Contacts of the helix formed by residues 434 - 447 (chain O) in PDB entry 5G04
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 ARG 434 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132I GLU* 5.9 4.8 - - - +
361I TYR* 2.9 50.2 + - + -
364I SER* 6.5 0.9 - - - -
365I GLU* 3.2 21.2 + - - +
395O ALA* 5.3 3.0 - - - +
429O TRP* 2.9 45.8 + - + +
432O TYR* 3.1 15.0 + - - +
433O GLY* 1.3 76.7 - - - +
435O SER* 1.3 59.6 + - - +
436O THR 3.6 1.3 - - - -
437O MET* 3.5 10.5 - - + +
438O ALA* 3.1 23.2 + - - +
617O GLN* 4.7 21.3 + - - +
650O PRO* 6.2 1.4 - - - +
654O ASP* 3.8 16.2 - - - +
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Residues in contact with SER 435 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430O ARG* 5.7 1.8 - - - +
433O GLY* 3.0 4.7 + - - -
434O ARG* 1.3 70.7 - - - +
436O THR* 1.3 64.4 + - - +
438O ALA* 3.3 6.7 + - - +
439O LEU* 3.2 23.3 + - - +
476O LEU* 3.3 23.8 - - - +
480O GLN* 3.8 19.1 + - - -
618O TYR* 3.7 28.5 + - - -
654O ASP* 3.4 22.0 + - - +
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Residues in contact with THR 436 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360I LEU* 4.9 3.5 - - + +
364I SER* 3.7 23.9 - - - +
367I LYS* 3.0 35.2 + - - +
390I ILE* 4.6 14.8 - - + -
514I PHE* 4.2 7.9 - - + -
435O SER* 1.3 78.2 + - - +
437O MET* 1.3 59.0 + - - +
439O LEU* 3.3 19.5 - - + +
440O GLN* 3.2 23.9 + - - +
480O GLN* 5.6 2.1 + - - -
654O ASP* 3.7 13.8 + - - +
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Residues in contact with MET 437 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357I GLU* 3.3 30.1 - - + +
360I LEU* 4.3 11.9 - - + +
361I TYR* 3.6 39.7 - - + -
364I SER* 4.8 4.5 - - - +
429O TRP* 3.4 53.3 - - + +
434O ARG* 3.5 17.9 + - + +
436O THR* 1.3 77.2 - - - +
438O ALA* 1.3 59.7 + - - +
439O LEU 3.2 0.2 - - - -
440O GLN* 3.3 30.6 + - - +
441O GLN* 3.1 21.3 + - - +
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Residues in contact with ALA 438 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426O THR* 3.5 29.9 + - - +
429O TRP* 4.0 8.0 - - + -
430O ARG* 4.1 11.4 - - - +
434O ARG 3.1 12.8 + - - +
435O SER* 3.3 9.8 + - - +
437O MET* 1.3 71.6 - - - +
439O LEU* 1.3 56.7 + - - +
441O GLN* 4.1 6.7 - - - -
442O ALA* 2.8 35.9 + - - +
476O LEU* 4.0 14.1 - - + +
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Residues in contact with LEU 439 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512I LEU* 3.5 52.7 - - + +
514I PHE* 3.8 11.4 - - + -
435O SER 3.2 18.0 + - - +
436O THR* 3.3 25.6 - - + +
437O MET 3.2 0.4 - - - -
438O ALA* 1.3 73.0 - - - +
440O GLN* 1.3 61.1 + - - +
442O ALA* 3.8 3.9 + - - +
443O GLN* 2.9 31.2 + - + +
473O LEU* 4.0 24.2 - - + +
476O LEU* 3.8 19.1 - - + -
477O HIS* 5.2 0.4 - - + -
480O GLN* 4.4 10.1 - - - +
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Residues in contact with GLN 440 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357I GLU* 3.5 9.9 - - - +
360I LEU* 3.5 28.5 - - + -
394I GLY 5.0 0.9 - - - +
397I ILE* 3.5 27.5 - - + +
398I LEU* 4.2 2.0 - - + +
514I PHE* 3.0 22.8 - - + -
436O THR 3.2 5.6 + - - +
437O MET* 3.3 20.4 + - + +
439O LEU* 1.3 79.1 - - - +
441O GLN* 1.3 79.7 + - - +
443O GLN* 3.2 4.7 - - - +
444O MET* 2.9 60.3 + - - +
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Residues in contact with GLN 441 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357I GLU* 4.0 12.6 + - - +
