Contacts of the helix formed by residues 495 - 508 (chain K) 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 PRO 495 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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433K THR* 3.6 0.2 - - - -
437K GLY 5.8 0.9 - - - +
440K HIS* 3.5 26.7 - - + +
469K GLN* 3.2 51.8 - - + +
470K GLN* 4.4 2.7 - - + -
494K VAL* 1.3 92.5 - - + +
496K TYR* 1.3 61.9 + - - +
497K SER* 3.1 17.0 - - - +
498K GLU* 2.8 31.9 + - + +
499K PHE 3.1 8.1 + - - -
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Residues in contact with TYR 496 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411K LEU* 4.6 7.3 - - + +
433K THR* 3.3 26.9 + - + -
434K HIS 3.4 15.7 - - - +
435K PRO* 3.6 47.1 - - + +
437K GLY* 3.8 18.0 - - - -
440K HIS* 5.0 0.4 + - - -
495K PRO* 1.3 72.9 - - - +
497K SER* 1.3 58.4 + - - +
498K GLU 2.9 5.1 + - - -
499K PHE* 3.1 36.7 + + + +
500K ALA 4.5 1.6 + - - -
554K PRO 5.7 5.4 - - - +
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Residues in contact with SER 497 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437K GLY* 5.6 0.8 - - - -
495K PRO* 3.9 13.7 - - - +
496K TYR* 1.3 77.2 - - - +
498K GLU* 1.3 66.2 + - - +
500K ALA* 5.5 0.8 - - - +
501K CYS* 6.0 0.5 - - - -
530K HIS 4.6 1.9 - - - +
531K ALA* 5.4 3.5 - - - +
553K THR* 5.2 7.9 + - - +
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Residues in contact with GLU 498 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469K GLN* 4.3 16.1 + - - +
470K GLN* 2.9 19.0 + - - +
494K VAL* 4.5 0.7 - - + -
495K PRO* 2.8 22.7 + - + +
497K SER* 1.3 89.5 + - - +
499K PHE* 1.3 57.0 + - - +
500K ALA* 3.4 2.9 + - - -
501K CYS* 3.4 5.3 + - - +
502K ALA* 2.8 29.9 + - - +
530K HIS* 2.7 58.6 + - - +
531K ALA* 5.2 1.8 - - + -
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Residues in contact with PHE 499 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411K LEU* 3.8 24.2 - - + -
413K VAL* 4.4 13.2 - - + -
431K LEU* 3.7 31.6 - - + -
433K THR* 3.4 26.0 - - + +
494K VAL* 4.2 2.5 - - + -
495K PRO 3.1 5.2 + - - +
496K TYR* 3.1 40.8 + + + +
498K GLU* 1.3 77.9 - - - +
500K ALA* 1.3 60.8 + - + +
502K ALA* 4.1 4.0 - - - -
503K LEU* 2.7 64.3 + - + +
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Residues in contact with ALA 500 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496K TYR 4.5 1.4 + - - -
497K SER 5.5 0.4 - - - -
498K GLU 3.4 0.8 - - - -
499K PHE* 1.3 83.3 - - - +
501K CYS* 1.3 59.0 + - - +
503K LEU* 3.7 4.5 - - - +
504K LEU* 3.0 28.8 + - - +
553K THR* 3.0 31.6 - - - +
554K PRO 3.5 16.7 + - - +
555K THR* 3.6 20.4 - - - +
556K GLU* 4.0 8.6 - - - +
559K VAL* 5.1 1.8 - - + -
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Residues in contact with CYS 501 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497K SER 6.0 0.4 - - - -
498K GLU* 3.4 3.8 + - - +
500K ALA* 1.3 76.3 - - - +
502K ALA* 1.3 60.9 + - - +
504K LEU* 3.2 8.7 + - - +
505K TYR* 2.8 32.1 + - - +
527K LEU* 4.4 5.6 - - + -
528K SER 3.8 15.3 - - - +
529K GLU* 3.8 2.4 - - - -
530K HIS 3.7 16.8 - - - +
531K ALA* 3.2 26.7 - - - -
532K LEU 3.7 7.2 - - - -
553K THR* 3.3 23.6 - - - -
559K VAL* 4.3 12.6 - - - -
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Residues in contact with ALA 502 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431K LEU* 4.0 6.3 - - + -
