Contacts of the helix formed by residues 1575 - 1580 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1433D TYR* 4.4 14.1 - - + +
1434D TYR 4.2 15.4 + - - +
1435D TYR* 4.7 19.3 - - + -
1452D TRP* 5.7 7.0 - - + -
1574D PRO* 1.3 73.8 - - - +
1576D SER* 1.3 60.0 + - - +
1578D ALA* 3.3 5.9 + - - +
1579D MET* 2.9 28.3 + - - +
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Residues in contact with SER1576 (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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1566D LEU* 5.8 5.2 - - - +
1574D PRO* 3.8 6.8 - - - +
1575D LEU* 1.3 76.9 - - - +
1577D ALA* 1.3 62.4 + - - +
1579D MET* 3.5 13.8 + - - +
1580D PHE* 3.6 15.4 + - - +
1583D GLU 5.1 0.3 - - - +
1588D ALA 3.6 14.1 + - - -
1589D PRO* 3.8 12.0 + - - +
1590D GLN 3.3 27.7 + - - -
1591D CYS* 4.7 7.6 - - - -
1592D PRO* 5.0 8.3 - - - +
1595D LEU* 5.9 2.9 - - - -
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Residues in contact with ALA1577 (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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1433D TYR* 5.2 1.6 - - + -
1573D MET* 4.9 7.6 - - + -
1574D PRO* 3.4 17.8 + - + +
1575D LEU 3.2 0.8 - - - -
1576D SER* 1.3 82.3 + - - +
1578D ALA* 1.3 57.5 + - - +
1580D PHE 3.0 17.8 - - - +
1583D GLU 3.9 10.0 - - - +
1584D ARG* 3.4 39.2 - - - +
1586D ASN 3.8 16.6 - - - +
1587D PRO* 5.7 0.4 - - + -
1588D ALA 5.3 2.4 + - - +
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Residues in contact with ALA1578 (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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1294D PRO 4.7 2.6 - - - +
1295D VAL* 4.7 19.4 - - + +
1296D GLN 5.5 4.1 + - - +
1433D TYR* 3.5 41.3 - - + +
1574D PRO 3.9 0.6 + - - -
1575D LEU* 3.3 8.0 + - - +
1577D ALA* 1.3 77.2 - - - +
1579D MET* 1.3 66.4 + - - +
1580D PHE 3.8 3.7 - - - +
1584D ARG* 6.0 0.2 - - - -
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Residues in contact with MET1579 (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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1293D LEU* 4.2 33.9 - - + +
1294D PRO* 4.0 19.1 - - - +
1295D VAL* 5.7 1.8 - - - +
1575D LEU 2.9 17.2 + - - +
1576D SER* 3.9 9.2 - - - +
1577D ALA 3.4 0.4 - - - -
1578D ALA* 1.3 79.6 - - - +
1580D PHE* 1.3 59.3 + - + +
1592D PRO* 6.0 4.9 - - + -
1595D LEU* 5.7 6.3 - - + -
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Residues in contact with PHE1580 (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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591D ASP* 5.3 10.5 - - + +
592D LYS* 5.9 7.9 - - + -
1293D LEU* 5.6 4.9 - - + -
1576D SER 3.6 10.6 + - - +
1577D ALA 3.0 19.8 - - - +
1578D ALA* 3.8 4.2 - - - +
1579D MET* 1.3 81.1 - - + +
1581D LEU* 1.3 62.1 + - - +
1582D SER* 3.7 12.6 - - - +
1583D GLU 5.2 3.8 - - - +
1584D ARG* 4.9 2.6 - - - +
1592D 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