Contacts of the helix formed by residues 508 - 520 (chain K) in PDB entry 2A07
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 THR 508 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9C A 3.6 36.3 - - - +
10C A 3.2 15.0 - - - +
507K PHE* 1.3 78.4 - - - +
509K TYR* 1.3 64.7 + - - +
510K ALA* 3.6 8.1 + - - +
511K THR* 3.0 29.8 + - - +
512K LEU* 3.0 22.4 + - - +
584K ARG* 5.5 2.1 + - - -
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Residues in contact with TYR 509 (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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10C A 3.1 28.7 + - + +
11C C 3.5 14.7 + - - -
504K ARG* 3.4 27.5 + - - -
508K THR* 1.3 75.1 - - - +
510K ALA* 1.3 58.1 + - - +
512K LEU* 3.3 5.8 + - + +
513K ILE* 2.9 37.6 + - + +
534K PHE* 3.8 28.9 - + - -
540K TYR* 4.4 2.3 - - - -
541K PHE* 3.4 15.4 - + - -
547K THR* 5.6 0.7 - - - +
548K TRP* 3.2 25.8 - - - +
551K ALA* 3.5 25.7 - - + +
552K VAL* 4.1 17.0 - - + -
555K ASN* 3.4 26.0 - - + +
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Residues in contact with ALA 510 (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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508K THR* 3.2 8.3 + - - +
509K TYR* 1.3 80.3 - - - +
511K THR* 1.3 63.3 + - - +
513K ILE* 4.6 0.2 - - - -
514K ARG* 3.0 22.9 + - - +
555K ASN* 3.8 13.1 - - - +
559K HIS* 4.4 5.2 - - + +
562K PHE* 3.4 32.3 - - + -
580K TYR* 4.3 3.6 - - + -
584K ARG* 3.5 29.2 - - - +
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Residues in contact with THR 511 (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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507K PHE* 4.0 26.0 - - + -
508K THR* 3.0 29.8 + - - +
510K ALA* 1.3 77.6 - - - +
512K LEU* 1.3 57.8 + - + +
514K ARG* 3.5 4.1 + - - +
515K GLN* 3.0 29.4 + - + +
580K TYR* 2.9 27.4 + - - +
584K ARG* 5.0 2.8 + - - -
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Residues in contact with LEU 512 (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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505K PRO* 4.3 9.4 - - + -
507K PHE* 3.9 35.2 - - + +
508K THR 3.0 19.3 + - - +
509K TYR* 3.3 6.9 + - + +
511K THR* 1.3 73.5 - - + +
513K ILE* 1.3 66.5 + - - +
515K GLN* 3.2 7.5 + - + +
516K ALA* 3.0 19.8 + - - +
533K TRP* 3.5 16.2 - - + -
534K PHE* 3.7 30.1 - - + -
538K PHE* 4.1 26.2 - - + -
541K PHE* 4.1 19.1 - - + -
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Residues in contact with ILE 513 (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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509K TYR* 2.9 22.6 + - + +
510K ALA 3.8 3.1 - - - +
512K LEU* 1.3 72.7 - - - +
514K ARG* 1.3 67.3 + - - +
516K ALA* 3.1 5.7 + - - +
517K ILE* 3.1 29.4 + - + +
530K ILE* 4.4 8.1 - - + -
534K PHE* 3.8 23.8 - - + -
552K VAL* 3.9 27.8 - - + +
555K ASN* 3.8 27.6 - - + -
556K LEU* 3.6 27.4 - - + +
562K PHE* 3.6 17.0 - - + -
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Residues in contact with ARG 514 (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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510K ALA 3.0 18.1 + - - +
511K THR* 3.6 5.4 - - - +
513K ILE* 1.3 76.2 - - - +
515K GLN* 1.3 55.3 + - - +
517K ILE* 3.3 1.7 + - - +
518K MET* 2.8 65.9 + - + +
562K PHE* 3.9 6.9 - - + -
575K VAL* 4.0 22.9 - - + -
577K GLU* 2.6 38.4 + - - -
580K TYR* 2.9 48.5 + - + -
581K GLN* 3.8 4.6 - - - +
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Residues in contact with GLN 515 (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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511K THR* 3.0 18.0 + - + +
512K LEU* 3.4 13.2 - - + +
513K ILE 3.1 0.2 - - - -
514K ARG* 1.3 79.1 - - - +
516K ALA* 1.3 63.7 + - - +
518K MET* 3.3 7.5 + - - +
519K GLU* 2.7 64.6 + - - +
533K TRP* 3.8 16.2 - - + -
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Residues in contact with ALA 516 (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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512K LEU 3.0 8.6 + - - +
513K ILE* 3.1 11.2 + - - +
515K GLN* 1.3 76.7 - - - +
517K ILE* 1.3 64.5 + - + +
519K GLU* 3.3 9.4 + - - +
520K SER* 3.4 9.0 + - - -
525K LEU* 3.5 20.4 - - + +
530K ILE* 4.7 9.9 - - + -
533K TRP* 3.5 49.5 - - + +
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Residues in contact with ILE 517 (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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513K ILE* 3.1 26.1 + - + +
514K ARG 3.7 5.6 - - - +
516K ALA* 1.3 76.7 - - - +
518K MET* 1.3 62.7 + - - +
520K SER* 2.4 27.0 + - - -
523K ARG* 3.5 32.9 - - + +
524K GLN 3.9 2.0 - - - +
525K LEU* 4.1 9.4 - - + -
530K ILE* 4.4 13.0 - - + -
562K PHE* 4.5 2.0 - - + -
573K TRP* 3.8 34.3 - - + +
574K THR* 4.1 5.2 - - - +
575K VAL* 3.6 32.5 - - + +
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Residues in contact with MET 518 (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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514K ARG* 2.8 69.0 + - + +
515K GLN* 3.9 9.0 - - - +
517K ILE* 1.3 72.7 - - + +
519K GLU* 1.3 61.5 + - + +
520K SER 3.9 5.4 - - - +
523K ARG* 3.8 46.5 - - - +
575K VAL* 5.0 6.7 - - + -
577K GLU* 4.2 11.2 - - + +
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Residues in contact with GLU 519 (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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515K GLN* 2.7 52.9 + - - +
516K ALA 3.7 5.2 - - - +
517K ILE 3.1 0.4 - - - -
518K MET* 1.3 75.2 - - + +
520K SER* 1.3 65.8 + - - +
521K SER* 3.7 1.0 + - - -
533K TRP* 3.0 28.9 + - + +
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Residues in contact with SER 520 (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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516K ALA 3.4 4.8 + - - -
517K ILE* 2.4 22.9 + - - -
518K MET 3.9 6.2 - - - +
519K GLU* 1.3 82.9 - - - +
521K SER* 1.3 65.5 + - - +
522K ASP 3.3 1.0 + - - -
523K ARG* 3.1 8.9 + - - +
524K GLN 3.0 35.9 + - - -
525K LEU* 3.7 20.6 - - - -
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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