Contacts of the helix formed by residues 1468 - 1479 (chain A) in PDB entry 6FF7
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 ASN1468 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1371A TYR* 6.0 0.2 - - - +
1466A ASN* 3.3 12.9 + - + +
1467A LEU* 1.3 75.6 - - - +
1469A ASN* 1.3 65.3 + - + +
1470A TYR 3.4 1.9 + - - +
1471A ARG* 3.7 18.4 + - - +
1472A THR* 4.0 4.9 + - - -
433C TYR* 6.0 2.7 - - - +
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Residues in contact with ASN1469 (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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1371A TYR* 5.4 5.7 - - + +
1468A ASN* 1.3 77.5 - - - +
1470A TYR* 1.3 58.7 + - - +
1471A ARG 3.3 1.8 - - - -
1472A THR* 3.8 11.4 - - - +
1473A ASP* 2.9 30.3 + - - +
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Residues in contact with TYR1470 (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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1366A PRO* 5.7 5.7 - - + +
1367A ASN 5.5 3.1 - - - +
1368A LEU* 5.5 9.9 - - - +
1371A TYR* 4.4 21.7 - - + +
1467A LEU* 5.0 13.0 - - + -
1468A ASN 3.4 2.0 - - - +
1469A ASN* 1.3 77.2 - - - +
1471A ARG* 1.3 57.9 + - - +
1473A ASP* 3.5 5.3 + - - +
1474A MET* 2.9 28.9 + - - +
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Residues in contact with ARG1471 (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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1319A PRO* 5.0 15.3 - - + -
1467A LEU 5.9 0.2 - - - -
1468A ASN* 3.7 12.1 + - - +
1469A ASN 3.3 0.4 - - - -
1470A TYR* 1.3 79.4 - - - +
1472A THR* 1.3 57.1 + - - +
1474A MET* 3.2 8.5 + - - +
1475A ILE* 3.0 26.7 + - - +
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Residues in contact with THR1472 (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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1468A ASN 4.0 4.1 + - - -
1469A ASN* 3.4 15.8 + - - -
1470A TYR 3.4 0.4 - - - -
1471A ARG* 1.3 77.4 - - - +
1473A ASP* 1.3 59.1 + - - +
1475A ILE* 3.2 8.2 + - - +
1476A GLN* 2.9 27.5 + - - +
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Residues in contact with ASP1473 (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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1366A PRO* 5.3 13.9 - - + +
1469A ASN 2.9 17.9 + - - +
1470A TYR* 4.0 5.6 - - - +
1472A THR* 1.3 73.0 - - - +
1474A MET* 1.3 59.7 + - - +
1476A GLN* 3.7 7.0 - - - +
1477A ALA* 2.8 30.5 + - - +
464T GLN* 5.5 7.9 - - + -
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Residues in contact with MET1474 (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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1317A TYR* 5.3 14.9 - - + +
1318A THR* 6.3 1.1 - - - -
1366A PRO* 5.7 5.1 - - + +
1470A TYR 2.9 18.0 + - - +
1471A ARG* 3.4 9.4 - - - +
1473A ASP* 1.3 76.2 - - - +
1475A ILE* 1.3 57.1 + - - +
1477A ALA* 3.3 5.6 + - - +
1478A LEU* 3.0 31.0 + - - +
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Residues in contact with ILE1475 (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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1471A ARG 3.0 12.7 + - - +
1472A THR* 3.4 12.1 - - - +
1474A MET* 1.3 77.0 - - - +
1476A GLN* 1.3 51.7 + - - +
1478A LEU* 3.3 1.2 + - - -
1479A GLY 2.7 48.0 + - - +
1480A GLY* 5.5 4.0 - - - -
1925A LYS 5.7 4.5 - - - +
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Residues in contact with GLN1476 (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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1472A THR 2.9 16.8 + - - +
1473A ASP* 3.7 7.2 - - - +
1475A ILE* 1.3 75.7 - - - +
1477A ALA* 1.3 59.0 + - - +
1479A GLY* 4.0 6.6 + - - +
1925A LYS* 6.0 6.7 - - + -
457T ARG* 6.1 0.3 - - - +
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Residues in contact with ALA1477 (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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1363A GLN* 3.5 22.7 - - - +
1364A LEU* 3.7 24.0 - - + +
1365A ILE* 5.0 4.5 - - - -
1366A PRO* 5.3 2.9 - - + -
1473A ASP 2.8 19.3 + - - +
1474A MET* 3.8 6.3 - - - +
1475A ILE 3.2 0.2 - - - -
1476A GLN* 1.3 77.6 - - - +
1478A LEU* 1.3 60.1 + - - +
1479A GLY 3.5 0.4 + - - -
461T LEU* 5.7 6.3 - - + -
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Residues in contact with LEU1478 (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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1314A VAL* 6.4 2.9 - - + -
1317A TYR 5.1 9.6 - - - +
1363A GLN* 6.1 2.2 - - + -
1474A MET 3.0 16.5 + - - +
1475A ILE* 4.4 0.9 - - - +
1477A ALA* 1.3 77.5 - - + +
1479A GLY* 1.3 61.4 + - - +
1481A VAL 4.9 0.3 - - - -
1482A GLU* 3.4 27.6 - - + +
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Residues in contact with GLY1479 (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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1475A ILE* 2.7 25.8 + - - +
1476A GLN* 4.0 6.0 + - - -
1477A ALA 3.5 3.2 - - - -
1478A LEU* 1.3 78.4 - - - +
1480A GLY* 1.3 62.1 + - - -
1481A VAL 3.1 7.0 - - - -
1482A GLU* 3.3 11.8 - - - +
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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