Contacts of the helix formed by residues 526 - 538 (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 526 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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525K LEU* 1.3 79.5 - - - +
527K LEU* 1.3 65.2 + - - +
528K ASN* 3.6 7.4 + - - +
529K GLU* 2.9 42.9 + - - +
530K ILE* 3.0 19.4 + - - +
571K ALA 3.8 23.1 - - - +
572K VAL* 4.2 10.5 - - + -
573K TRP* 4.4 1.3 - - - +
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Residues in contact with LEU 527 (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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8D A 3.5 48.2 - - + +
9D A 3.4 15.4 + - - +
526K THR* 1.3 73.2 - - - +
528K ASN* 1.3 63.6 + - - +
530K ILE* 3.1 8.3 + - + +
531K TYR* 3.0 60.3 + - + +
552K VAL* 4.2 4.9 - - + -
553K ARG* 3.9 14.1 - - + -
556K LEU* 3.6 28.3 - - + -
571K ALA 4.8 1.2 + - - -
573K TRP* 4.0 9.8 - - - +
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Residues in contact with ASN 528 (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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8D A 4.0 20.7 + - - +
526K THR* 3.3 6.7 + - - +
527K LEU* 1.3 80.1 - - - +
529K GLU* 1.3 57.7 + - + +
531K TYR* 3.3 25.1 + - - +
532K SER* 3.0 37.0 + - - -
549K LYS* 5.5 1.8 - - - +
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Residues in contact with GLU 529 (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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524K GLN 4.5 0.7 - - - +
525K LEU* 3.4 30.6 - - + +
526K THR* 2.9 46.7 + - - +
528K ASN* 1.3 74.7 - - + +
530K ILE* 1.3 66.2 + - - +
532K SER* 3.4 8.8 + - - -
533K TRP* 3.1 20.8 + - - +
536K ARG* 4.8 2.8 + - - -
572K VAL* 5.5 0.7 - - - +
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Residues in contact with ILE 530 (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* 4.4 6.7 - - + -
516K ALA* 4.7 6.3 - - + -
517K ILE* 4.4 13.5 - - + -
525K LEU* 3.7 24.2 - - + +
526K THR 3.0 18.3 + - - +
527K LEU* 3.1 8.0 + - - +
529K GLU* 1.3 75.1 - - - +
531K TYR* 1.3 65.6 + - - +
533K TRP* 3.1 4.6 + - - +
534K PHE* 3.1 45.1 + - + -
552K VAL* 4.0 16.6 - - + -
556K LEU* 4.2 21.5 - - + -
573K TRP* 4.0 28.0 - - + -
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Residues in contact with TYR 531 (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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8D A 3.8 19.8 + - - -
527K LEU* 3.0 49.8 + - + +
528K ASN* 3.5 24.5 - - - +
530K ILE* 1.3 75.8 - - - +
532K SER* 1.3 64.0 + - - +
534K PHE* 3.1 4.0 + - - +
535K THR* 3.0 27.8 + - + +
548K TRP* 3.9 20.0 - + + -
549K LYS* 3.6 57.4 - - + +
552K VAL* 4.3 8.7 - - + -
553K ARG* 2.9 29.0 + - - +
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Residues in contact with SER 532 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528K ASN* 3.0 24.6 + - - -
529K GLU* 3.6 9.5 - - - -
530K ILE 3.2 0.4 - - - -
531K TYR* 1.3 77.6 - - - +
533K TRP* 1.3 56.5 + - - +
535K THR* 3.2 9.3 + - - -
536K ARG* 3.0 46.0 + - - +
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Residues in contact with TRP 533 (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* 3.5 33.9 - - + -
515K GLN* 3.8 27.8 - - + -
516K ALA* 3.5 34.4 - - + +
519K GLU* 3.0 27.2 + - + -
525K LEU* 5.0 3.8 - - + -
529K GLU 3.1 13.3 + - - +
530K ILE* 3.1 7.8 + - - +
532K SER* 1.3 76.9 - - - +
534K PHE* 1.3 78.2 + + - +
536K ARG* 3.7 28.7 - - - +
537K THR* 2.5 48.9 + - + +
538K PHE* 3.8 30.1 - + - -
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Residues in contact with PHE 534 (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* 3.8 16.6 - + - -
512K LEU* 3.7 26.7 - - + -
513K ILE* 3.8 22.9 - - + -
530K ILE* 3.1 44.0 + - + -
531K TYR 3.1 8.8 + - - +
533K TRP* 1.3 97.5 - + - +
535K THR* 1.3 63.3 + - - +
537K THR* 4.8 0.2 - - - -
538K PHE* 3.1 20.7 + - - -
541K PHE* 3.4 56.8 - + + +
548K TRP* 3.7 19.3 - + + -
552K VAL* 3.9 11.7 - - + -
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Residues in contact with THR 535 (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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531K TYR* 3.0 11.2 + - + +
532K SER* 3.2 13.3 + - - -
534K PHE* 1.3 76.6 - - - +
536K ARG* 1.3 60.8 + - - +
537K THR 3.5 0.2 + - - -
538K PHE 3.7 1.7 - - - +
541K PHE* 3.4 15.0 - - - +
542K ARG* 2.7 40.9 + - - +
548K TRP* 3.4 31.6 - - + -
549K LYS* 5.6 1.8 - - - -
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Residues in contact with ARG 536 (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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529K GLU 4.8 2.2 + - - -
532K SER* 3.0 38.0 + - - +
533K TRP* 3.7 32.0 - - - +
535K THR* 1.3 78.2 + - - +
537K THR* 1.3 65.1 + - - +
542K ARG* 3.1 14.8 + - - +
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Residues in contact with THR 537 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533K TRP* 2.5 49.7 + - + +
535K THR 3.3 0.2 - - - -
536K ARG* 1.3 85.4 - - - +
538K PHE* 1.3 96.7 + - + +
542K ARG* 4.1 2.7 + - - -
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Residues in contact with PHE 538 (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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503K VAL 5.6 1.8 - - - +
505K PRO* 3.3 40.6 - - + -
507K PHE* 5.6 4.0 - + - -
512K LEU* 4.1 13.5 - - + -
533K TRP* 3.8 23.1 - + - -
534K PHE 3.1 12.3 + - - +
535K THR 3.7 6.8 - - - +
536K ARG 3.7 0.2 - - - -
537K THR* 1.3 109.9 - - + +
539K ALA* 1.3 66.1 + - - +
540K TYR* 4.1 5.8 - - + +
541K PHE* 3.1 35.9 + + + -
542K ARG* 3.8 6.4 + - - +
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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