Contacts of the helix formed by residues 425 - 437 (chain J) in PDB entry 6H25
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 GLU 425 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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422J ASP* 3.6 27.3 + - - +
423J VAL 3.6 3.0 + - - -
424J GLY* 1.3 79.6 - - - +
426J LYS* 1.3 66.2 + - - +
427J GLU* 3.5 4.0 - - + +
428J THR* 4.1 9.9 - - - +
429J GLU* 3.4 22.5 + - - +
834J PHE* 4.4 0.4 - - - -
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Residues in contact with LYS 426 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424J GLY 3.8 0.6 + - - -
425J GLU* 1.3 72.6 - - - +
427J GLU* 1.3 59.0 + - - +
429J GLU* 3.4 2.4 + - - +
430J THR* 2.7 46.0 + - - +
534J GLU* 4.6 16.6 - - + +
645J THR 4.5 2.0 + - - -
646J HIS* 2.4 48.2 + - + +
834J PHE* 4.2 18.2 - - + -
835J HIS* 3.1 34.3 - - - +
838J LEU* 4.9 12.3 - - + -
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Residues in contact with GLU 427 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425J GLU* 3.5 2.8 - - + +
426J LYS* 1.3 80.7 - - - +
428J THR* 1.3 58.6 + - - +
430J THR* 3.4 3.9 + - - -
431J GLU* 3.0 57.6 + - - +
535J LYS* 4.2 21.9 + - - -
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Residues in contact with THR 428 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397J ARG* 4.2 20.2 - - + -
420J LEU* 4.0 11.4 + - + +
421J GLY* 3.3 49.5 + - - +
422J ASP* 3.7 15.7 + - - +
425J GLU* 3.8 11.5 + - - +
426J LYS 3.3 0.6 - - - -
427J GLU* 1.3 78.9 - - - +
429J GLU* 1.3 58.8 + - - +
431J GLU* 3.3 5.7 + - - +
432J VAL* 2.9 33.5 + - + +
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Residues in contact with GLU 429 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397J ARG* 2.5 46.3 + - - -
423J VAL* 4.1 12.8 - - - +
424J GLY* 4.2 11.0 + - - +
425J GLU 3.4 17.5 + - - +
426J LYS 4.0 0.2 - - - +
428J THR* 1.3 78.8 - - - +
430J THR* 1.3 57.4 + - - +
432J VAL* 3.8 6.6 - - - +
433J LEU* 3.0 37.0 + - + +
834J PHE* 3.8 36.5 - - + -
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Residues in contact with THR 430 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426J LYS* 2.7 33.6 + - - +
427J GLU* 3.6 7.8 - - - -
428J THR 3.2 0.2 - - - -
429J GLU* 1.3 76.5 - - - +
431J GLU* 1.3 59.4 + - + +
433J LEU* 3.3 13.5 + - - +
434J LEU* 3.0 38.2 + - + +
532J LEU* 3.8 25.0 - - + +
534J GLU* 6.1 0.7 - - - +
535J LYS* 3.5 28.3 - - - +
834J PHE* 5.0 4.9 - - - -
835J HIS* 5.7 1.2 + - - -
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Residues in contact with GLU 431 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418J ARG* 5.0 6.2 + - - -
420J LEU* 4.4 22.4 - - + +
427J GLU* 3.0 43.9 + - - +
428J THR* 4.0 3.9 - - - +
430J THR* 1.3 78.8 - - + +
432J VAL* 1.3 57.8 + - - +
434J LEU* 3.4 10.8 + - + +
435J LEU* 2.9 35.9 + - + +
441J HIS* 4.6 23.0 + - + +
535J LYS* 5.9 0.9 - - - +
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Residues in contact with VAL 432 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357J CYS* 4.1 24.7 - - + -
376J ALA* 5.2 1.1 - - + -
397J ARG* 3.7 50.5 - - + +
399J ILE* 6.1 0.2 - - + -
420J LEU* 3.7 20.4 - - + -
428J THR 2.9 20.4 + - - +
429J GLU* 3.8 8.1 - - - +
431J GLU* 1.3 77.6 - - - +
433J LEU* 1.3 59.7 + - - +
435J LEU* 3.2 1.6 + - - +
436J GLU* 2.9 35.5 + - + +
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Residues in contact with LEU 433 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429J GLU* 3.0 28.3 + - + +
430J THR* 3.3 12.8 - - - +
432J VAL* 1.3 78.9 - - + +
434J LEU* 1.3 68.2 + - + +
436J GLU* 4.1 3.1 - - - -
437J HIS* 3.2 30.4 + - + +
532J LEU* 4.1 20.6 - - + -
827J ALA* 3.8 27.7 - - - +
830J ALA* 4.4 17.0 - - + +
831J SER* 4.3 19.3 - - - +
834J PHE* 4.7 13.5 - - + -
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Residues in contact with LEU 434 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430J THR* 3.0 35.9 + - + +
431J GLU* 3.7 9.9 - - + +
432J VAL 3.1 0.2 - - - -
433J LEU* 1.3 87.6 - - + +
435J LEU* 1.3 65.1 + - - +
437J HIS 3.6 1.2 + - - -
438J ASP* 3.2 3.5 + - - -
439J VAL* 3.2 50.4 + - + +
441J HIS* 4.0 24.0 - - + +
530J VAL* 4.9 0.9 - - + -
532J LEU* 4.3 17.5 - - + -
535J LYS* 5.2 4.5 - - - +
537J ILE* 3.7 33.0 - - + -
827J ALA* 4.9 4.9 - - + -
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Residues in contact with LEU 435 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354J ARG* 4.1 10.4 + - - -
355J PRO 5.5 1.6 - - - +
357J CYS* 4.0 16.4 - - - -
399J ILE* 4.6 17.0 - - + -
418J ARG* 5.4 4.9 - - - +
420J LEU* 4.2 20.9 - - + -
431J GLU* 2.9 22.4 + - + +
432J VAL 3.2 2.4 + - - +
434J LEU* 1.3 75.4 - - - +
436J GLU* 1.3 64.9 + - - +
438J ASP* 3.6 10.9 + - - +
439J VAL 5.5 0.9 - - - +
441J HIS* 3.5 28.7 - - + +
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Residues in contact with GLU 436 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354J ARG* 3.9 31.1 + - - +
356J TYR* 4.1 5.8 - - - +
357J CYS* 3.1 37.4 + - + +
376J ALA* 3.4 23.9 - - + +
377J ASP* 4.0 18.6 - - - +
432J VAL* 2.9 23.3 + - + +
433J LEU* 4.5 1.6 - - - +
434J LEU 3.3 0.2 - - - -
435J LEU* 1.3 79.5 - - - +
437J HIS* 1.3 76.1 + - + +
438J ASP* 3.2 2.5 + - - +
823J MET* 4.5 1.7 - - - +
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Residues in contact with HIS 437 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433J LEU* 3.2 23.3 + - + +
434J LEU 3.6 2.9 + - - +
436J GLU* 1.3 86.1 - - + +
438J ASP* 1.3 66.9 + - - +
439J VAL* 3.4 5.0 + - + +
823J MET* 2.5 64.4 - - + +
826J TYR* 3.8 30.2 + + + +
827J ALA* 4.8 9.1 - - + -
830J ALA* 4.8 18.6 - - + -
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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