Contacts of the helix formed by residues 433 - 446 (chain B) in PDB entry 5JG8
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 LYS 433 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B PHE 6.0 2.5 - - - +
173B SER* 6.5 0.2 - - - -
432B LEU* 1.3 82.7 - - + +
434B SER* 1.3 73.9 + - - +
435B TRP 3.4 1.5 - - - +
436B SER* 3.4 5.7 + - - +
437B TRP* 2.9 51.3 + - + +
601B ALA* 5.1 1.6 - - - -
602B ASP* 3.3 47.4 + - + +
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Residues in contact with SER 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B PHE 5.2 0.9 + - - -
172B SER 3.6 4.3 + - - -
173B SER* 3.4 25.5 + - - -
174B TRP* 3.2 39.9 - - - -
432B LEU* 4.9 0.8 - - - +
433B LYS* 1.3 81.2 - - - +
435B TRP* 1.3 66.3 + - - +
437B TRP* 3.2 5.3 + - - +
438B ASN* 2.7 33.5 + - - +
705B NAG 6.0 0.9 - - - -
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Residues in contact with TRP 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B TRP* 3.4 28.7 - + + -
380B LEU* 4.4 5.2 - - + -
382B MET* 4.0 21.8 - - + -
384B PHE* 3.5 28.7 + - - +
385B CYS* 3.2 35.2 - - + +
396B SER 5.4 0.4 - - - -
398B ASP* 4.9 1.8 + - - -
399B PRO* 4.1 12.7 - - + +
402B GLN* 3.7 26.9 - - - +
403B LEU* 3.3 36.5 - - + +
428B PRO* 5.2 3.4 - - + -
431B CYS* 4.7 3.6 - - + -
432B LEU* 5.0 10.0 - - + +
433B LYS 3.4 0.8 - - - +
434B SER* 1.3 79.4 - - - +
436B SER* 1.3 64.3 + - - +
438B ASN* 3.3 2.1 + - - +
439B TYR* 2.9 52.2 + + + -
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Residues in contact with SER 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428B PRO* 4.6 2.2 - - - -
429B GLY 3.7 9.7 + - - +
431B CYS* 4.2 16.6 - - - +
433B LYS 3.4 10.6 + - - +
434B SER 3.2 0.8 - - - -
435B TRP* 1.3 82.4 - - - +
437B TRP* 1.3 58.5 + - - +
439B TYR* 3.1 9.2 + - - +
440B TYR* 2.9 28.1 + - - +
599B ALA 3.7 2.3 + - - +
600B ARG* 3.2 10.8 - - - +
601B ALA* 2.9 38.9 + - - -
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Residues in contact with TRP 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B LYS* 2.9 51.8 + - + +
434B SER* 3.2 5.8 + - - +
436B SER* 1.3 76.5 - - - +
438B ASN* 1.3 60.4 + - - +
440B TYR* 3.4 2.8 + - - +
441B ARG* 2.9 28.2 + - - +
469B GLU* 5.0 2.7 - - - +
600B ARG* 3.3 55.5 + - + +
601B ALA 2.9 21.7 + - - -
602B ASP 3.5 12.8 + - - -
603B SER* 3.4 14.4 - - - -
705B NAG 5.1 23.6 - - + +
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Residues in contact with ASN 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B TRP* 3.2 34.4 + - - -
175B ASN* 3.4 5.3 + - - +
176B ILE* 3.0 38.6 + - + +
403B LEU* 4.1 15.3 - - + -
434B SER* 2.7 32.6 + - - +
435B TRP 3.8 2.9 - - - +
437B TRP* 1.3 74.4 - - - +
439B TYR* 1.3 60.9 + - - +
441B ARG* 3.3 13.8 + - - +
442B ILE* 2.8 36.7 + - + +
705B NAG 4.8 7.0 + - - +
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Residues in contact with TYR 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B LEU* 4.1 20.4 - - + -
382B MET* 5.9 0.4 - - - -
403B LEU* 4.4 2.2 - - + +
406B LEU* 4.2 16.2 - - + -
422B ILE* 3.6 14.2 - - + +
428B PRO* 3.3 37.7 - - + -
435B TRP* 2.9 41.8 + + + +
436B SER* 3.4 9.9 - - - +
438B ASN* 1.3 76.3 - - - +
440B TYR* 1.3 64.9 + - - +
442B ILE* 2.9 8.6 + - + +
443B VAL* 2.9 43.3 + - + +
453B GLN* 2.7 29.9 + - - -
455B PHE* 3.5 16.7 - + - -
466B PHE* 3.9 7.2 - + - -
