Contacts of the helix formed by residues 1456 - 1461 (chain r) 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 VAL1456 (chain r).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1453r VAL* 4.6 20.0 - - + +
1454r ASP 3.4 1.7 - - - -
1455r GLU* 1.3 69.1 - - - +
1457r HIS* 1.3 62.6 + - - +
1458r LEU 2.9 6.1 - - - -
1459r ILE* 2.9 24.0 + - - +
1467r LEU* 6.6 0.2 - - - -
1489r ALA* 4.7 10.8 - - + -
1490r LEU 2.9 15.6 + - - +
1491r SER* 4.2 5.8 - - - +
1500r VAL* 6.4 2.2 - - + -
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Residues in contact with HIS1457 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1455r GLU* 3.2 1.9 - - - -
1456r VAL* 1.3 79.1 - - - +
1458r LEU* 1.3 55.6 + - - +
1459r ILE* 2.9 6.8 + - - +
1460r GLY* 2.9 17.2 + - - -
1491r SER* 4.0 19.1 - - - -
1492r SER* 4.5 15.5 - - - +
1493r SER 5.9 1.1 - - - +
1494r LEU* 5.6 6.3 - - + -
1722r LEU* 6.3 3.6 - - + -
1724r VAL* 4.2 19.1 - - + +
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Residues in contact with LEU1458 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1381r PRO* 4.0 22.4 - - + -
1455r GLU* 3.2 22.5 + - + +
1456r VAL 2.9 0.2 - - - -
1457r HIS* 1.3 76.1 - - - +
1459r ILE* 1.3 64.9 + - - +
1460r GLY 3.0 0.7 - - - -
1461r GLY* 2.9 20.7 + - - +
1462r GLU 5.0 0.7 - - - +
1463r ASN 5.2 0.2 - - - -
1464r GLY* 3.9 6.7 + - - -
1467r LEU* 5.8 1.3 - - - -
1682r TYR* 6.1 7.0 - - + -
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Residues in contact with ILE1459 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1456r VAL* 2.9 17.9 + - - +
1457r HIS* 4.1 1.1 - - - +
1458r LEU* 1.3 76.2 - - - +
1460r GLY* 1.3 63.8 + - - +
1461r GLY 3.2 9.4 - - - +
1464r GLY* 3.5 22.2 - - - +
1465r PRO 4.5 0.7 - - - -
1467r LEU* 5.2 6.2 - - + +
1468r GLU* 5.2 12.3 - - + +
1724r VAL* 5.6 4.0 - - + -
1725r GLU 4.2 9.1 - - - +
1726r SER* 5.4 2.2 - - - -
1727r HIS* 4.8 7.6 + - - +
1759r PHE* 6.2 3.6 - - + -
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Residues in contact with GLY1460 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1457r HIS 2.9 13.8 + - - -
1459r ILE* 1.3 80.3 - - - +
1461r GLY* 1.3 59.7 + - - +
1724r VAL* 4.8 4.5 - - - +
1725r GLU 3.6 24.6 + - - +
1727r HIS* 5.0 7.4 - - - +
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Residues in contact with GLY1461 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1457r HIS 4.5 0.2 + - - -
1458r LEU* 2.9 13.2 + - - +
1459r ILE 3.2 9.0 - - - +
1460r GLY* 1.3 78.0 - - - +
1462r GLU* 1.3 64.1 + - - -
1464r GLY* 3.0 17.1 + - - -
1465r PRO 4.7 0.3 - - - -
1727r HIS* 5.2 4.7 - - - +
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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
------------------------------------------------------------
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