Contacts of the strand formed by residues 1233 - 1237 (chain A) in PDB entry 6BM0
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 LEU1233 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1221A PHE* 4.6 13.0 - - + -
1222A ILE 3.3 11.0 - - - +
1223A LEU* 3.7 19.5 - - + +
1231A ILE* 4.2 2.0 - - - +
1232A SER* 1.3 72.7 - - - +
1234A LEU* 1.3 67.4 + - - +
1245A LEU* 3.3 8.0 - - - +
1246A VAL* 3.2 44.6 + - + -
1247A SER* 3.3 21.9 + - - +
1269A PHE* 3.6 35.2 - - + -
1283A TYR* 4.9 5.2 - - + -
1296A LEU* 3.7 31.6 - - + -
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Residues in contact with LEU1234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1190A ILE* 4.1 31.0 - - + -
1206A ILE* 3.9 20.4 - - + -
1221A PHE* 3.9 6.1 - - - -
1222A ILE* 2.6 49.3 + - + +
1224A ALA* 5.4 1.1 - - + -
1232A SER* 3.8 11.4 - - - +
1233A LEU* 1.3 92.5 - - - +
1235A ARG* 1.3 64.4 + - - +
1243A LEU* 4.0 27.1 - - + -
1244A SER 3.3 17.9 - - - +
1245A LEU* 3.8 17.3 - - + -
1246A VAL* 3.9 2.4 - - - +
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Residues in contact with ARG1235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1220A ASN* 3.9 19.3 - - - +
1221A PHE* 3.4 35.9 - - + +
1222A ILE 4.8 0.4 - - - +
1234A LEU* 1.3 78.7 - - - +
1236A TYR* 1.3 64.2 + - - +
1237A GLN* 3.4 28.9 + - + +
1243A LEU* 3.3 5.0 - - - +
1244A SER* 2.9 36.1 + - - +
1246A VAL* 3.6 28.4 - - + +
1283A TYR* 4.8 11.3 + - - -
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Residues in contact with TYR1236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1178A CYS* 5.7 7.2 - - + -
1181A HIS* 4.2 22.9 + + - -
1192A LEU* 4.0 31.2 - - + -
1203A MET* 3.3 32.3 - - + +
1204A ALA* 4.1 13.0 - - + -
1220A ASN* 2.9 39.0 + - + +
1222A ILE* 5.4 3.5 - - + +
1235A ARG* 1.3 73.9 - - - +
1237A GLN* 1.3 77.3 + - - +
1238A GLU* 3.7 15.2 + - + +
1241A LYS* 4.2 7.0 - - - -
1242A THR 3.2 33.7 - - - -
1243A LEU* 3.8 13.9 - - + +
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Residues in contact with GLN1237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1220A ASN* 5.0 0.7 - - - -
1235A ARG* 3.4 36.9 - - + +
1236A TYR* 1.3 90.6 - - - +
1238A GLU* 1.3 59.4 + - - +
1239A GLU* 4.9 5.2 - - - +
1240A SER* 2.9 26.1 - - - +
1242A THR* 3.4 27.6 + - + +
1244A SER* 4.2 13.3 + - - -
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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