Contacts of the helix formed by residues 390 - 400 (chain a) in PDB entry 6QX2
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 HIS 390 (chain a).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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386a ILE* 3.1 40.3 + - + +
387a ALA 3.4 4.3 - - - -
389a ASP* 1.3 103.1 - - + +
391a ILE* 1.3 61.8 + - - +
392a ASP 3.3 2.7 - - - -
393a GLU* 3.1 29.1 + - - +
394a ILE* 3.1 20.1 + - + +
415a PHE* 4.1 24.2 - + + -
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Residues in contact with ILE 391 (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 ALA 3.0 22.2 + - - +
388a LEU* 3.6 21.0 + - + +
389a ASP 3.7 0.4 - - - -
390a HIS* 1.3 75.6 - - - +
392a ASP* 1.3 63.5 + - - +
394a ILE* 3.3 9.0 + - + -
395a ILE* 3.0 46.8 + - + +
428a MET* 5.2 2.0 - - + -
433a LEU* 3.7 37.7 - - + -
395c ILE* 5.4 2.0 - - + -
399c ARG* 3.2 42.2 - - - +
430c LEU* 4.5 13.0 - - + -
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Residues in contact with ASP 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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390a HIS 3.3 1.2 - - - -
391a ILE* 1.3 81.9 - - + +
393a GLU* 1.3 64.3 + - + +
395a ILE* 3.6 6.9 + - - +
396a SER* 3.3 21.0 + - - -
395c ILE* 6.5 0.9 - - - -
399c ARG* 4.6 17.3 - - - +
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Residues in contact with GLU 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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390a HIS* 3.1 32.6 + - - +
392a ASP* 1.3 76.0 - - + +
394a ILE* 1.3 57.9 + - - +
396a SER* 2.6 23.3 + - - -
397a THR* 2.8 23.1 + - - +
415a PHE* 3.9 18.4 - - + -
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Residues in contact with ILE 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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386a ILE* 5.0 1.1 - - + +
387a ALA* 3.6 31.9 - - + +
390a HIS* 3.1 16.7 + - + +
391a ILE* 3.5 12.8 - - + +
393a GLU* 1.3 74.8 - - - +
395a ILE* 1.3 61.6 - - - +
397a THR* 3.4 8.1 - - - -
398a ILE* 3.1 42.2 + - + +
411a LEU* 3.9 11.2 - - + -
415a PHE* 3.8 33.7 - - + -
417a LEU* 5.0 2.0 - - + -
425a ILE* 3.9 21.5 - - + -
430c LEU* 4.5 8.3 - - + -
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Residues in contact with ILE 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 ILE* 3.0 39.1 + - + +
392a ASP* 3.8 7.2 - - - +
393a GLU 3.3 0.2 - - - -
394a ILE* 1.3 74.8 - - - +
396a SER* 1.3 52.9 + - - +
398a ILE* 3.1 9.0 + - + +
399a ARG* 2.8 62.9 + - - +
433a LEU* 4.8 0.2 - - + -
391c ILE* 5.1 1.3 - - + -
392c ASP* 5.1 6.3 - - - +
395c ILE* 4.4 28.5 - - + -
430c LEU* 3.7 32.3 - - + -
433c LEU* 3.9 17.5 - - + -
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Residues in contact with SER 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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392a ASP 3.3 11.8 + - - -
393a GLU* 2.6 26.9 + - - -
395a ILE* 1.3 77.2 - - - +
397a THR* 1.3 52.1 + - - -
399a ARG* 3.1 8.2 + - - +
400a GLU* 2.9 43.6 + - - +
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Residues in contact with THR 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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393a GLU* 2.8 15.4 + - - +
394a ILE 3.4 9.0 - - - -
396a SER* 1.3 75.3 + - - +
398a ILE* 1.3 52.8 + - - +
400a GLU* 3.5 18.7 + - - +
401a SER* 2.6 32.6 + - - +
407a ALA 4.8 0.2 - - - +
410a SER* 3.6 33.8 - - - +
411a LEU* 3.9 22.9 - - + +
414a ARG* 5.2 3.7 - - + +
415a PHE* 3.8 15.3 - - + -
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Residues in contact with ILE 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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394a ILE* 3.1 38.8 + - + +
395a ILE* 3.5 9.4 - - + +
397a THR* 1.3 74.6 - - - +
399a ARG* 1.3 63.9 + - - +
401a SER* 3.3 24.0 + - - +
407a ALA* 4.5 3.4 - - + -
411a LEU* 4.1 17.3 - - + -
425a ILE* 4.7 2.0 - - + -
426a LEU* 4.0 23.6 - - + -
430c LEU* 3.7 39.7 - - + +
433c LEU* 4.0 11.2 - - + -
434c THR* 3.7 24.2 - - + +
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Residues in contact with ARG 399 (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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395a ILE* 2.8 36.9 + - + +
396a SER* 3.1 8.0 + - - +
398a ILE* 1.3 73.4 - - - +
400a GLU* 1.3 59.9 + - - +
401a SER 3.1 12.2 + - - +
388c LEU 4.9 3.4 + - - -
389c ASP 6.3 0.4 - - - -
391c ILE* 2.9 34.8 - - - +
392c ASP* 2.6 36.2 + - - -
433c LEU* 3.6 27.3 - - + +
434c THR 5.1 0.2 - - - -
435c GLY* 4.8 4.0 + - - -
438c ARG* 5.3 19.6 + - - +
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Residues in contact with GLU 400 (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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396a SER* 2.9 20.5 + - - +
397a THR* 3.5 25.6 + - - +
399a ARG* 1.3 73.9 - - - +
401a SER* 1.3 61.7 + - - +
402a ASP* 3.6 12.1 - - - +
410a SER* 5.6 2.6 - - - -
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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