Contacts of the strand formed by residues 1346 - 1351 (chain A) in PDB entry 2H7C
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 TYR1346 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1227A VAL* 4.2 1.8 - - + -
1228A SER* 3.3 25.5 + - - -
1231A VAL* 4.5 16.2 - - + -
1243A ALA* 3.3 28.9 - - + -
1245A SER* 2.6 35.1 + - - -
1249A VAL* 4.1 4.0 - - - +
1344A VAL* 3.3 1.5 + - + +
1345A PRO* 1.3 76.0 - - - +
1347A MET* 1.3 75.2 + - - +
1348A VAL* 3.7 19.3 - - + -
1433A VAL* 3.8 16.4 - - + -
1437A HIS* 3.3 41.7 - + + +
1443A PRO 2.9 8.9 + - - -
1444A THR* 3.4 8.2 - - + +
1445A TYR* 3.1 22.8 + - - +
1503A PHE* 3.7 4.6 - - - -
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Residues in contact with MET1347 (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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1243A ALA 2.8 14.2 + - - +
1244A ILE* 3.2 22.7 - - + +
1245A SER 2.9 26.5 + - - +
1346A TYR* 1.3 75.4 - - - +
1348A VAL* 1.3 61.7 + - - +
1445A TYR* 3.3 12.8 - - + +
1447A TYR* 4.1 13.2 - - + -
1499A PHE 4.7 0.4 - - - +
1500A TRP* 3.9 29.4 - - + -
1503A PHE* 3.6 41.2 - - + -
1509A PRO* 4.2 8.3 - - + -
1517A TRP* 3.7 37.0 - - + -
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Residues in contact with VAL1348 (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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1245A SER 3.6 5.8 - - - +
1249A VAL* 4.0 15.7 - - + -
1346A TYR* 3.7 38.1 - - + +
1347A MET* 1.3 78.8 - - - +
1349A GLY* 1.3 62.9 + - - +
1430A SER* 3.9 35.9 - - - +
1433A VAL* 4.7 4.0 - - + -
1434A ALA* 4.6 11.2 - - + -
1444A THR* 5.2 1.8 - - + -
1445A TYR 2.8 11.8 + - - +
1446A MET* 3.0 39.1 - - + +
1447A TYR* 3.3 2.4 + - - -
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Residues in contact with GLY1349 (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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1245A SER 3.1 9.8 + - - +
1247A SER* 2.9 24.4 + - - -
1248A GLY 4.7 0.2 + - - -
1348A VAL* 1.3 76.6 - - - +
1350A ILE* 1.3 68.5 + - - +
1430A SER* 4.6 2.3 + - - -
1446A MET* 5.0 1.6 - - - -
1447A TYR* 3.3 37.5 - - - -
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Residues in contact with ILE1350 (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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1247A SER* 4.2 3.1 - - - -
1349A GLY* 1.3 80.2 - - - +
1351A ASN* 1.3 66.8 + - - +
1354A GLU* 3.4 13.7 - - + +
1426A PHE* 4.1 14.6 - - + +
1427A GLY* 4.0 12.6 - - - +
1430A SER* 3.5 27.8 - - - +
1446A MET* 5.5 0.9 - - + -
1447A TYR* 3.1 12.3 + - - +
1448A GLU* 3.1 15.6 - - + +
1449A PHE 2.7 29.8 + - - -
1539A LEU* 4.3 22.0 - - + -
1540A LYS* 3.8 30.1 - - + -
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Residues in contact with ASN1351 (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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1247A SER* 3.9 7.2 + - - -
1350A ILE* 1.3 86.5 - - - +
1352A LYS* 1.3 65.7 + - - +
1353A GLN 3.3 1.1 + - - -
1354A GLU* 2.7 29.5 + - - +
1447A TYR* 4.5 2.4 + - - -
1448A GLU* 4.6 2.2 - - - -
1449A PHE* 3.1 31.6 - - - +
1466A GLY 3.2 15.5 - - - +
1467A ASP 2.9 22.1 + - - +
1468A HIS* 4.0 1.4 - - - +
1469A GLY 3.4 8.3 - - - +
1470A ASP* 3.5 3.6 - - - +
1471A GLU* 3.0 31.9 + - - +
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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