Contacts of the helix formed by residues 432 - 447 (chain P) 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 ASP 432 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277P ARG* 5.6 7.6 + - - +
399P TYR* 3.9 5.7 + - - -
426P HIS* 4.8 0.2 - - - -
429P ARG* 3.4 47.8 - - - +
430P PRO 3.3 1.2 - - - +
431P ASN* 1.3 79.6 - - - +
433P SER* 1.3 65.4 + - - +
434P ARG* 3.5 5.2 + - + +
435P MET* 3.7 38.2 + - - +
436P LEU* 3.9 16.1 + - - +
462P VAL* 4.4 0.9 - - - -
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Residues in contact with SER 433 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431P ASN 3.5 5.1 + - - -
432P ASP* 1.3 72.1 - - - +
434P ARG* 1.3 64.6 + - - +
436P LEU* 3.1 7.9 + - - +
437P VAL* 3.0 27.7 + - - +
459P ALA* 4.3 1.2 - - - +
462P VAL* 4.0 14.4 - - - -
463P GLY* 4.5 1.6 - - - -
464P ASP* 2.9 49.9 + - - -
465P VAL* 4.2 15.4 + - - +
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Residues in contact with ARG 434 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277P ARG* 4.0 25.2 - - - +
403P TYR* 4.1 39.1 + - + +
432P ASP* 3.3 5.1 - - + -
433P SER* 1.3 80.2 - - - +
435P MET* 1.3 72.2 + - - +
437P VAL* 3.4 9.0 + - - +
438P ALA* 3.0 28.9 + - - +
465P VAL* 5.4 7.6 - - + -
466P GLU* 3.8 31.4 + - - +
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Residues in contact with MET 435 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399P TYR* 3.6 37.7 - - + -
403P TYR* 4.1 32.5 - - + -
422P TYR* 5.0 4.9 - - + +
425P ALA* 4.1 9.4 - - + +
426P HIS* 3.9 39.9 - - + +
429P ARG* 4.5 1.8 - - + +
432P ASP* 3.7 32.3 - - + +
433P SER 3.3 0.6 - - - -
434P ARG* 1.3 88.0 - - - +
436P LEU* 1.3 59.8 + - - +
438P ALA* 3.2 8.2 + - - +
439P LEU* 2.9 32.3 + - - +
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Residues in contact with LEU 436 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532J ALA 5.2 0.2 - - - +
533J TYR 4.9 2.0 - - - -
426P HIS* 3.5 34.3 - - + +
430P PRO 4.5 1.6 - - - +
432P ASP 3.9 8.3 + - - +
433P SER 3.1 6.1 + - - +
435P MET* 1.3 76.0 - - - +
437P VAL* 1.3 66.1 + - - +
439P LEU* 3.3 9.3 + - + +
440P GLY* 3.0 18.7 + - - -
455P CYS* 3.9 33.4 - - - +
456P TYR 4.9 0.3 + - - -
458P ARG* 3.6 30.5 - - - +
459P ALA* 3.8 22.0 - - + +
462P VAL* 3.6 31.0 - - + -
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Residues in contact with VAL 437 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433P SER* 3.0 24.9 + - - +
434P ARG* 3.6 10.3 - - - +
435P MET 3.3 0.2 - - - -
436P LEU* 1.3 75.9 - - - +
438P ALA* 1.3 61.7 + - - +
440P GLY* 3.1 11.8 + - - -
441P GLU* 3.2 23.5 + - - +
456P TYR* 3.5 19.8 - - + -
459P ALA* 4.1 3.8 - - + -
464P ASP* 4.5 0.2 - - - +
468P MET* 5.7 4.7 - - + -
469P ALA* 3.8 32.5 - - + +
472P LYS* 4.8 9.2 - - + -
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Residues in contact with ALA 438 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403P TYR* 4.7 4.5 - - + -
410P GLU* 5.5 0.8 - - - +
422P TYR* 3.6 38.7 - - + +
434P ARG 3.0 14.8 + - - +
435P MET* 3.2 9.2 + - - +
437P VAL* 1.3 76.1 - - - +
439P LEU* 1.3 61.4 + - - +
441P GLU* 3.3 18.6 + - - +
442P CYS* 3.2 27.2 + - - -
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Residues in contact with LEU 439 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532J ALA* 4.6 8.3 - - + +
419P LEU* 3.8 31.4 - - + +
422P TYR* 3.9 12.8 - - + -
423P ARG* 3.8 41.7 - - + +
426P HIS* 4.1 23.6 - - + +
435P MET 2.9 13.1 + - - +
436P LEU* 3.3 9.2 + - + +
438P ALA* 1.3 76.0 - - - +