470K GLN* 4.0 7.2 - - - +
494K VAL* 3.8 26.7 - - + -
498K GLU 2.8 22.7 + - - +
499K PHE 3.5 3.1 - - - +
501K CYS* 1.3 72.6 - - - +
503K LEU* 1.3 63.1 + - - +
505K TYR* 3.1 2.4 + - - +
506K PHE* 2.9 38.0 + - + -
529K GLU 3.3 16.2 + - - +
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Residues in contact with LEU 503 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413K VAL* 4.5 9.9 - - + -
415K CYS* 3.4 27.8 - - - -
419K ARG* 3.9 22.2 - - - +
431K LEU* 3.4 15.4 - - + +
499K PHE* 2.7 47.5 + - + +
500K ALA* 3.7 4.3 - - - +
502K ALA* 1.3 72.8 - - - +
504K LEU* 1.3 58.6 + - - +
506K PHE* 3.3 1.0 + - - +
507K THR* 2.6 37.6 + - - +
556K GLU* 3.4 22.7 - - + +
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Residues in contact with LEU 504 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500K ALA 3.0 15.8 + - - +
501K CYS* 3.4 5.6 - - - +
503K LEU* 1.3 78.8 - - - +
505K TYR* 1.3 64.4 + - - +
507K THR* 3.5 8.1 + - - -
508K GLY 3.6 8.3 + - - +
512K PHE* 4.2 12.3 - - + -
513K ASN* 3.7 8.3 - - - +
516K MET* 4.4 7.4 - - + -
527K LEU* 4.1 18.2 - - + -
556K GLU* 3.5 15.4 + - + +
559K VAL* 3.7 39.5 - - + -
560K PHE* 3.8 22.2 - - + -
573K ARG* 3.4 24.2 - - - +
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Residues in contact with TYR 505 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472K LYS* 6.0 0.9 - - - -
501K CYS 2.8 20.6 + - - +
502K ALA 3.4 3.4 - - - +
504K LEU* 1.3 74.5 - - - +
506K PHE* 1.3 83.5 + + - +
507K THR 3.2 4.0 + - - -
508K GLY 3.2 3.5 + - - -
513K ASN* 3.0 42.2 + - + -
517K ARG* 4.3 10.8 - - - -
527K LEU 6.0 0.7 - - - -
528K SER* 4.7 4.3 - - - +
529K GLU* 3.4 45.6 + - + -
703K D3T 3.7 32.3 + + - -
5L A 2.9 43.0 + + - -
6L A 4.5 5.5 + - - -
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Residues in contact with PHE 506 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415K CYS* 3.1 17.7 - - + +
416K GLY* 2.7 29.8 + - - -
429K ASP* 4.5 9.3 - - + +
431K LEU* 4.2 9.6 - - + -
470K GLN* 4.2 16.6 - - - -
472K LYS* 4.7 11.7 - - + -
492K ILE* 3.3 50.5 - - + -
502K ALA* 2.9 39.0 + - + +
503K LEU 4.3 0.7 - - - +
505K TYR* 1.3 98.8 - + - +
507K THR* 1.3 51.1 - - - +
508K GLY 3.4 0.2 - - - -
529K GLU* 4.2 8.5 - - + -
703K D3T 3.8 32.7 - - - +
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Residues in contact with THR 507 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415K CYS* 3.8 4.9 - - - +
416K GLY* 3.4 11.0 - - - +
419K ARG* 2.7 46.9 + - + +
420K ARG* 3.2 32.5 + - + +
503K LEU* 2.6 28.1 + - - +
504K LEU 3.7 5.6 - - - -
505K TYR 3.1 0.6 - - - -
506K PHE* 1.3 79.3 - - - +
508K GLY* 1.3 66.7 + - - +
570K PRO* 4.2 5.4 - - + -
573K ARG* 4.0 12.3 - - - +
703K D3T 4.9 0.2 - - - -
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Residues in contact with GLY 508 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420K ARG* 4.0 1.9 - - - -
504K LEU 3.6 4.5 + - - +
505K TYR 3.2 6.8 + - - -
506K PHE 3.4 0.6 - - - -
507K THR* 1.3 85.2 - - - +
509K SER* 1.3 69.4 + - - -
510K ALA 4.0 0.2 - - - -
512K PHE* 3.7 10.2 - - - -
513K ASN* 3.6 12.6 - - - -
573K ARG* 3.6 27.4 - - - +
703K D3T 4.2 6.1 - - - -
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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