Contacts of the helix formed by residues 362 - 371 (chain A) in PDB entry 5IVH
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 MET 362 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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360A LYS 3.5 0.4 + - - -
361A GLN* 1.3 66.7 - - - +
363A PRO* 1.3 60.0 - - - +
364A LEU* 2.0 57.2 + - + -
365A LEU* 2.8 32.1 - - + +
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Residues in contact with PRO 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 LEU 3.4 14.3 - - - +
360A LYS* 3.5 16.2 - - - +
362A MET* 1.3 84.6 - - - +
364A LEU* 1.3 55.0 + - + +
365A LEU* 2.9 6.3 - - + +
366A VAL* 2.8 38.5 + - + +
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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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362A MET* 2.0 56.7 + - + +
363A PRO* 1.3 63.6 - - + +
365A LEU* 1.3 63.9 + - - +
366A VAL 2.8 3.7 + - - -
367A LYS* 3.0 25.0 + - + +
368A GLU* 4.0 3.3 + - - +
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Residues in contact with LEU 365 (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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306A LYS* 6.3 0.2 - - - +
358A ILE* 4.3 13.7 - - + +
359A LEU* 3.4 32.8 - - + +
361A GLN 3.1 22.9 - - - +
362A MET* 2.8 52.2 + - + +
363A PRO* 2.9 3.1 - - + +
364A LEU* 1.3 75.1 - - - +
366A VAL* 1.3 60.7 + - - +
368A GLU* 2.6 41.6 - - - +
412A PHE* 3.3 8.3 - - + -
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Residues in contact with VAL 366 (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* 4.4 17.3 - - + -
363A PRO* 2.8 25.4 + - + +
364A LEU 2.8 0.6 + - - -
365A LEU* 1.3 77.8 - - - +
367A LYS* 1.3 57.3 + - - +
369A LEU* 2.9 27.6 + - + +
407A PRO* 3.7 26.5 - - + +
408A THR* 3.4 30.7 - - - +
409A ALA* 4.9 4.9 - - + +
412A PHE* 4.1 9.9 - - + -
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Residues in contact with LYS 367 (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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363A PRO 4.5 0.2 + - - -
364A LEU* 3.0 17.6 + - + +
366A VAL* 1.3 75.4 - - - +
368A GLU* 1.3 54.8 + - - +
369A LEU 2.9 1.6 - - - -
370A GLU* 2.5 62.7 + - + +
407A PRO* 5.1 5.8 - - + -
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Residues in contact with GLU 368 (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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306A LYS* 3.1 27.4 + - - -
364A LEU 4.0 3.1 + - - +
365A LEU* 2.6 39.5 + - - +
367A LYS* 1.3 73.1 - - - +
369A LEU* 1.3 56.3 + - + +
370A GLU 3.0 3.1 + - - -
371A THR* 3.3 4.5 + - - -
372A CYS* 2.8 31.6 + - - -
373A VAL 4.4 0.7 + - - -
374A ASN* 4.1 22.4 + - + +
375A PHE* 2.8 33.4 - - + -
412A PHE* 3.2 12.2 - - - -
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Residues in contact with LEU 369 (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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366A VAL 2.9 12.4 + - - +
367A LYS 2.8 3.8 + - - -
368A GLU* 1.3 74.0 - - - +
370A GLU* 1.3 63.6 + - - +
371A THR 3.2 0.7 - - - -
372A CYS* 3.3 28.6 - - - -
375A PHE* 4.0 20.0 - - + -
398A LYS* 3.5 13.9 - - - +
401A HIS* 5.4 0.9 - - + -
402A VAL* 4.3 10.4 - - + +
407A PRO* 3.7 19.9 - - + +
408A THR 4.5 0.9 - - - +
411A ASN* 3.7 18.2 - - + +
412A PHE* 3.3 61.0 - - + +
415A LEU* 3.9 11.7 - - + -
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Residues in contact with GLU 370 (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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366A VAL 4.5 0.2 + - - -
367A LYS* 2.5 53.2 + - + +
369A LEU* 1.3 71.2 - - - +
371A THR* 1.3 70.0 + - + +
398A LYS* 3.0 27.8 + - - +
407A PRO* 4.5 12.7 - - + +
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Residues in contact with THR 371 (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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368A GLU 3.3 3.7 + - - -
370A GLU* 1.3 90.6 - - + +
372A CYS* 1.3 72.5 + - - +
373A VAL* 3.1 22.7 + - - +
391A LEU* 3.7 30.5 - - + +
394A GLY* 3.4 19.4 - - - +
395A ALA* 4.1 1.2 + - - -
398A LYS* 4.3 8.0 - - - +
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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