Contacts of the helix formed by residues 390 - 406 (chain T) in PDB entry 6FF7
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 ASN 390 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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388T ASP* 3.3 3.3 - - + +
389T PRO* 1.3 75.9 - - + +
391T PHE* 1.3 53.7 + - - +
392T MET* 3.3 2.7 - - - -
393T GLU* 3.4 16.1 + - + +
394T ASN* 2.7 39.6 + - + +
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Residues in contact with PHE 391 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155T GLN* 5.6 10.5 - - + -
388T ASP* 3.0 31.2 + - + +
389T PRO 3.1 4.8 + - - +
390T ASN* 1.3 76.0 - - - +
392T MET* 1.3 57.4 + - - +
394T ASN* 3.9 3.7 - - - +
395T GLU* 2.8 32.8 + - - +
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Residues in contact with MET 392 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389T PRO 4.7 2.6 + - - +
390T ASN* 5.1 0.7 - - - -
391T PHE* 1.3 80.0 - - - +
393T GLU* 1.3 63.9 + - - +
395T GLU* 3.2 5.1 + - - +
396T GLU* 3.0 24.1 + - - +
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Residues in contact with GLU 393 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390T ASN* 3.4 18.8 + - + +
392T MET* 1.3 78.4 - - - +
394T ASN* 1.3 53.2 + - - +
396T GLU* 3.2 6.3 + - - +
397T LYS* 2.8 36.3 + - - +
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Residues in contact with ASN 394 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388T ASP* 6.1 2.0 - - + -
390T ASN* 2.7 26.9 + - + +
391T PHE* 3.9 4.5 - - - +
393T GLU* 1.3 74.0 - - - +
395T GLU* 1.3 62.7 + - - +
397T LYS* 3.4 8.1 + - - +
398T TYR* 3.2 20.8 + - - +
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Residues in contact with GLU 395 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391T PHE 2.8 22.4 + - - +
392T MET* 3.5 6.1 - - - +
394T ASN* 1.3 71.5 - - - +
396T GLU* 1.3 66.8 + - - +
398T TYR* 3.0 16.7 + - - +
399T LYS* 3.3 12.3 + - - +
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Residues in contact with GLU 396 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392T MET 3.0 16.4 + - - +
393T GLU* 3.9 4.3 - - - +
395T GLU* 1.3 76.0 - - - +
397T LYS* 1.3 62.5 + - - +
399T LYS* 3.6 6.6 + - - +
400T ALA* 3.3 20.6 + - - +
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Residues in contact with LYS 397 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393T GLU 2.8 18.7 + - - +
394T ASN* 3.5 10.5 - - - +
395T GLU 3.1 0.2 - - - -
396T GLU* 1.3 78.1 - - - +
398T TYR* 1.3 61.9 + - - +
400T ALA* 3.3 14.9 + - - +
401T ILE* 3.3 11.1 + - - +
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Residues in contact with TYR 398 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189T ASN* 4.6 23.6 - - + -
191T VAL* 5.5 9.9 - - + -
394T ASN 3.2 11.5 + - - +
395T GLU* 3.0 10.6 + - - +
397T LYS* 1.3 75.0 - - - +
399T LYS* 1.3 58.0 + - - +
401T ILE* 2.7 30.8 + - + +
402T LYS* 2.8 13.0 + - - +
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Residues in contact with LYS 399 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395T GLU 3.3 8.9 + - - +
396T GLU* 4.2 8.7 - - - +
397T LYS 3.4 0.2 - - - -
398T TYR* 1.3 79.0 - - - +
400T ALA* 1.3 57.0 + - - +
402T LYS* 3.7 10.3 - - + +
403T LYS* 3.1 29.1 + - - +
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Residues in contact with ALA 400 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396T GLU 3.3 10.8 + - - +
397T LYS* 3.3 14.0 + - - +
398T TYR 3.0 0.4 - - - -
399T LYS* 1.3 77.4 - - - +
401T ILE* 1.3 62.3 + - - +
403T LYS* 3.9 5.6 + - - +
404T GLU* 3.6 16.1 + - - +
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Residues in contact with ILE 401 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397T LYS 3.3 6.0 + - - +
398T TYR* 2.7 20.2 + - - +
400T ALA* 1.3 73.1 - - - +
402T LYS* 1.3 59.6 + - - +
404T GLU* 2.9 29.9 + - - +
405T ILE* 3.3 8.5 + - - +
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Residues in contact with LYS 402 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186T LEU* 4.4 17.9 - - - +
187T GLN* 5.7 4.0 - - - +
398T TYR 2.8 11.9 + - - +
399T LYS* 3.7 13.0 - - + +
401T ILE* 1.3 77.1 - - - +
403T LYS* 1.3 52.4 + - - +
405T ILE* 5.6 0.9 - - - +
406T LEU* 2.7 44.7 + - - +
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Residues in contact with LYS 403 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399T LYS 3.1 17.5 + - - +
400T ALA* 4.2 6.1 - - - +
402T LYS* 1.3 76.8 - - - +
404T GLU* 1.3 63.0 + - - +
406T LEU* 3.9 7.2 + - - +
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Residues in contact with GLU 404 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400T ALA 3.6 11.6 + - - +
401T ILE* 2.9 14.8 + - - +
403T LYS* 1.3 82.4 - - - +
405T ILE* 1.3 60.6 + - + +
406T LEU* 3.2 2.0 + - - +
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Residues in contact with ILE 405 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225T LYS* 5.2 14.1 - - + -
401T ILE 3.3 7.2 + - - +
402T LYS* 4.9 0.9 - - - +
404T GLU* 1.3 77.0 - - + +
406T LEU* 1.3 70.9 + - - +
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Residues in contact with LEU 406 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183T GLN* 5.2 4.1 - - - +
186T LEU* 4.4 21.2 - - - +
187T GLN* 5.5 0.5 + - - -
402T LYS* 2.7 30.3 + - - +
403T LYS* 3.9 6.3 + - - +
404T GLU 3.2 4.6 - - - +
405T ILE* 1.3 82.5 - - - +
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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