Contacts of the strand formed by residues 1278 - 1282 (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 LEU1278 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A TYR* 4.8 0.2 - - + -
1270A LEU* 4.1 17.9 - - + -
1271A VAL 3.4 7.6 - - - +
1272A SER* 3.9 20.0 - - - +
1277A ASN* 1.3 84.1 - - - +
1279A MET* 1.3 65.2 + - - +
1301A ASP* 3.5 3.6 - - - +
1302A PHE* 2.6 46.7 + - + +
1304A VAL* 3.7 26.0 - - + -
1308A VAL* 4.5 11.7 - - + -
1311A PHE* 4.6 6.1 - - + -
1338A PHE* 3.7 23.3 - - + -
1348A LEU* 4.1 20.6 - - + -
1384A LEU* 4.6 0.7 - - - +
1398A VAL* 6.5 0.2 - - + -
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Residues in contact with MET1279 (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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1253A LEU* 3.7 16.2 - - + -
1269A PHE 3.3 2.4 - - - +
1270A LEU* 3.5 2.3 - - - +
1271A VAL* 2.8 43.3 + - + +
1273A ASP* 3.3 24.2 - - - +
1277A ASN* 4.6 1.6 - - + +
1278A LEU* 1.3 74.7 - - - +
1280A VAL* 1.3 64.1 + - - +
1281A TYR* 2.9 40.8 + - + -
1298A ARG* 3.4 28.3 - - + +
1300A ALA 3.3 6.3 - - - -
1301A ASP* 3.5 12.1 - - - +
1384A LEU* 4.0 19.5 - - + -
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Residues in contact with VAL1280 (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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1A MET 5.0 7.0 - - - +
1261A MET* 4.0 18.4 - - + -
1268A GLY* 3.7 29.6 - - - -
1269A PHE 3.5 4.3 - - - +
1270A LEU* 3.8 20.9 - - + -
1279A MET* 1.3 77.7 - - - +
1281A TYR* 1.3 61.8 - - - +
1282A MET* 4.7 11.2 - - + -
1298A ARG* 3.3 1.2 - - - -
1299A ARG* 2.8 34.8 + - + +
1300A ALA* 3.2 25.9 + - + +
1348A LEU* 5.1 4.5 - - + -
1398A VAL* 5.9 2.2 - - + -
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Residues in contact with TYR1281 (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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1231A ILE* 4.6 9.6 - - + -
1249A ASP* 2.8 33.4 + - - -
1253A LEU* 3.8 3.9 - - + +
1268A GLY 3.9 0.2 - - - -
1269A PHE* 3.1 41.8 + - + +
1271A VAL* 4.1 24.9 - - + -
1279A MET* 2.9 31.8 - - + -
1280A VAL* 1.3 74.4 - - - +
1282A MET* 1.3 64.1 + - - +
1296A LEU* 3.8 32.5 - - + -
1297A LEU* 3.3 5.8 - - - +
1298A ARG* 2.7 59.9 + - + -
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Residues in contact with MET1282 (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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1A MET* 3.3 54.7 - - + +
1266A GLN* 3.9 27.6 - - + -
1267A LEU 4.1 12.3 - - - +
1268A GLY* 4.2 17.9 - - - +
1269A PHE* 4.6 2.2 - - - -
1280A VAL* 4.7 4.9 - - + -
1281A TYR* 1.3 78.6 - - - +
1283A TYR* 1.3 60.7 + - - +
1284A LEU* 3.7 23.3 + - + +
1296A LEU* 3.3 15.5 - - - +
1297A LEU* 3.0 23.1 + - - +
1299A ARG* 4.3 16.2 - - + -
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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