422O ILE* 3.2 38.0 - - - +
425O LYS* 3.2 48.4 + - + +
426O THR* 3.5 14.6 - - - +
429O TRP* 3.9 17.0 - - + +
437O MET 3.1 12.7 + - - +
438O ALA* 3.2 5.4 + - - +
440O GLN* 1.3 95.1 + - - +
442O ALA* 1.3 67.4 + - - +
443O GLN 3.0 1.1 - - - -
444O MET* 3.0 31.6 + - - +
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Residues in contact with ALA 442 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426O THR* 4.0 15.8 - - - +
438O ALA 2.8 21.0 + - - +
439O LEU* 4.0 4.3 - - - +
441O GLN* 1.3 70.0 - - - +
443O GLN* 1.3 54.6 + - - +
445O LEU* 2.8 32.8 + - - +
446O LEU* 3.2 13.9 + - + +
469O ALA* 4.1 27.1 - - - +
472O HIS* 5.4 0.2 - - + -
473O LEU* 4.5 22.4 - - + +
476O LEU* 5.9 0.7 - - + -
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Residues in contact with GLN 443 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398I LEU* 3.5 23.3 - - + +
497I TRP* 4.7 1.4 - - - -
501I LEU* 6.0 1.0 - - - +
512I LEU 6.0 0.4 - - - +
513I LEU* 3.4 27.0 - - + +
514I PHE* 3.2 54.6 + - + +
516I TYR* 4.6 9.6 + - - -
439O LEU* 2.9 20.8 + - + +
440O GLN 3.2 12.3 + - - +
441O GLN 3.0 1.0 - - - -
442O ALA* 1.3 80.2 - - - +
444O MET* 1.3 51.0 + - - +
445O LEU 2.9 0.3 + - - -
446O LEU* 3.0 18.6 + - - +
447O SER* 2.5 40.0 + - - -
473O LEU* 4.4 3.6 - - + +
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Residues in contact with MET 444 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353I GLN* 3.7 19.3 - - + -
357I GLU* 3.4 23.3 - - - +
397I ILE* 3.8 10.1 - - + -
398I LEU* 4.0 5.6 - - + +
401I ASN* 3.3 33.4 - - + +
422O ILE* 3.8 22.0 - - + +
425O LYS* 5.2 3.1 - - - +
440O GLN* 2.9 37.1 + - - +
441O GLN* 3.0 35.1 + - - +
443O GLN* 1.3 75.1 - - - +
445O LEU* 1.3 59.5 + - - +
447O SER* 3.7 10.7 + - - -
448O MET* 3.3 18.7 - - - +
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Residues in contact with LEU 445 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419O ASP* 3.7 40.4 - - + +
422O ILE* 3.7 17.5 - - + +
423O ALA* 4.1 7.6 - - + +
441O GLN 3.4 1.0 + - - +
442O ALA 2.8 12.0 + - - +
444O MET* 1.3 79.7 - - - +
446O LEU* 1.3 60.2 + - + +
447O SER 3.2 2.2 - - - -
448O MET* 3.0 40.2 + - - +
465O SER 4.0 16.6 - - - +
466O PHE* 3.2 36.3 - - + -
469O ALA* 3.9 22.2 - - + -
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Residues in contact with LEU 446 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497I TRP* 2.7 45.0 - - + +
498I TYR* 4.5 2.1 - - - -
516I TYR* 3.0 5.9 + - - -
442O ALA* 3.4 17.9 - - + +
443O GLN* 3.0 16.4 + - - +
445O LEU* 1.3 72.3 - - - +
447O SER* 1.3 62.0 + - - +
448O MET 3.2 0.9 - - - -
460O GLN* 3.5 13.5 + - - +
466O PHE* 3.7 24.7 - - + -
469O ALA* 4.0 18.8 - - + -
470O LEU* 4.1 24.0 - - + -
473O LEU* 3.6 35.7 - - + -
496O ARG* 4.4 3.4 - - - +
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Residues in contact with SER 447 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398I LEU* 3.6 37.2 - - - +
401I ASN* 5.2 4.5 - - - -
402I GLU* 5.4 5.3 - - - +
405I GLN* 4.0 9.7 + - - -
498I TYR* 3.3 20.7 + - - -
516I TYR* 4.0 14.1 + - - -
443O GLN 2.5 26.3 + - - -
444O MET* 3.7 11.3 - - - -
446O LEU* 1.3 78.2 - - - +
448O MET* 1.3 62.5 + - - -
449O ASN* 4.3 1.0 + - - -
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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