Contacts of the helix formed by residues 498 - 508 (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 GLU 498 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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469P GLN* 3.5 32.9 + - - +
470P GLN* 3.1 12.6 + - - +
494P VAL* 4.9 0.7 - - + -
495P PRO* 2.7 20.9 + - + +
497P SER* 1.3 88.4 - - - +
499P PHE* 1.3 63.1 + - - +
500P ALA 3.0 4.9 + - - -
501P CYS* 3.3 3.9 + - - +
502P ALA* 2.8 25.9 + - + +
529P GLU 4.6 1.8 - - - +
530P HIS* 2.8 56.7 + - - +
531P ALA* 5.1 3.1 - - + -
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Residues in contact with PHE 499 (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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411P LEU* 3.7 28.3 - - + -
413P VAL* 4.4 13.2 - - + -
431P LEU* 4.0 28.9 - - + -
433P THR* 3.3 26.7 - - + +
494P VAL* 4.2 1.8 - - - -
495P PRO 3.1 5.9 + - - +
496P TYR* 3.5 45.8 + + + +
498P GLU* 1.3 77.3 - - - +
500P ALA* 1.3 64.5 + - - +
502P ALA* 4.0 4.7 - - - -
503P LEU* 2.9 47.5 + - + +
554P PRO 5.4 4.5 - - - +
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Residues in contact with ALA 500 (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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496P TYR 4.9 1.0 + - - -
497P SER 5.4 0.6 - - - +
498P GLU* 3.0 3.0 + - - +
499P PHE* 1.3 84.4 - - - +
501P CYS* 1.3 63.0 + - - +
503P LEU* 3.7 4.0 - - - +
504P LEU* 3.2 20.2 + - - +
553P THR* 2.9 37.2 - - - +
554P PRO 3.3 20.0 + - - +
555P THR* 4.1 12.3 - - - +
556P GLU* 4.1 6.3 - - - +
559P VAL* 4.8 4.3 - - + -
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Residues in contact with CYS 501 (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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498P GLU* 3.3 2.5 + - - -
500P ALA* 1.3 77.1 - - - +
502P ALA* 1.3 65.4 + - - +
504P LEU* 3.9 7.4 - - - +
505P TYR* 3.0 25.8 + - - +
527P LEU* 3.8 12.4 - - + +
528P SER 3.7 17.6 - - - +
529P GLU 3.9 1.8 - - - -
530P HIS 3.8 6.7 - - - +
531P ALA* 3.3 31.9 - - - -
532P LEU* 3.3 12.1 - - - -
553P THR* 3.4 20.4 - - - -
559P VAL* 4.2 11.7 - - - -
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Residues in contact with ALA 502 (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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431P LEU* 4.0 7.6 - - + -
494P VAL* 3.9 30.7 - - + -
498P GLU* 2.8 23.4 + - + +
499P PHE 3.7 3.4 - - - +
501P CYS* 1.3 76.9 - - - +
503P LEU* 1.3 63.6 + - - +
505P TYR* 3.1 2.9 + - - +
506P PHE* 3.1 34.3 + - + -
529P GLU 3.4 17.4 + - - +
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Residues in contact with LEU 503 (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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413P VAL* 3.7 23.3 - - + -
415P CYS* 3.6 25.6 - - - -
419P ARG* 3.7 20.0 - - - +
431P LEU* 3.4 16.3 - - + +
499P PHE* 2.9 39.8 + - + +
500P ALA* 3.7 3.4 - - - +
502P ALA* 1.3 77.1 - - - +
504P LEU* 1.3 58.2 + - - +
506P PHE* 3.5 0.5 + - - -
507P THR* 2.6 33.5 + - - -
556P GLU* 3.0 28.5 - - + +
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Residues in contact with LEU 504 (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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500P ALA 3.2 13.8 + - - +
501P CYS* 3.9 6.7 - - - +
503P LEU* 1.3 80.4 - - - +
505P TYR* 1.3 63.7 + - - +
507P THR* 3.6 4.4 + - - -
508P GLY 3.6 10.6 + - - +
512P PHE* 3.8 22.9 - - + -
513P ASN* 3.5 8.4 - - - +
516P MET* 4.9 4.9 - - + -
527P LEU* 4.1 15.3 - - + -
556P GLU* 3.5 16.3 + - + +
559P VAL* 3.5 39.7 - - + -
560P PHE* 4.3 13.9 - - + -
573P ARG* 3.3 24.9 - - - +
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Residues in contact with TYR 505 (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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501P CYS 3.0 19.3 + - - +
502P ALA 3.1 3.3 + - - +
504P LEU* 1.3 78.4 - - - +
506P PHE* 1.3 74.5 + + - +
508P GLY* 3.0 8.1 + - - -
513P ASN* 2.9 45.4 + - + -
517P ARG* 4.3 9.4 - - - -
527P LEU* 6.4 1.1 - - + -
528P SER* 4.4 4.7 - - - +
529P GLU* 3.2 49.4 + - + +
704P D3T 3.4 37.7 + + + +
5Q A 2.7 46.4 + + - -
6Q A 4.9 3.3 - - - -
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Residues in contact with PHE 506 (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* 3.5 17.7 - - + -
416P GLY 2.9 17.3 + - - -
429P ASP* 4.7 8.8 - - + +
431P LEU* 4.5 2.9 - - + -
467P ASN* 6.1 0.7 - - - -
470P GLN* 3.8 18.8 - - - -
490P ASP* 6.2 0.4 - - - -
492P ILE* 3.5 51.8 - - + -
502P ALA* 3.1 27.9 + - - +
505P TYR* 1.3 92.2 - + - +
507P THR* 1.3 62.3 + - - +
508P GLY 3.2 0.2 - - - -
529P GLU* 4.3 7.6 - - + -
704P D3T 3.2 47.2 - - - +
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Residues in contact with THR 507 (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* 3.6 3.0 - - - +
416P GLY* 3.6 13.0 - - - +
419P ARG* 3.0 52.1 + - + +
420P ARG* 2.9 37.1 + - + +
503P LEU 2.6 23.2 + - - -
504P LEU 3.7 7.0 - - - -
505P TYR 3.1 0.4 - - - -
506P PHE* 1.3 78.8 - - - +
508P GLY* 1.3 62.6 + - - +
570P PRO* 4.4 4.5 - - + -
573P ARG* 3.9 13.0 - - - +
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Residues in contact with GLY 508 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420P ARG* 4.3 0.7 - - - -
504P LEU 3.6 3.4 + - - +
505P TYR 3.0 7.2 + - - -
506P PHE 3.2 0.4 - - - -
507P THR* 1.3 84.0 - - - +
509P SER* 1.3 69.9 + - - -
512P PHE* 3.5 19.2 - - - -
513P ASN* 3.3 13.7 - - - -
573P ARG* 3.6 18.8 - - - +
704P D3T 3.9 7.0 - - - -
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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