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Residues in contact with TYR 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B SER 2.9 12.2 + - - +
437B TRP 3.6 8.3 - - - +
439B TYR* 1.3 74.9 - - - +
441B ARG* 1.3 64.1 + - - +
443B VAL* 3.3 7.8 - - - +
444B ALA* 2.9 27.4 + - + +
465B VAL 3.9 1.3 + - - -
466B PHE* 3.5 29.1 - + - -
467B TYR* 2.8 58.5 + - - +
468B ASP 5.1 0.7 - - - -
469B GLU* 5.1 7.0 - - + -
472B LEU* 4.1 17.3 - - + -
599B ALA* 3.7 21.5 + - + -
600B ARG* 3.6 45.3 - - + +
606B LEU* 4.1 13.1 - - + +
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Residues in contact with ARG 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B ASN* 4.3 9.8 - - - +
176B ILE* 3.9 18.0 - - - +
177B SER* 4.1 6.7 - - - +
178B LEU* 3.7 44.0 - - + +
437B TRP 2.9 16.9 + - - +
438B ASN* 3.6 27.8 + - - +
440B TYR* 1.3 75.6 - - - +
442B ILE* 1.3 58.2 + - - +
444B ALA* 3.6 2.2 + - - +
445B ARG* 2.9 27.9 + - - +
469B GLU* 3.4 39.7 + - - +
705B NAG 4.5 17.5 - - + +
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Residues in contact with ILE 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B ILE* 4.3 10.8 - - + -
178B LEU* 3.9 18.2 - - + -
403B LEU* 4.0 29.6 - - + +
406B LEU* 4.6 7.4 - - + -
407B VAL* 3.7 21.3 - - + -
410B LEU* 3.3 33.2 - - + -
438B ASN 2.8 29.0 + - - +
439B TYR* 2.9 7.4 + - + +
441B ARG* 1.3 74.0 - - + +
443B VAL* 1.3 69.2 + - + +
445B ARG* 2.9 6.2 + - - -
446B TYR* 2.9 33.6 + - + +
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Residues in contact with VAL 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B LEU* 6.0 1.1 - - + -
422B ILE* 5.3 1.1 - - + -
439B TYR* 2.9 49.4 + - + +
440B TYR* 3.3 9.4 - - + +
442B ILE* 1.3 72.6 - - + +
444B ALA* 1.3 69.6 + - + +
446B TYR* 3.3 3.4 + - - +
447B GLU* 3.0 26.0 + - - +
450B LEU* 4.2 23.2 - - + +
453B GLN* 4.2 10.3 - - - +
466B PHE* 3.1 39.5 - - + -
476B LEU* 4.0 5.9 - - + +
477B ALA* 5.6 0.8 - - + +
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Residues in contact with ALA 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B LYS* 3.0 20.4 + - - +
440B TYR* 2.9 16.2 + - + +
441B ARG* 3.7 6.1 - - - +
443B VAL* 1.3 85.0 - - + +
445B ARG* 1.3 62.4 + - - +
446B TYR 3.4 0.2 + - - -
447B GLU* 3.6 8.8 + - - +
467B TYR 4.2 7.0 - - - +
469B GLU* 4.5 19.3 - - + +
476B LEU* 3.5 29.4 - - + +
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Residues in contact with ARG 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B LEU* 3.8 25.8 - - + +
179B PRO 5.2 4.6 + - - -
181B VAL 3.2 25.9 + - - -
182B PRO 4.0 0.6 + - - -
183B LYS* 3.4 53.5 - - - +
184B PRO* 3.8 0.8 - - - +
411B GLN* 3.6 12.9 + - - -
414B GLU* 2.7 36.8 + - - -
441B ARG 2.9 17.3 + - - +
442B ILE 2.9 5.6 + - - +
444B ALA* 1.3 76.0 - - - +
446B TYR* 1.3 90.0 + - + +
447B GLU* 3.4 0.6 - - - +
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Residues in contact with TYR 446 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B LEU* 4.8 4.9 - - + -
179B PRO* 3.3 23.0 - - - +
407B VAL* 3.7 16.9 - - + +
410B LEU* 3.9 28.3 - - + -
411B GLN* 2.9 44.9 + - - +
414B GLU* 3.8 8.5 - - - -
442B ILE* 2.9 40.4 + - + +
443B VAL* 3.6 4.5 - - - +
445B ARG* 1.3 110.3 + - + +
447B GLU* 1.3 65.4 + - - +
448B ASN 3.4 2.2 - - - -
449B THR* 2.7 26.8 + - - -
450B LEU* 2.9 14.4 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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