Contacts of the helix formed by residues 415 - 420 (chain P) in PDB entry 3HX0
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 CYS 415 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413P VAL* 3.9 11.4 - - - -
414P ALA* 1.3 72.1 - - - +
416P GLY* 1.3 72.5 + - - +
417P SER 3.7 0.2 + - - -
418P TYR* 3.2 20.1 + - - +
419P ARG* 3.7 9.0 - - - -
429P ASP* 2.7 23.2 + - + +
431P LEU* 3.9 18.4 - - - -
503P LEU* 3.6 34.5 - - - -
506P PHE* 3.3 25.6 - - + +
507P THR* 3.6 7.2 - - - +
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Residues in contact with GLY 416 (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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415P CYS* 1.3 83.2 - - - +
417P SER* 1.3 64.8 + - - -
418P TYR 2.9 1.7 + - - -
419P ARG* 3.2 7.3 + - - +
420P ARG* 3.3 20.3 + - - +
429P ASP* 3.5 8.9 + - - -
506P PHE 2.9 15.8 + - - -
507P THR* 3.6 9.1 - - - +
704P D3T 3.4 15.3 - - - -
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Residues in contact with SER 417 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386P ARG* 4.3 3.4 - - - -
416P GLY* 1.3 70.7 - - - -
418P TYR* 1.3 64.9 + - - +
420P ARG* 3.2 20.0 + - - +
421P GLY 3.3 0.2 + - - -
422P LYS* 3.1 41.7 + - - +
425P CYS* 3.2 22.0 - - - +
427P ASP 4.2 3.5 + - - -
704P D3T 2.7 44.9 + - - -
804P MG 4.1 0.2 - - - -
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Residues in contact with TYR 418 (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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389P ARG* 3.0 56.5 + - + +
392P ALA* 4.0 17.7 - - + -
393P THR* 2.9 49.7 + - - +
396P GLU* 5.5 3.5 - - + +
414P ALA* 3.3 32.8 - - + +
415P CYS 3.2 11.4 + - - +
416P GLY 2.9 1.2 + - - -
417P SER* 1.3 76.7 + - - +
419P ARG* 1.3 58.1 + - - +
420P ARG 2.9 3.6 - - - -
421P GLY* 2.7 24.4 + - - -
425P CYS* 4.2 9.2 - - + -
427P ASP 5.9 2.0 - - - +
428P VAL* 6.0 3.6 - - + -
429P ASP 6.0 2.0 - - - +
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Residues in contact with ARG 419 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389P ARG* 5.9 0.2 - - - +
413P VAL* 4.1 15.5 - - - +
414P ALA 3.2 19.9 + - - +
415P CYS* 3.3 11.4 + - - +
416P GLY 3.2 3.3 + - - +
418P TYR* 1.3 80.7 - - - +
420P ARG* 1.3 58.5 + - - +
421P GLY 3.3 0.6 + - - -
503P LEU* 3.7 18.4 - - - +
507P THR* 3.0 42.7 + - + +
556P GLU* 3.0 33.8 + - - -
567P TYR* 4.6 3.2 + - - -
570P PRO* 3.4 36.4 - - + +
571P ALA* 5.5 0.2 - - - +
573P ARG* 3.7 1.6 - - - +
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Residues in contact with ARG 420 (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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416P GLY* 3.3 12.6 - - - +
417P SER* 3.2 17.9 + - - +
418P TYR 2.8 1.4 + - - -
419P ARG* 1.3 78.4 - - - +
421P GLY* 1.3 61.9 + - - +
422P LYS* 3.4 25.6 + - - +
507P THR* 2.9 32.4 + - + +
508P GLY* 4.3 0.6 - - - -
509P SER* 3.8 23.7 - - - +
570P PRO 3.0 22.0 - - - +
571P ALA* 3.6 22.8 - - - +
573P ARG* 3.4 23.0 + - - +
574P ASP* 3.3 18.8 + - - -
704P D3T 3.0 28.9 + - - -
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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