Contacts of the helix formed by residues 1575 - 1580 (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 LEU1575 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1295F VAL* 6.1 0.2 - - - +
1433F TYR* 4.4 14.5 - - + +
1434F TYR 4.2 16.1 + - - +
1435F TYR* 4.7 19.1 - - + -
1452F TRP* 5.7 7.2 - - + -
1574F PRO* 1.3 72.5 - - - +
1576F SER* 1.3 60.2 + - - +
1577F ALA 3.2 0.2 - - - -
1578F ALA* 3.3 3.9 + - - +
1579F MET* 2.9 29.8 + - - +
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Residues in contact with SER1576 (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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1566F LEU* 5.8 5.0 - - - +
1574F PRO* 3.8 6.8 - - - +
1575F LEU* 1.3 77.5 - - - +
1577F ALA* 1.3 60.8 + - - +
1579F MET* 3.5 13.8 + - - +
1580F PHE* 3.6 15.6 + - - +
1583F GLU 5.1 0.5 - - - +
1588F ALA 3.6 14.1 + - - -
1589F PRO* 3.8 11.6 + - - +
1590F GLN 3.3 27.9 + - - -
1591F CYS* 4.7 7.6 - - - -
1592F PRO* 5.0 7.8 - - - +
1595F LEU* 5.9 3.8 - - - -
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Residues in contact with ALA1577 (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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1433F TYR* 5.2 1.8 - - + -
1573F MET* 5.0 8.1 - - + -
1574F PRO* 3.4 17.8 + - + +
1575F LEU 3.2 0.6 - - - -
1576F SER* 1.3 82.0 + - - +
1578F ALA* 1.3 56.0 + - - +
1580F PHE* 3.0 18.5 - - - +
1583F GLU 3.9 8.8 - - - +
1584F ARG* 3.4 38.8 - - - +
1586F ASN 3.8 16.8 - - - +
1587F PRO* 5.7 0.2 - - + -
1588F ALA 5.3 2.9 + - - +
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Residues in contact with ALA1578 (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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1294F PRO 4.7 2.6 - - - +
1295F VAL* 4.7 20.2 - - + +
1296F GLN 5.5 3.6 + - - +
1433F TYR* 3.5 41.7 - - + +
1574F PRO 3.9 0.8 + - - -
1575F LEU* 3.3 8.2 + - - +
1577F ALA* 1.3 77.7 - - - +
1579F MET* 1.3 65.3 + - - +
1580F PHE 3.4 4.3 - - - +
1584F ARG* 6.0 0.4 - - - -
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Residues in contact with MET1579 (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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1293F LEU* 4.2 34.4 - - + +
1294F PRO* 4.0 18.4 - - - +
1295F VAL* 5.7 2.4 - - + +
1575F LEU 2.9 17.9 + - - +
1576F SER* 3.9 10.1 - - - +
1577F ALA 3.4 0.4 - - - -
1578F ALA* 1.3 79.6 - - - +
1580F PHE* 1.3 59.5 + - + +
1592F PRO* 6.0 4.5 - - + -
1595F LEU* 5.7 5.8 - - + -
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Residues in contact with PHE1580 (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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591F ASP* 5.3 10.8 - - - +
592F LYS* 5.9 7.4 - - + -
1293F LEU* 5.6 4.0 - - + -
1576F SER 3.6 11.4 + - - +
1577F ALA 3.0 19.6 - - - +
1578F ALA* 3.8 4.4 - - - +
1579F MET* 1.3 82.2 - - + +
1581F LEU* 1.3 62.1 + - - +
1582F SER* 3.7 12.8 - - - +
1583F GLU 5.2 3.6 - - - +
1584F ARG* 4.9 2.6 - - - +
1592F PRO* 5.3 13.7 - - + -
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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
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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