PRO* 3.4 6.2 - - - +
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Residues in contact with THR1213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A GLN 3.0 6.8 - - - +
19A PHE* 3.3 3.3 - - - -
20A GLY* 2.8 50.9 + - - -
21A LEU 3.4 1.0 + - - -
22A PHE* 3.4 58.3 - - + +
1168B LEU* 4.7 3.1 - - - -
1212B ILE* 1.3 74.3 - - - +
1214B PRO* 1.3 63.6 - - - +
1215B ARG* 3.6 31.9 + - - +
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Residues in contact with PRO1214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A VAL* 4.6 3.1 - - + -
18A GLN 3.7 2.0 - - - +
19A PHE* 3.9 23.6 - - + -
1167B GLY 3.1 12.1 - - - +
1168B LEU* 4.3 7.3 - - + +
1204B PHE* 4.0 46.2 - - + +
1207B LEU* 5.0 5.4 - - + -
1208B MET* 4.0 15.5 - - + -
1212B ILE* 3.4 11.4 - - + +
1213B THR* 1.3 82.6 - - - +
1215B ARG* 1.3 63.9 + - - +
1216B LEU* 3.5 7.2 + - + +
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Residues in contact with ARG1215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A GLU 3.3 1.2 - - - +
17A VAL* 3.0 28.8 - - - -
18A GLN* 2.6 52.5 + - + +
19A PHE 5.5 0.4 - - - -
20A GLY* 5.5 0.4 - - - +
21A LEU 5.1 3.6 + - - -
26A GLU* 3.3 28.3 + - - -
227A VAL 5.7 0.2 + - - -
228A PHE* 4.8 17.9 + - + +
1166B CYS* 3.5 29.1 - - - +
1167B GLY* 3.1 19.3 - - - +
1168B LEU* 3.7 11.0 - - - +
1213B THR* 3.6 30.9 + - - +
1214B PRO* 1.3 73.6 - - - +
1216B LEU* 1.3 64.6 + - - +
1217B TYR* 3.7 20.4 + - + +
15D LEU* 3.8 19.9 - - - +
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Residues in contact with LEU1216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A VAL* 3.3 32.5 - - + -
16A GLU 4.0 2.5 - - - -
17A VAL* 4.9 6.5 - - + -
1430A LEU* 4.7 2.7 - - + -
1162B ILE* 3.7 34.9 - - + +
1163B CYS 4.7 1.7 - - - +
1167B GLY* 2.9 16.8 + - - +
1168B LEU* 5.9 1.6 - - - -
1169B MET* 6.0 6.7 - - + -
1194B ILE* 3.6 18.2 - - + -
1196B ILE* 5.1 2.2 - - + -
1204B PHE* 4.0 38.1 - - + -
1214B PRO* 3.6 15.7 - - + +
1215B ARG* 1.3 81.8 - - - +
1217B TYR* 1.3 66.3 + - - +
1218B THR* 4.1 1.0 + - - +
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Residues in contact with TYR1217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A VAL* 3.6 2.8 - - - -
15A LYS 2.8 24.8 + - - -
16A GLU* 3.2 41.2 + - + +
18A GLN* 5.3 12.3 - - + -
228A PHE* 4.9 10.6 - + - -
1163B CYS 5.3 0.7 - - - -
1164B GLY 4.9 8.3 - - - -
1165B ILE 2.5 26.2 + - - -
1166B CYS* 4.2 1.2 - - - -
1167B GLY* 3.3 26.5 + - - -
1215B ARG* 3.7 22.7 - - + -
1216B LEU* 1.3 81.3 - - - +
1218B THR* 1.3 62.0 + - - +
1219B ASP* 3.3 13.9 - - - +
1221B SER* 5.8 1.8 - - - -
13D ARG* 4.7 16.8 - - - -
14D ARG* 5.9 1.3 - - - -
15D LEU* 4.4 10.2 + - - +
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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