Contacts of the helix formed by residues 389 - 398 (chain A) in PDB entry 2WJP
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 THR 389 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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369A PHE* 3.7 6.8 - - - +
387A THR* 2.9 17.5 + - - -
388A GLU* 1.3 91.2 - - + +
390A MET* 1.3 63.3 + - - +
391A GLU* 3.6 8.8 + - - +
392A GLN* 2.9 39.8 + - - +
393A ALA 3.0 8.3 + - - -
418A GLN* 4.0 15.9 - - - +
428A GLU* 6.0 0.2 - - - -
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Residues in contact with MET 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A LEU* 4.4 10.3 - - + -
369A PHE* 3.6 39.2 - - + -
389A THR* 1.3 71.7 - - - +
391A GLU* 1.3 66.1 + - - +
393A ALA* 3.1 2.7 + - - +
394A MET* 2.9 27.8 + - + +
409A LEU* 4.0 20.2 - - + -
418A GLN* 4.9 1.4 + - - -
419A PHE* 4.2 13.8 - - + -
425A ARG* 3.5 30.3 - - - +
428A GLU* 3.6 23.3 - - + +
429A PHE* 3.5 35.7 - - - +
432A LEU* 4.6 4.7 - - + -
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Residues in contact with GLU 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A THR* 3.3 8.7 + - - +
390A MET* 1.3 78.8 - - - +
392A GLN* 1.3 62.5 + - + +
394A MET* 3.2 2.1 + - - +
395A ARG* 2.9 62.7 + - - +
428A GLU* 3.9 12.9 + - - +
431A ARG* 4.0 12.8 + - - -
432A LEU* 3.8 28.3 - - + -
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Residues in contact with GLN 392 (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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387A THR* 3.7 12.9 - - + +
388A GLU* 2.9 22.1 + - - +
389A THR* 2.9 44.3 + - - +
391A GLU* 1.3 77.4 - - + +
393A ALA* 1.3 63.0 + - - +
395A ARG* 3.4 6.9 + - - +
396A LEU* 3.0 24.3 + - - +
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Residues in contact with ALA 393 (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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342A LEU* 3.6 20.4 - - + -
367A TYR* 4.0 18.2 - - + +
369A PHE* 4.4 7.0 - - + -
387A THR* 3.5 22.1 + - + +
389A THR 3.0 8.4 + - - +
390A MET* 3.1 10.3 + - - +
392A GLN* 1.3 77.2 - - - +
394A MET* 1.3 56.5 + - - +
396A LEU* 3.3 5.4 + - - +
397A LEU* 3.0 32.5 + - - +
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Residues in contact with MET 394 (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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314A TRP* 3.7 22.0 - - + -
342A LEU* 3.8 18.8 - - + -
390A MET* 2.9 22.8 + - + +
391A GLU* 3.6 9.0 - - - +
393A ALA* 1.3 75.9 - - - +
395A ARG* 1.3 58.9 + - - +
397A LEU* 3.3 10.8 + - - +
398A ALA* 3.0 32.6 + - - +
429A PHE* 3.6 41.5 - - + +
432A LEU* 3.9 18.4 - - + -
433A ALA* 3.7 26.5 - - - +
436A LEU* 3.7 11.7 - - + +
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Residues in contact with ARG 395 (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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391A GLU* 2.9 51.4 + - + +
392A GLN* 4.0 6.1 - - - +
394A MET* 1.3 75.7 - - - +
396A LEU* 1.3 57.7 + - - +
398A ALA* 4.8 1.1 - - - -
399A PRO* 3.2 23.2 - - - +
431A ARG* 4.8 3.0 - - - +
432A LEU* 3.5 13.2 - - + +
435A GLU* 2.9 41.2 + - - -
436A LEU* 3.8 24.2 - - + +
1454A CL 3.6 17.9 - - + +
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Residues in contact with LEU 396 (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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367A TYR* 4.5 7.4 - - + -
385A GLU* 3.8 36.8 - - + +
386A GLN 5.6 0.2 - - - +
387A THR* 4.0 20.6 - - + -
392A GLN 3.0 15.5 + - - +
393A ALA 3.5 5.2 - - - +
394A MET 3.2 0.2 - - - -
395A ARG* 1.3 78.3 - - - +
397A LEU* 1.3 61.6 + - - +
399A PRO* 3.4 10.4 - - - +
400A ARG* 3.9 36.3 + - - +
1454A CL 3.9 16.5 - - + +
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Residues in contact with LEU 397 (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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314A TRP* 4.3 7.0 - - + -
340A HIS* 4.4 4.7 + - + +
342A LEU* 3.9 37.0 - - + -
367A TYR* 3.4 42.4 - - + +
393A ALA 3.0 17.3 + - - +
394A MET* 3.3 13.9 + - - +
396A LEU* 1.3 78.3 - - - +
398A ALA* 1.3 72.0 + - - +
399A PRO 3.4 0.2 - - - -
400A ARG* 2.9 19.4 + - - +
401A VAL* 3.5 24.8 + - + +
407A VAL* 3.9 21.1 - - + -
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Residues in contact with ALA 398 (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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314A TRP* 4.4 9.5 - - + -
394A MET 3.0 17.0 + - - +
395A ARG 4.5 0.9 - - - +
397A LEU* 1.3 85.9 - - - +
399A PRO* 1.3 68.8 - - + +
400A ARG 3.1 0.9 + - - -
401A VAL* 3.2 20.2 + - - +
436A LEU* 3.9 39.2 - - + +
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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