Contacts of the helix formed by residues 357 - 363 (chain A) in PDB entry 3REP
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 ALA 357 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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355A TRP 3.8 0.6 + - - -
356A VAL* 1.3 80.3 - - - +
358A PRO* 1.3 71.3 - - + +
359A GLU* 3.2 30.3 - - - +
360A ALA* 3.0 13.4 + - + +
361A LEU* 3.1 10.6 + - - +
373A ALA* 3.9 18.4 + - + +
376A TRP* 3.5 29.8 - - + +
377A SER* 4.8 0.2 + - - -
436A ARG* 3.9 0.4 - - - +
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Residues in contact with PRO 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 VAL 4.2 0.2 - - - +
357A ALA* 1.3 86.0 - - + +
359A GLU* 1.3 68.2 + - - +
361A LEU* 3.2 26.2 + - + +
362A GLN* 2.8 25.1 + - - +
376A TRP* 3.6 33.7 - - + -
404A VAL* 3.8 13.5 - - + +
410A ARG* 3.6 35.7 - - - +
431A GLU* 4.8 2.2 - - - +
436A ARG* 4.3 1.1 - - - +
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Residues in contact with GLU 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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357A ALA* 3.3 16.4 - - - +
358A PRO* 1.3 80.8 - - - +
360A ALA* 1.3 56.0 + - + +
362A GLN* 3.1 8.1 + - - +
363A LYS* 2.8 56.3 + - - +
368A THR* 4.4 16.8 - - + -
369A ASN 4.9 1.7 - - - +
373A ALA* 3.8 10.0 + - + +
431A GLU 4.9 1.0 - - - +
433A PRO* 3.7 21.9 - - + +
436A ARG* 2.7 44.3 + - - -
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Residues in contact with ALA 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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350A MET* 3.5 15.8 - - + +
356A VAL* 3.6 20.9 - - + -
357A ALA* 3.0 6.5 + - + +
359A GLU* 1.3 78.9 - - + +
361A LEU* 1.3 62.8 + - - +
362A GLN 3.2 0.8 + - - -
363A LYS 4.0 12.3 - - - +
368A THR* 4.6 4.7 - - + -
370A ARG* 3.9 26.6 + - - +
373A ALA* 4.2 19.5 - - + -
311B HIS* 4.5 4.5 + - - -
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Residues in contact with LEU 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 MET* 3.9 10.8 - - - -
353A PRO* 4.0 15.3 - - + +
356A VAL* 3.7 25.6 - - + +
357A ALA 3.1 12.9 + - - +
358A PRO* 3.2 11.6 + - + +
360A ALA* 1.3 77.6 - - - +
362A GLN* 1.3 60.3 + - - +
401A GLY* 3.7 14.4 - - - +
404A VAL* 3.4 40.8 - - + -
405A ALA* 3.8 11.0 - - + +
307B PHE* 3.5 29.0 - - + -
309B PRO* 3.4 10.4 - - - +
310B LEU 3.2 21.3 + - - -
311B HIS* 4.9 0.2 - - - -
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Residues in contact with GLN 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 PRO* 2.8 27.1 + - - +
359A GLU* 3.1 6.7 + - - +
361A LEU* 1.3 84.6 - - - +
363A LYS* 1.3 66.7 + - + +
405A ALA* 3.3 41.5 + - + +
406A LEU* 3.8 12.5 - - - +
310B LEU* 3.7 21.0 - - + +
311B HIS* 3.5 24.9 + - - +
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Residues in contact with LYS 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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359A GLU* 2.8 34.4 + - - +
360A ALA* 4.0 8.3 - - - +
362A GLN* 1.3 79.0 - - + +
364A LYS* 1.3 66.4 + - - +
365A PRO* 3.5 2.3 - - - +
367A ASP* 3.1 35.5 + - + +
368A THR* 3.7 17.8 - - + +
370A ARG* 5.3 1.0 + - - -
311B HIS* 3.1 17.1 + - - -
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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