Contacts of the helix formed by residues 356 - 364 (chain A) in PDB entry 4P4P
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 SER 356 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281A PRO* 3.7 12.8 - - - +
354A VAL* 3.6 3.2 - - - +
355A ARG* 1.3 104.9 + - - +
357A GLU* 1.3 64.8 + - - +
358A GLN* 3.5 12.6 + - - +
359A ASP* 3.0 39.7 + - - +
360A VAL* 3.7 2.6 + - - +
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Residues in contact with GLU 357 (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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186A ARG* 2.9 38.0 + - - -
281A PRO* 3.9 14.3 - - + +
284A MET* 3.6 11.1 - - + +
285A LEU* 3.5 39.3 + - + -
356A SER* 1.3 72.0 - - - +
358A GLN* 1.3 57.6 + - - +
360A VAL* 2.8 23.0 + - - +
361A PHE* 3.3 17.6 + - + -
368A TYR* 4.0 9.0 + - + -
374A ARG* 2.8 42.5 + - - +
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Residues in contact with GLN 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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356A SER* 3.1 10.8 + - - +
357A GLU* 1.3 78.6 - - - +
359A ASP* 1.3 65.3 + - - +
360A VAL 3.1 0.2 + - - -
361A PHE* 3.3 4.5 + - - +
362A ASP* 2.7 61.1 + - - +
368A TYR* 3.7 52.2 - - + +
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Residues in contact with ASP 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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353A GLU 5.4 0.7 - - - -
354A VAL* 3.6 21.6 - - + -
355A ARG* 2.7 40.6 + - - +
356A SER* 3.0 23.1 + - - +
358A GLN* 1.3 79.1 - - - +
360A VAL* 1.3 56.5 + - - +
362A ASP* 3.3 10.5 + - - +
363A VAL* 3.0 35.5 + - + +
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Residues in contact with VAL 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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282A THR* 4.1 21.1 - - + +
285A LEU* 3.6 31.0 - - + -
297A MET* 4.1 9.2 - - - -
308A LEU* 4.2 11.9 - - + -
313A LEU* 4.5 12.8 - - + -
354A VAL* 4.1 17.0 - - + -
356A SER 4.3 5.2 - - - +
357A GLU* 2.8 11.5 + - - +
359A ASP* 1.3 74.1 - - - +
361A PHE* 1.3 64.0 + - - +
363A VAL* 3.4 1.9 + - - +
364A LEU* 3.1 42.7 + - + +
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Residues in contact with PHE 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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285A LEU* 3.9 18.8 - - + -
293A PHE* 3.5 27.8 - + - -
297A MET* 3.2 23.3 - - + -
357A GLU 3.3 21.7 + - - -
358A GLN* 3.3 6.4 + - - +
360A VAL* 1.3 78.4 - - - +
362A ASP* 1.3 63.8 + - - +
364A LEU* 3.2 4.0 + - - -
365A GLY 3.0 4.3 + - - -
366A MET* 2.9 49.7 + - + +
367A PRO 3.4 17.9 - - - -
368A TYR* 3.6 34.5 - + - +
369A ALA* 3.6 26.7 - - + -
374A ARG* 4.0 4.7 - - - -
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Residues in contact with ASP 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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358A GLN* 2.7 53.9 + - - +
359A ASP* 3.6 10.5 - - - +
361A PHE* 1.3 77.9 - - - +
363A VAL* 1.3 66.1 + - + +
365A GLY* 3.0 14.0 + - - +
366A MET 4.7 4.4 - - - +
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Residues in contact with VAL 363 (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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304A LYS* 4.5 6.2 - - - +
306A TYR* 3.4 37.4 + - + +
313A LEU* 3.8 23.6 - - + -
352A VAL* 4.4 20.6 - - + -
354A VAL* 5.3 2.5 - - + -
359A ASP* 3.0 22.2 + - + +
360A VAL 4.1 0.2 - - - +
362A ASP* 1.3 77.6 - - + +
364A LEU* 1.3 60.0 + - + +
365A GLY 3.7 0.5 + - - -
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Residues in contact with LEU 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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297A MET* 3.9 32.5 - - + +
300A ALA* 5.0 5.0 - - + +
301A ALA* 3.7 31.2 - - + +
304A LYS* 3.0 29.2 - - + +
306A TYR* 4.0 22.2 - - + -
308A LEU* 4.2 3.4 - - + -
313A LEU* 4.1 12.8 - - + -
360A VAL* 3.1 35.2 + - + +
361A PHE 3.9 2.7 - - - +
362A ASP 3.1 0.6 - - - -
363A VAL* 1.3 79.1 - - + +
365A GLY* 1.3 61.7 + - - +
366A MET* 3.3 18.1 + - - +
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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