440P GLY* 1.3 56.5 + - - +
442P CYS* 3.4 4.0 + - + +
443P TYR* 3.0 42.6 + - + -
455P CYS* 3.9 20.0 - - - -
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Residues in contact with GLY 440 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436P LEU 3.0 12.4 + - - -
437P VAL 3.1 1.7 + - - -
439P LEU* 1.3 72.9 - - - +
441P GLU* 1.3 57.1 + - - +
443P TYR 3.4 0.3 + - - -
444P GLU* 2.9 29.5 + - - +
452P ALA* 3.6 19.4 - - - +
455P CYS* 4.5 2.8 - - - +
456P TYR* 3.0 31.4 + - - -
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Residues in contact with GLU 441 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410P GLU* 3.0 24.2 - - - +
437P VAL* 3.2 17.2 + - - +
438P ALA* 3.5 20.4 - - - +
440P GLY* 1.3 75.3 - - - +
442P CYS* 1.3 63.1 + - - +
444P GLU* 3.3 3.5 + - - +
445P LYS* 3.1 45.7 + - - +
456P TYR* 3.0 9.0 + - - -
472P LYS* 3.1 37.9 + - - +
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Residues in contact with CYS 442 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410P GLU* 5.1 3.8 - - - -
415P PRO* 5.1 6.3 - - - +
418P CYS* 3.8 23.1 - - - -
419P LEU* 4.1 26.7 - - + -
422P TYR* 3.4 29.6 - - - -
438P ALA 3.2 15.0 + - - -
439P LEU* 3.5 9.4 - - - +
441P GLU* 1.3 76.9 - - - +
443P TYR* 1.3 59.1 + - - +
445P LYS* 3.4 7.1 + - - +
446P LEU* 2.8 31.1 + - - +
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Residues in contact with TYR 443 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527J ILE* 4.9 10.3 + - + +
530J SER* 4.6 12.1 - - - -
531J GLU 4.8 2.0 + - - -
532J ALA* 3.5 27.5 - - + +
419P LEU* 3.9 18.9 - - + +
423P ARG* 4.8 1.7 - - - -
439P LEU* 3.0 43.0 + - + +
442P CYS* 1.3 79.7 - - - +
444P GLU* 1.3 55.1 + - - +
446P LEU* 3.2 24.3 - - + +
447P ASN 3.0 21.3 + - - -
448P GLN* 3.0 21.7 + - + +
451P GLU* 3.8 39.8 + - + -
452P ALA* 3.6 20.9 - - + -
455P CYS* 4.9 6.7 - - - -
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Residues in contact with GLU 444 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440P GLY 2.9 17.9 + - - +
441P GLU* 3.7 4.3 - - - +
442P CYS 3.3 0.2 - - - -
443P TYR* 1.3 72.8 - - - +
445P LYS* 1.3 64.3 + - + +
447P ASN* 3.0 20.4 + - - +
449P LEU* 4.0 17.8 - - + +
452P ALA* 4.0 2.4 - - - +
456P TYR* 3.8 2.4 + - - -
472P LYS* 3.3 26.0 + - - +
475P LYS* 5.0 9.2 - - - +
476P LEU* 3.6 35.4 - - + +
479P GLN* 5.0 8.6 + - + +
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Residues in contact with LYS 445 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410P GLU* 3.6 33.1 + - - +
415P PRO* 5.4 15.4 - - + +
441P GLU* 3.1 33.4 + - - +
442P CYS* 4.0 5.1 - - - +
444P GLU* 1.3 80.5 - - + +
446P LEU* 1.3 61.0 + - - +
447P ASN* 3.2 3.8 + - - +
472P LYS* 6.0 1.3 - - - +
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Residues in contact with LEU 446 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527J ILE* 4.5 3.4 - - + -
415P PRO* 5.6 10.4 - - + +
416P PHE* 4.0 34.8 - - + -
419P LEU* 3.7 26.7 - - + -
442P CYS 2.8 13.6 + - - +
443P TYR* 3.2 30.3 - - + +
444P GLU 3.2 0.2 - - - -
445P LYS* 1.3 75.4 - - - +
447P ASN* 1.3 65.6 + - - +
448P GLN* 3.5 31.6 + - + +
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Residues in contact with ASN 447 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443P TYR 3.0 3.4 + - - -
444P GLU 3.0 16.1 + - - +
445P LYS 3.2 3.2 + - - +
446P LEU* 1.3 79.4 - - - +
448P GLN* 1.3 60.6 + - - +
449P LEU* 3.4 27.3 + - - +
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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