Contacts of the strand formed by residues 1560 - 1565 (chain F) in PDB entry 6X34
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 ASN1560 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1272F LEU 3.6 7.9 - - - +
1273F THR* 5.0 2.9 - - + +
1440F PHE* 3.6 42.7 - - + +
1443F GLN* 3.9 12.3 - - - +
1558F HIS* 3.3 22.6 + - + +
1559F GLN* 1.3 77.3 - - + +
1561F VAL* 1.3 66.9 + - - +
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Residues in contact with VAL1561 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1272F LEU* 3.3 37.2 + - + -
1274F HIS* 6.2 1.1 - - + -
1289F LEU* 6.0 1.3 - - + -
1439F VAL* 4.7 4.9 - - - +
1440F PHE* 5.0 1.7 - - - -
1443F GLN* 4.3 5.2 - - - +
1554F VAL* 3.4 35.2 - - + +
1555F LEU 4.4 11.2 - - - +
1556F PRO* 4.7 10.8 - - + -
1558F HIS 4.9 2.2 - - - +
1559F GLN 3.6 3.6 + - - +
1560F ASN* 1.3 75.5 - - - +
1562F ILE* 1.3 65.8 + - + +
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Residues in contact with ILE1562 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1270F LEU 3.9 1.8 - - - +
1271F ARG* 3.4 1.6 - - - +
1272F LEU* 3.0 27.8 + - + +
1289F LEU* 5.2 8.1 - - + -
1437F VAL* 5.0 6.1 - - + -
1438F ARG 4.3 4.7 - - - +
1439F VAL* 5.2 6.3 - - + +
1440F PHE* 4.4 8.5 - - - -
1448F VAL* 6.5 0.2 - - + -
1552F VAL* 4.3 20.2 - - + -
1554F VAL* 3.8 16.2 - - + -
1560F ASN 3.7 0.8 - - - -
1561F VAL* 1.3 82.6 - - + +
1563F GLN* 1.3 61.8 + - - +
1564F PHE* 5.8 3.8 - - + -
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Residues in contact with GLN1563 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1269F CYS* 4.8 6.1 - - + -
1270F LEU 3.6 5.4 - - - -
1271F ARG* 3.8 17.5 - - + +
1437F VAL* 3.3 4.8 - - - +
1438F ARG* 3.0 44.4 + - + +
1440F PHE* 3.6 24.2 - - + -
1562F ILE* 1.3 76.3 - - - +
1564F PHE* 1.3 68.4 + - - +
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Residues in contact with PHE1564 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1269F CYS* 3.2 22.1 - - - +
1270F LEU* 3.2 54.5 + - + +
1289F LEU* 5.0 19.1 - - + -
1290F ARG 5.8 1.6 - - - -
1291F LEU* 3.6 31.9 - - + -
1435F TYR* 4.1 15.9 - - + +
1436F SER 4.4 0.7 - - - -
1437F VAL* 4.5 10.5 - - + +
1438F ARG* 4.5 4.3 - - - +
1550F PRO 5.4 0.2 - - - -
1552F VAL* 3.9 30.7 - - + -
1562F ILE* 5.8 3.4 - - + -
1563F GLN* 1.3 81.2 - - - +
1565F GLU* 1.3 66.4 + - - +
1597F MET* 4.7 16.6 - - + -
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Residues in contact with GLU1565 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1267F PRO* 5.3 9.2 - - + -
1268F PRO 3.7 7.4 + - - -
1269F CYS* 5.0 0.4 - - + -
1435F TYR* 4.2 13.6 - - - -
1436F SER* 3.0 48.4 + - - +
1438F ARG* 4.2 21.3 - - + -
1564F PHE* 1.3 79.6 - - - +
1566F LEU* 1.3 60.1 + - - +
1567F GLY 3.9 1.8 + - - +
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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