Contacts of the helix formed by residues 436 - 446 (chain W) in PDB entry 6G0L
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 436 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433W PRO* 3.0 12.6 + - - +
435W SER* 1.4 82.1 + - - +
437W MET* 1.3 51.9 + - - -
438W PRO* 3.7 2.7 - - - -
439W ALA* 3.6 16.2 - - + +
440W TRP* 2.3 42.1 - - + +
513W ASP* 3.6 7.9 - - - +
514W GLU* 3.1 16.7 + - - +
777W GLY* 3.8 10.4 - - - -
778W ILE* 4.7 11.2 - - - +
1501W BEF 2.9 33.7 - - - -
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Residues in contact with MET 437 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432W VAL* 4.1 6.5 - - + +
433W PRO 3.1 11.2 + - - +
434W LEU* 4.0 12.1 - - - +
436W THR* 1.3 70.9 - - - +
438W PRO* 1.4 87.6 - - + +
439W ALA 3.1 2.5 - - - -
440W TRP* 2.7 30.7 + - - +
441W LEU* 2.9 20.3 + - + +
455W CYS* 3.3 31.0 - - + -
456W TYR 5.6 0.2 - - - +
457W MET* 3.0 45.5 - - - +
489W LEU* 4.2 18.2 - - + +
491W THR* 4.5 15.5 - - - +
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Residues in contact with PRO 438 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313W ARG* 4.5 11.3 + - - +
434W LEU 4.2 3.1 - - - +
435W SER 3.9 13.5 - - - +
436W THR 3.7 1.8 - - - -
437W MET* 1.4 105.6 - - + +
439W ALA* 1.3 63.7 - - - +
441W LEU* 3.2 19.6 + - + +
442W ASP* 3.2 18.2 + - - +
747W SER* 6.5 1.8 - - - -
751W ARG* 3.3 40.5 + - + +
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Residues in contact with ALA 439 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436W THR* 3.6 20.6 - - + +
438W PRO* 1.3 77.9 - - - +
440W TRP* 1.3 54.5 + - + +
442W ASP* 3.2 8.0 + - - +
443W THR* 2.4 43.2 + - - +
751W ARG* 4.7 1.9 - - - +
778W ILE* 6.4 1.8 - - + -
779W ASN* 6.3 1.1 - - - +
1501W BEF 5.8 1.6 - - - -
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Residues in contact with TRP 440 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408W THR* 2.8 53.4 - - + -
411W THR* 3.7 19.3 - - + -
412W VAL* 4.6 6.9 - - + +
430W ILE* 6.1 2.7 - - + -
432W VAL* 2.8 39.7 - - + +
436W THR* 2.3 38.7 + - + +
437W MET* 2.7 15.2 + - - +
439W ALA* 1.3 78.9 - - + +
441W LEU* 1.3 48.9 + - - +
443W THR* 3.0 10.4 + - - -
444W PHE* 2.6 38.0 + + - +
489W LEU* 4.1 15.3 - - + -
512W VAL 6.1 0.4 - - - -
513W ASP* 2.9 34.9 + - + -
540W ILE* 4.6 12.3 - - + -
1501W BEF 4.7 1.8 - - - -
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Residues in contact with LEU 441 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288W GLU* 5.9 2.9 - - - +
313W ARG* 5.3 13.0 - - - +
437W MET* 2.9 18.1 + - + +
438W PRO* 3.2 13.9 + - + +
440W TRP* 1.3 72.3 - - - +
442W ASP* 1.3 76.1 + - - +
444W PHE* 3.0 7.2 + - - +
445W GLU* 2.8 42.5 + - + +
453W CYS* 4.2 21.1 - - - +
455W CYS* 6.1 4.3 - - + -
489W LEU* 4.6 10.5 - - + +
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Residues in contact with ASP 442 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313W ARG* 4.2 13.8 + - - -
438W PRO 3.2 9.7 + - - +
439W ALA* 3.2 8.9 + - - +
441W LEU* 1.3 93.8 - - - +
443W THR* 1.4 57.1 + - - +
444W PHE 3.0 0.2 - - - -
445W GLU* 4.3 9.4 - - - +
446W LYS* 3.1 44.6 + - + +
751W ARG* 4.6 11.6 + - - -
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Residues in contact with THR 443 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408W THR* 3.3 29.7 - - + +
409W VAL* 4.4 9.9 - - + -
412W VAL* 3.8 10.3 - - + +
439W ALA* 2.4 32.5 + - - +
440W TRP* 3.1 12.0 - - - -
442W ASP* 1.4 76.6 - - - +
444W PHE* 1.3 55.4 + - - +
447W TRP* 3.3 39.8 - - + +
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Residues in contact with PHE 444 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412W VAL* 3.7 31.6 - - + +
415W ILE* 4.1 31.6 - - + -
440W TRP* 2.6 19.6 + + - +
441W LEU* 3.6 7.9 - - - +
442W ASP 3.0 0.4 - - - -
443W THR* 1.3 76.6 - - - +
445W GLU* 1.4 54.5 + - - +
446W LYS 3.4 3.4 - - - -
447W TRP 4.2 0.7 - - - -
448W ALA* 3.3 34.5 + - + +
451W LEU* 4.1 22.2 - - + +
452W ASN 4.7 0.7 - - - -
453W CYS* 3.5 31.9 - - + -
487W VAL* 3.8 35.2 - - + -
489W LEU* 6.4 2.2 - - + -
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Residues in contact with GLU 445 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289W ARG* 5.9 6.1 - - - +
441W LEU* 2.8 33.2 + - + +
442W ASP* 3.3 7.0 + - - +
444W PHE* 1.4 73.9 - - - +
446W LYS* 1.3 92.5 + - - +
447W TRP 3.8 0.2 - - - -
448W ALA 4.6 8.7 - - - -
449W PRO* 4.8 10.5 - - + +
453W CYS* 4.7 10.1 - - - -
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Residues in contact with LYS 446 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372W LYS* 4.2 11.1 + - - +
373W GLY* 3.3 24.4 + - - -
442W ASP* 3.1 26.3 + - + +
445W GLU* 1.3 118.6 + - - +
447W TRP* 1.3 64.1 + - + +
448W ALA 3.5 1.6 - - - -
449W PRO* 5.1 3.4 - - - -
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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