Contacts of the helix formed by residues 335 - 338 (chain A) in PDB entry 1T9A
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 LEU 335 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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334A THR* 1.3 75.9 - - - +
336A GLN* 1.3 63.2 + - - +
337A GLY 3.3 0.9 + - - -
338A LEU* 3.5 15.2 + - - +
351A MET* 4.0 10.9 - - - -
501A GLN* 4.1 9.9 - - + +
502A MET* 4.0 14.1 - - + -
505A ALA* 3.5 31.9 - - + -
516A PHE* 3.6 27.0 - - + -
518A THR* 3.8 22.2 - - + -
520A GLY* 4.3 4.9 - - - -
701A FAD 3.0 61.1 + - + +
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Residues in contact with GLN 336 (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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151A ARG* 2.9 33.2 + - - +
180A ASP* 3.3 21.8 + - - +
308A ALA* 3.5 23.7 - - + +
311A LEU* 3.6 13.2 - - - +
334A THR* 3.1 2.3 + - - -
335A LEU* 1.3 77.7 - - + +
337A GLY* 1.3 56.4 + - - +
338A LEU 3.5 1.3 - - - +
516A PHE* 5.0 4.2 - - - +
518A THR* 3.1 34.4 + - - +
520A GLY* 3.4 11.6 - - - +
701A FAD 3.6 47.8 - - - +
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Residues in contact with GLY 337 (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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307A GLY* 3.9 21.1 - - - -
311A LEU* 4.4 3.8 - - - -
333A THR* 3.7 15.0 - - - +
334A THR* 3.1 13.0 + - - -
336A GLN* 1.3 78.3 - - - +
338A LEU* 1.3 64.6 + - - +
339A GLY 3.2 0.2 + - - -
340A SER* 2.6 31.4 + - - -
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Residues in contact with LEU 338 (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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311A LEU* 4.6 7.6 - - - +
333A THR* 3.3 18.4 - - - +
334A THR 3.3 6.9 + - - +
335A LEU* 3.5 22.7 - - - +
336A GLN 3.5 2.3 - - - +
337A GLY* 1.3 78.0 - - - +
339A GLY* 1.3 59.5 + - - +
343A GLN* 3.8 14.8 - - - +
351A MET* 4.3 16.6 - - + +
505A ALA* 3.8 19.5 - - + +
510A TRP* 3.7 36.1 - - + +
512A ASN 4.8 0.2 - - - +
514A HIS 5.4 0.9 + - - -
515A THR 5.3 1.0 + - - -
516A PHE* 3.6 43.7 + - + +
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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