Contacts of the strand formed by residues 1201 - 1204 (chain B) in PDB entry 2BOA
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 LEU1201 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39B LYS* 6.0 2.7 - - - -
50B ARG* 5.6 3.8 - - - +
1199B SER* 3.9 27.6 - - - +
1200B GLN* 1.3 78.9 - - - +
1202B LEU* 1.3 61.1 + - - +
1203B MET* 3.9 18.8 - - + -
1238B TYR* 3.3 10.6 - - - -
1239B GLN* 3.5 39.5 - - + +
1246B THR* 4.2 11.2 - - + +
1247B VAL* 3.4 33.7 - - + -
1268B THR 4.3 0.2 - - - -
1269B PHE* 3.5 2.1 - - - -
1270B GLU* 2.8 42.4 + - + -
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Residues in contact with LEU1202 (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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1201B LEU* 1.3 73.7 - - - +
1203B MET* 1.3 61.1 + - - +
1223B ALA* 3.4 35.7 - - + +
1226B ALA* 3.9 8.1 - - + -
1227B ALA* 3.9 16.8 - - + +
1230B LEU* 6.0 0.2 - - + -
1238B TYR* 4.0 9.9 - - + -
1239B GLN 3.0 11.4 + - - +
1240B VAL* 3.4 16.4 - - + +
1241B GLY 3.3 22.0 + - - +
1267B PHE* 4.5 8.7 - - + -
1268B THR 3.3 16.4 - - - +
1269B PHE* 3.6 45.1 - - + -
1300B ILE* 4.5 7.9 - - + -
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Residues in contact with MET1203 (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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1201B LEU* 3.9 15.5 - - + -
1202B LEU* 1.3 80.4 - - - +
1204B TYR* 1.3 64.2 + - - +
1241B GLY 3.1 15.3 - - - +
1243B THR* 4.0 22.0 - - + +
1246B THR* 3.9 13.9 - - + -
1247B VAL* 3.7 40.2 - - + -
1255B ILE* 4.5 1.3 - - - -
1267B PHE* 3.3 12.1 - - - -
1268B THR* 2.9 51.2 + - + -
1270B GLU* 3.7 30.3 - - + +
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Residues in contact with TYR1204 (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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1203B MET* 1.3 78.8 - - - +
1205B PRO* 1.3 97.8 - - + +
1212B LYS* 6.0 0.2 + - - -
1216B ALA* 3.8 26.5 + - + +
1219B LEU* 4.0 29.4 - - + -
1220B ASP* 2.7 49.8 + - + +
1223B ALA* 4.4 9.0 - - + -
1241B GLY* 3.3 18.0 + - - -
1242B PRO* 3.3 27.7 - - + +
1243B THR* 2.9 26.9 + - - -
1255B ILE* 3.8 8.3 - - - -
1266B ALA 3.7 9.0 - - - +
1267B PHE* 4.1 5.2 - - + -
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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