Contacts of the helix formed by residues 358 - 364 (chain A) in PDB entry 6DWM
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 ARG 358 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A THR* 2.7 50.2 + - - +
156A SER* 3.7 9.5 + - - +
160A GLU* 3.0 43.5 + - - +
355A ARG* 4.4 11.7 - - - +
356A ARG* 3.9 8.5 - - - +
357A PRO* 1.3 80.5 - - - +
359A LEU* 1.3 65.8 + - - +
360A SER* 3.1 20.4 + - - +
361A ASP* 2.9 25.8 + - - +
468A PHE* 3.6 12.5 - - - -
469A LEU* 4.4 3.1 - - - -
436D ASP* 5.2 4.3 - - - -
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Residues in contact with LEU 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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157A CYS* 3.9 13.9 - - - -
159A LEU* 5.0 2.5 - - + -
160A GLU* 3.3 35.3 + - + +
358A ARG* 1.3 74.5 - - - +
360A SER* 1.3 63.2 + - - +
362A ARG* 3.0 22.3 + - + +
363A SER 4.6 0.3 + - - -
465A TRP* 3.6 58.6 - - + +
468A PHE* 4.2 10.8 - - + -
469A LEU* 3.7 29.6 - - + +
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Residues in contact with SER 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A GLU* 5.3 0.6 + - - -
358A ARG* 3.9 18.3 + - - +
359A LEU* 1.3 78.3 - - - +
361A ASP* 1.3 70.7 + - - +
362A ARG 3.5 0.7 + - - -
363A SER* 4.2 5.7 + - - -
364A HIS* 3.5 18.7 + - - -
436D ASP* 4.2 10.2 + - - -
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Residues in contact with ASP 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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350A VAL* 5.6 3.0 - - + +
351A ILE* 3.3 30.0 - - + +
355A ARG* 3.1 38.2 + - - -
358A ARG 2.9 23.8 + - - +
360A SER* 1.3 86.7 + - - +
362A ARG* 1.3 64.9 + - - +
363A SER 3.3 2.0 - - - -
364A HIS* 3.2 22.1 + - + +
365A LEU* 3.4 17.9 - - + +
468A PHE* 4.1 2.2 - - + -
436D ASP* 3.9 7.1 - - - +
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Residues in contact with ARG 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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359A LEU* 3.0 17.9 + - + +
361A ASP* 1.3 76.9 - - - +
363A SER* 1.3 63.8 + - - +
364A HIS 3.2 1.4 + - - -
365A LEU* 3.3 17.3 + - - +
369A GLU* 3.4 40.3 + - + +
461A THR* 6.1 0.2 - - - +
464A ARG* 3.7 33.0 + - - +
465A TRP* 3.0 41.5 - - - +
468A PHE* 3.4 46.1 - - + +
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Residues in contact with SER 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A LEU 4.6 0.2 + - - -
360A SER 4.2 5.2 + - - -
361A ASP 3.3 1.0 - - - -
362A ARG* 1.3 79.5 - - - +
364A HIS* 1.3 77.3 + - - +
365A LEU 3.4 0.8 + - - -
366A PRO* 4.9 4.9 - - - +
441D LYS* 4.8 13.2 + - - +
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Residues in contact with HIS 364 (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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350A VAL* 3.8 30.0 - - + +
360A SER 3.5 22.8 + - - -
361A ASP* 3.2 12.2 + - - +
362A ARG 3.1 1.0 - - - -
363A SER* 1.3 93.7 + - - +
365A LEU* 1.3 62.5 + - - +
366A PRO* 3.4 13.8 - - - +
363D SER 5.2 3.3 - - - +
364D HIS* 5.2 1.4 - - - -
434D THR* 5.3 4.4 - - - +
438D ALA* 3.4 28.4 - - + +
439D ILE* 3.0 30.7 + - - +
441D LYS* 4.2 15.6 + - + -
604D GOL 5.3 1.2 + - - -
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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