Contacts of the helix formed by residues 1464 - 1481 (chain D) in PDB entry 6AH0
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 GLY1464 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1458D LEU 3.9 9.4 - - - -
1459D ILE* 3.5 21.0 - - - -
1461D GLY 3.0 15.7 + - - -
1462D GLU* 2.9 6.7 + - - +
1463D ASN* 1.3 75.9 - - - +
1465D PRO* 1.4 67.1 - - - +
1466D VAL 3.1 2.2 - - - -
1467D LEU* 2.8 14.4 + - - -
1468D GLU* 2.9 10.7 + - - -
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Residues in contact with PRO1465 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1459D ILE 4.5 1.0 - - - -
1461D GLY 4.7 0.4 - - - -
1463D ASN* 3.7 1.2 - - - -
1464D GLY* 1.4 73.3 - - - +
1466D VAL* 1.3 56.3 + - - +
1468D GLU* 3.2 2.7 + - - +
1469D VAL* 2.8 28.6 + - - -
1727D HIS* 5.3 5.2 - - - +
1728D LEU* 4.9 21.5 - - - +
1731D CYS 5.6 3.6 - - - +
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Residues in contact with VAL1466 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1429D PRO* 5.0 14.8 - - - +
1463D ASN* 4.3 7.2 + - - +
1464D GLY 3.1 1.4 - - - -
1465D PRO* 1.3 75.0 - - - +
1467D LEU* 1.3 62.5 + - - +
1469D VAL* 3.9 1.0 - - - +
1470D ILE* 3.0 20.1 + - - -
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Residues in contact with LEU1467 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1429D PRO* 5.3 9.7 - - - +
1459D ILE* 6.3 0.4 - - - +
1463D ASN 4.1 6.5 + - - -
1464D GLY* 2.8 10.6 + - - -
1466D VAL* 1.3 76.7 - - - +
1468D GLU* 1.3 60.3 + - - +
1470D ILE* 3.1 2.6 + - - -
1471D CYS* 3.0 20.4 + - - -
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Residues in contact with GLU1468 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1459D ILE* 5.7 2.7 - - - +
1464D GLY 2.9 11.9 + - - -
1465D PRO* 3.6 4.3 - - - -
1467D LEU* 1.3 75.0 - - - +
1469D VAL* 1.3 56.5 + - - +
1471D CYS* 3.2 2.9 + - - -
1472D SER* 2.9 26.9 + - - -
1758D THR* 5.9 2.3 - - - -
1759D PHE 5.9 3.0 + - - +
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Residues in contact with VAL1469 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1465D PRO 2.8 18.9 + - - -
1466D VAL* 3.9 1.6 - - - +
1468D GLU* 1.3 71.6 - - - +
1470D ILE* 1.3 57.1 + - - +
1472D SER* 3.9 1.5 - - - +
1473D ARG* 2.9 26.0 + - - -
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Residues in contact with ILE1470 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1432D TRP 5.6 5.2 - - - -
1433D ASP* 6.1 3.4 - - - +
1466D VAL 3.0 15.2 + - - -
1467D LEU* 3.1 2.9 + - - +
1469D VAL* 1.3 75.5 - - - +
1471D CYS* 1.3 59.9 + - - +
1473D ARG* 3.9 1.2 - - - +
1474D MET* 2.9 24.3 + - - -
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Residues in contact with CYS1471 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1467D LEU 3.0 13.9 + - - -
1468D GLU* 3.8 2.0 - - - +
1470D ILE* 1.3 72.1 - - - +
1472D SER* 1.3 67.8 + - - +
1474D MET* 3.1 3.7 + - - +
1475D ARG* 3.0 18.4 + - - -
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Residues in contact with SER1472 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1468D GLU 2.9 15.9 + - - -
1469D VAL* 3.9 1.8 - - - +
1471D CYS* 1.3 73.9 - - - +
1473D ARG* 1.3 63.0 - - - +
1475D ARG* 2.8 14.0 + - - -
1476D TYR* 3.0 10.2 + - - -
1757D TRP 4.1 20.8 - - - +
1758D THR* 5.6 2.0 - - - +
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Residues in contact with ARG1473 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1469D VAL 2.9 17.4 + - - -
1470D ILE* 3.9 1.6 - - - +
1472D SER* 1.3 73.7 - - - +
1474D MET* 1.3 62.8 + - - +
1476D TYR* 2.9 14.6 + - - +
1477D ILE* 2.9 11.4 + - - -
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Residues in contact with MET1474 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1470D ILE 2.9 16.4 + - - -
1471D CYS* 3.1 5.1 + - - +
1473D ARG* 1.3 73.8 - - - +
1475D ARG* 1.3 63.3 + - - +
1477D ILE* 3.2 2.8 + - - +
1478D SER* 3.0 18.9 + - - -
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Residues in contact with ARG1475 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1471D CYS 3.0 8.7 + - - -
1472D SER 2.8 13.5 + - - -
1474D MET* 1.3 68.1 - - - +
1476D TYR* 1.3 64.1 + - - +
1478D SER* 3.1 3.8 + - - +
1479D SER* 2.9 19.1 + - - -
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Residues in contact with TYR1476 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1472D SER 3.0 8.2 + - - -
1473D ARG* 2.9 12.3 + - - +
1475D ARG* 1.3 71.0 - - - +
1477D ILE* 1.3 62.2 + - - +
1479D SER* 2.9 12.2 + - - +
1480D GLN* 3.0 11.1 + - - -
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Residues in contact with ILE1477 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1473D ARG 2.9 12.1 + - - -
1474D MET* 3.7 3.8 - - - +
1476D TYR* 1.3 76.1 - - - +
1478D SER* 1.3 56.4 + - - +
1480D GLN* 2.9 5.1 + - - +
1481D ILE* 2.8 29.1 + - - -
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Residues in contact with SER1478 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1474D MET 3.0 14.1 + - - -
1475D ARG* 3.1 5.1 + - - +
1477D ILE* 1.3 74.8 - - - +
1479D SER* 1.3 61.0 + - - +
1481D ILE* 4.1 1.3 - - - +
1482D GLU* 4.1 5.5 + - - -
1483D ARG 3.5 24.2 - - - +
1484D PRO* 5.1 1.4 - - - +
1485D ILE* 4.9 9.9 - - - +
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Residues in contact with SER1479 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1475D ARG 2.9 13.0 + - - -
1476D TYR* 2.9 6.4 + - - +
1478D SER* 1.3 81.2 - - - +
1480D GLN* 1.3 61.1 + - - +
1481D ILE 3.7 0.2 + - - -
1482D GLU* 3.9 6.9 + - - -
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Residues in contact with GLN1480 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1476D TYR 3.0 8.4 + - - -
1477D ILE* 2.9 5.3 + - - +
1479D SER* 1.3 74.7 - - - +
1481D ILE* 1.3 59.8 + - - +
1482D GLU* 3.1 6.9 + - - -
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Residues in contact with ILE1481 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1477D ILE 2.8 19.0 + - - -
1478D SER* 4.1 1.7 + - - +
1479D SER 3.5 0.4 - - - -
1480D GLN* 1.3 71.9 - - - +
1482D GLU* 1.3 57.1 + - - +
1483D ARG 2.8 15.2 + - - +
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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