Contacts of the helix formed by residues 403 - 416 (chain c) 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 THR 403 (chain c).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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434a THR* 4.3 6.4 - - - +
436a LEU* 4.1 21.1 - - + -
401c SER* 3.8 3.5 - - - -
402c ASP* 1.3 84.9 - - + +
404c ASP* 1.3 64.7 + - - +
405c LYS* 3.5 10.9 + - - +
406c VAL* 3.3 28.5 + - + +
407c ALA* 3.2 21.5 + - - +
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Residues in contact with ASP 404 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431a ARG* 3.4 41.7 + - - +
434a THR* 3.6 24.3 + - - +
437a GLU* 5.4 2.2 - - - +
403c THR* 1.3 73.2 - - - +
405c LYS* 1.3 57.1 + - - +
407c ALA* 3.3 8.7 + - - +
408c MET* 2.9 36.0 + - + +
426c LEU* 4.0 4.9 - - + +
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Residues in contact with LYS 405 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403c THR* 3.5 9.5 + - - +
404c ASP* 1.3 78.3 - - - +
406c VAL* 1.3 62.4 + - + +
408c MET* 3.4 9.7 - - - +
409c GLU* 3.1 47.5 + - + +
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Residues in contact with VAL 406 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400c GLU 5.5 0.2 - - - +
401c SER* 3.9 18.2 - - - +
402c ASP* 4.4 12.3 - - - +
403c THR* 3.3 28.4 + - + +
404c ASP 3.3 0.2 - - - -
405c LYS* 1.3 77.9 - - + +
407c ALA* 1.3 52.5 + - - +
409c GLU* 3.2 18.9 + - - +
410c SER* 2.8 48.0 + - - +
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Residues in contact with ALA 407 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434a THR* 4.7 2.2 - - + -
397c THR 5.0 0.4 - - - -
398c ILE* 4.5 13.9 - - + -
401c SER* 3.2 25.9 + - - -
403c THR 3.2 7.9 + - - +
404c ASP* 3.5 11.2 - - - +
406c VAL* 1.3 78.0 - - - +
408c MET* 1.3 56.5 + - - +
410c SER* 3.4 2.1 + - - -
411c LEU* 2.9 38.3 + - - +
426c LEU* 4.2 21.1 - - + -
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Residues in contact with MET 408 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404c ASP* 2.9 21.4 + - + +
405c LYS* 3.4 13.2 - - - +
407c ALA* 1.3 76.0 - - - +
409c GLU* 1.3 61.4 + - + +
411c LEU* 3.9 1.8 - - - +
412c GLN* 3.1 40.6 + - - +
419c GLU* 3.4 39.0 - - + +
422c ALA* 3.7 7.6 - - + +
423c GLN* 3.2 55.0 - - + +
426c LEU* 3.6 15.7 - - + +
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Residues in contact with GLU 409 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405c LYS* 3.1 40.5 - - + +
406c VAL* 3.2 18.4 + - - +
408c MET* 1.3 74.8 - - + +
410c SER* 1.3 57.2 + - - +
412c GLN* 3.3 10.5 + - - +
413c GLN* 3.0 35.4 + - - +
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Residues in contact with SER 410 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397c THR* 3.6 22.7 - - - -
400c GLU* 5.5 3.8 - - - +
401c SER* 3.9 8.8 + - - -
406c VAL* 2.8 30.5 + - - +
407c ALA 3.8 2.0 - - - -
409c GLU* 1.3 76.3 - - - +
411c LEU* 1.3 56.7 + - - +
413c GLN* 3.6 10.6 + - - +
414c ARG* 2.9 34.8 + - - +
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Residues in contact with LEU 411 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394c ILE* 3.9 38.4 - - + +
397c THR* 3.9 20.4 - - + -
398c ILE* 4.1 15.0 - - + -
407c ALA 2.9 24.0 + - - +
408c MET 3.9 3.6 - - - +
410c SER* 1.3 72.1 - - - +
412c GLN* 1.3 65.4 + - - +
415c PHE* 3.1 36.6 + - + +
417c LEU* 3.6 14.1 - - + +
422c ALA* 4.3 16.6 - - + +
425c ILE* 4.5 9.0 - - + -
426c LEU* 4.1 26.5 - - + -
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Residues in contact with GLN 412 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408c MET* 3.1 34.8 + - - +
409c GLU* 3.5 7.9 + - - +
411c LEU* 1.3 77.8 - - - +
413c GLN* 1.3 56.5 + - - +
416c LYS* 3.0 25.3 + - - -
417c LEU* 3.2 29.7 + - - +
418c SER* 3.7 10.9 - - - +
419c GLU* 3.7 33.4 - - - +
422c ALA* 4.1 4.7 - - + -
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Residues in contact with GLN 413 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409c GLU* 3.0 19.5 + - - +
410c SER* 4.0 9.1 - - - +
412c GLN* 1.3 78.3 - - - +
414c ARG* 1.3 65.5 + - - +
415c PHE 3.5 0.3 + - - -
416c LYS* 4.0 4.3 + - - +
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Residues in contact with ARG 414 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393c GLU* 5.9 1.1 - - - +
397c THR* 4.8 8.3 - - + +
410c SER 2.9 19.6 + - - +
413c GLN* 1.3 80.8 - - + +
415c PHE* 1.3 88.0 + - + +
416c LYS 3.7 0.2 - - - -
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Residues in contact with PHE 415 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386c ILE* 4.4 22.2 - - + +
390c HIS* 4.1 23.6 - + + -
393c GLU* 3.8 29.8 - - + -
394c ILE* 3.8 35.9 - - + -
397c THR* 3.7 14.8 - - - -
411c LEU* 3.1 26.5 + - + +
414c ARG* 1.3 103.0 - - + +
416c LYS* 1.3 72.5 + - - +
417c LEU* 3.3 21.0 + - + +
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Residues in contact with LYS 416 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386c ILE* 5.8 1.0 - - - +
412c GLN 3.0 11.3 + - - -
413c GLN 4.0 4.0 + - - +
414c ARG 3.7 1.4 - - - -
415c PHE* 1.3 82.4 - - - +
417c LEU* 1.3 62.0 + - - +
418c SER 4.4 0.2 + - - -
421c GLN* 4.7 1.4 - - - +
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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