Contacts of the helix formed by residues 357 - 362 (chain A) in PDB entry 4DVQ
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 LYS 357 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350A SER* 3.3 34.0 + - - +
351A ILE* 4.4 3.6 - - + -
353A GLU* 5.0 6.9 + - - -
354A HIS* 3.1 42.7 + - + +
356A GLN* 1.3 76.2 - - + +
358A ALA* 1.3 61.2 + - - +
359A THR 3.1 0.2 - - - -
360A THR* 2.8 15.1 + - - +
361A GLU* 2.8 55.3 + - + +
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Residues in contact with ALA 358 (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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158A LEU* 5.4 2.0 - - + -
351A ILE* 3.8 22.8 - - + +
355A PRO 3.0 17.1 + - - +
357A LYS* 1.3 77.9 - - - +
359A THR* 1.3 64.2 + - + +
362A LEU* 3.3 42.3 + - + +
461A LEU* 4.4 8.2 - - + +
462A LEU* 3.9 22.9 - - + -
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Residues in contact with THR 359 (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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154A VAL* 5.1 7.0 - - + -
155A GLN* 5.6 1.0 + - - -
158A LEU* 3.9 26.0 - - + -
356A GLN 2.9 14.9 + - - -
358A ALA* 1.3 80.4 - - + +
360A THR* 1.3 64.4 + - - +
362A LEU 4.5 2.4 + - - -
363A PRO* 5.4 0.7 - - - +
366A ARG* 3.3 39.6 - - - +
458A ALA* 5.8 4.7 - - + -
461A LEU* 5.2 6.7 - - + -
603A SO4 5.3 9.9 - - - +
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Residues in contact with THR 360 (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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356A GLN 4.4 0.3 + - - -
357A LYS* 2.9 22.5 + - - +
359A THR* 1.3 86.5 + - - +
361A GLU* 1.3 67.1 + - - +
362A LEU 3.5 1.3 + - - -
363A PRO* 3.9 12.8 - - - +
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Residues in contact with GLU 361 (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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343A GLU* 3.9 8.1 - - - +
347A ALA* 4.1 21.0 - - + +
350A SER* 3.6 15.9 + - - +
351A ILE* 4.7 5.6 - - + -
357A LYS* 2.8 54.5 + - + +
360A THR* 1.3 78.2 - - - +
362A LEU* 1.3 66.8 + - - +
363A PRO* 3.0 12.0 - - - +
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Residues in contact with LEU 362 (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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343A GLU* 3.6 13.5 - - + +
344A SER* 3.8 27.8 - - - +
347A ALA* 4.2 1.1 - - + -
351A ILE* 3.8 29.4 - - + -
358A ALA* 3.3 24.6 + - + +
359A THR 5.0 1.3 - - - -
360A THR 3.5 0.6 - - - -
361A GLU* 1.3 87.2 - - - +
363A PRO* 1.3 59.1 - - - +
364A LEU 3.3 3.4 - - - -
365A LEU* 3.3 13.1 + - + -
366A ARG* 3.0 30.2 + - - +
461A LEU* 3.4 26.5 - - + -
465A HIS* 3.9 19.5 - - + +
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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