Contacts of the helix formed by residues 478 - 491 (chain M) 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 478 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468M GLU* 5.4 0.2 - - - +
476M VAL* 3.6 9.4 - - + +
477M GLN* 1.3 82.6 - - - +
479M ARG* 1.3 62.0 + - - +
480M VAL* 3.3 5.1 + - - +
481M TYR* 4.6 7.4 + - + +
482M LYS* 4.8 6.4 + - - +
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Residues in contact with ARG 479 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467M ALA* 3.7 30.3 - - + -
468M GLU* 5.4 1.6 - - + -
477M GLN* 4.5 5.1 - - + +
478M ASN* 1.3 74.8 - - - +
480M VAL* 1.3 58.2 + - - +
481M TYR 3.5 1.6 - - - -
482M LYS* 5.4 1.8 - - - -
483M SER* 2.5 49.0 + - - +
511M LEU 4.2 8.0 - - - +
512M ASP* 5.3 3.8 - - - +
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Residues in contact with VAL 480 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478M ASN* 3.3 3.6 - - - -
479M ARG* 1.3 74.9 - - - +
481M TYR* 1.3 60.6 + - - +
484M LEU* 2.5 39.3 + - - +
512M ASP* 4.6 12.4 + - + +
515M ILE 4.2 9.2 - - - +
516M ALA* 3.6 28.9 - - + -
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Residues in contact with TYR 481 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478M ASN* 4.6 5.9 + - + +
479M ARG 3.5 0.2 - - - -
480M VAL* 1.3 79.5 - - - +
482M LYS* 1.3 59.4 + - + +
484M LEU* 3.8 0.5 - - - +
485M LYS* 2.9 31.6 + - - +
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Residues in contact with LYS 482 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430M ASP* 5.1 14.1 - - + +
433M ALA* 3.6 32.7 - - + +
434M SER* 5.2 0.7 - - - +
437M CYS* 5.8 0.5 - - - +
478M ASN 4.8 6.8 + - - +
479M ARG* 4.1 3.1 + - - -
481M TYR* 1.3 80.3 - - - +
483M SER* 1.3 59.9 + - - +
485M LYS* 3.1 6.8 + - - +
486M VAL* 2.9 29.3 + - - +
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Residues in contact with SER 483 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433M ALA* 5.8 0.9 - - - -
463M PRO* 5.2 15.9 - - - -
467M ALA* 5.7 1.8 - - - -
479M ARG* 2.5 35.1 + - - +
482M LYS* 1.3 78.3 - - - +
484M LEU* 1.3 56.7 + - - +
486M VAL* 3.3 6.7 + - - +
487M TRP* 2.9 30.2 + - - +
511M LEU* 4.0 18.5 - - - +
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Residues in contact with LEU 484 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479M ARG 3.5 0.4 + - - -
480M VAL* 2.5 27.0 + - + +
481M TYR 4.2 0.7 - - - +
483M SER* 1.3 78.6 - - - +
485M LYS* 1.3 56.1 + - - +
487M TRP* 4.1 5.9 - - - +
488M SER* 2.9 30.5 + - - -
508M ASP* 5.4 7.4 - - + +
511M LEU* 4.8 4.4 - - + +
512M ASP* 5.4 7.0 - - + +
516M ALA* 5.3 8.3 - - + -
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Residues in contact with LYS 485 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437M CYS* 5.3 10.8 - - + +
481M TYR 2.9 20.5 + - - +
482M LYS* 3.1 7.6 + - - +
484M LEU* 1.3 76.1 - - - +
486M VAL* 1.3 60.3 + - - +
488M SER* 3.8 5.0 - - - -
489M MET* 2.9 28.9 + - - +
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Residues in contact with VAL 486 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433M ALA* 5.4 6.5 - - + +
436M TRP* 6.4 1.8 - - + -
437M CYS* 5.1 14.3 - - + +
459M ALA 5.7 0.7 - - - +
460M THR* 4.0 23.5 - - - +
463M PRO* 6.1 4.5 - - + -
482M LYS 2.9 15.6 + - - +
483M SER* 3.9 5.6 - - - +
485M LYS* 1.3 73.7 - - - +
487M TRP* 1.3 61.7 + - - +
489M MET* 3.3 6.3 + - - +
490M LEU* 2.9 29.3 + - - +
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Residues in contact with TRP 487 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460M THR* 5.1 5.6 + - - +
483M SER 2.9 18.1 + - - +
484M LEU* 4.1 3.4 - - - +
486M VAL* 1.3 76.9 - - - +
488M SER* 1.3 57.5 + - - +
490M LEU* 3.4 6.1 + - - +
491M ALA* 2.9 28.9 + - - +
507M TYR* 4.8 3.4 - - + +
508M ASP* 4.6 15.4 - - + +
511M LEU* 4.0 21.1 - - + -
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Residues in contact with SER 488 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484M LEU 2.9 21.2 + - - -
485M LYS* 3.8 6.3 - - - -
486M VAL 3.3 0.2 - - - -
487M TRP* 1.3 77.0 - - - +
489M MET* 1.3 61.0 + - - +
491M ALA* 3.0 21.5 - - - +
492M ASP 3.9 12.5 - - - +
493M LEU* 3.9 14.8 - - - +
508M ASP* 5.8 2.0 - - - +
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Residues in contact with MET 489 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437M CYS* 5.6 10.3 - - + +
440M GLY* 5.8 9.2 - - - -
456M LEU* 5.4 4.4 - - + +
485M LYS 2.9 18.5 + - - +
486M VAL* 3.3 6.9 + - - +
488M SER* 1.3 76.0 - - - +
490M LEU* 1.3 63.0 + - - +
493M LEU* 5.8 1.2 - - - +
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Residues in contact with LEU 490 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453M LEU* 5.7 6.1 - - - +
456M LEU* 4.0 17.5 - - + +
457M ARG* 5.1 4.5 - - + -
460M THR* 3.8 21.5 - - - -
486M VAL 2.9 17.3 + - - +
487M TRP* 3.4 6.7 + - - +
488M SER 3.2 0.2 - - - -
489M MET* 1.3 80.1 - - - +
491M ALA* 1.3 62.6 + - + +
499M THR* 5.0 2.8 - - - +
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Residues in contact with ALA 491 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487M TRP 2.9 19.8 + - - +
488M SER* 3.0 7.6 - - - +
489M MET 3.5 0.6 - - - -
490M LEU* 1.3 81.0 - - + +
492M ASP* 1.3 73.7 + - - +
493M LEU 3.6 2.0 - - - -
498M GLY 5.0 4.0 - - - -
499M THR 3.9 20.0 - - - +
500M PHE* 4.2 7.2 - - - -
501M GLN 5.2 0.2 - - - +
504M LYS* 4.2 15.3 - - + -
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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