Contacts of the helix formed by residues 525 - 541 (chain A) in PDB entry 2IVF
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 525 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372A GLY 5.9 0.7 - - - +
517A THR* 4.9 0.5 - - - +
518A LEU* 6.0 0.4 - - - -
523A THR 4.3 2.2 - - - +
524A SER* 1.3 79.0 - - - +
526A ASP* 1.3 65.3 + - - +
527A GLU* 3.5 11.2 + - - +
528A MET* 2.9 38.0 + - + +
529A GLY* 3.0 10.6 + - - -
803A LYS* 3.9 26.6 - - + -
804A VAL* 3.6 31.4 + - + +
806A PRO* 5.5 0.2 - - - +
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Residues in contact with ASP 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A ASN* 4.5 20.0 + - - +
525A THR* 1.3 71.4 - - - +
527A GLU* 1.3 70.8 + - - +
529A GLY* 3.1 3.3 + - - +
530A ASN* 2.8 31.4 + - - +
780A TYR* 3.6 30.4 - - + -
797A TRP* 5.5 1.4 - - - -
803A LYS* 2.6 33.4 + - - -
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Residues in contact with GLU 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A LYS* 2.9 44.7 + - - +
525A THR* 3.1 9.9 + - - +
526A ASP* 1.3 85.7 + - - +
528A MET* 1.3 57.2 + - - +
530A ASN* 3.4 3.6 + - - +
531A ILE* 3.1 31.2 + - + +
777A VAL* 6.5 0.4 - - + -
780A TYR* 3.6 34.3 - - + +
781A ALA* 3.5 8.5 - - - +
783A ALA* 5.3 0.2 - - - +
798A HIS* 3.9 10.0 - - - -
803A LYS* 4.5 8.3 - - - +
804A VAL 4.4 3.3 - - - +
806A PRO* 3.5 27.7 - - + +
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Residues in contact with MET 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A THR* 4.3 5.2 - - + -
524A SER* 3.7 17.7 - - - +
525A THR* 2.9 36.6 + - - +
527A GLU* 1.3 75.0 - - - +
529A GLY* 1.3 65.1 + - - +
531A ILE* 3.3 10.9 + - - +
532A GLU* 3.2 28.2 + - + +
804A VAL* 3.7 13.0 - - + +
805A PHE 3.7 14.4 - - - +
806A PRO* 3.8 20.4 - - + -
810A ARG* 3.2 44.9 - - - +
950A GLU* 4.4 9.2 - - - +
953A ARG* 6.3 0.2 - - - +
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Residues in contact with GLY 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A PHE* 4.1 5.8 - - - +
514A ASN* 3.6 20.6 - - - -
517A THR* 3.6 23.8 - - - +
525A THR 3.0 11.5 + - - -
526A ASP 3.1 4.0 + - - -
528A MET* 1.3 76.8 - - - +
530A ASN* 1.3 60.5 + - - +
532A GLU* 3.4 3.1 + - - +
533A PHE* 3.2 22.2 + - - +
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Residues in contact with ASN 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A ASN* 4.1 3.4 + - - +
526A ASP 2.8 15.9 + - - +
527A GLU 3.6 4.5 - - - +
528A MET 3.2 0.2 - - - -
529A GLY* 1.3 76.5 - - - +
531A ILE* 1.3 57.5 + - - +
533A PHE* 3.3 13.9 - - - +
534A MET* 2.9 39.1 + - - +
775A THR 3.8 13.7 + - - -
776A GLY* 4.0 7.1 - - - -
777A VAL* 3.3 32.7 - - - +
780A TYR* 3.5 35.5 - - + +
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Residues in contact with ILE 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A GLY 4.4 3.8 - - - +
234A LYS* 5.8 1.6 - - + -
527A GLU* 3.1 21.4 + - + +
528A MET* 3.3 9.8 + - + +
530A ASN* 1.3 77.3 - - - +
532A GLU* 1.3 63.4 + - - +
534A MET* 3.0 8.3 + - - +
535A LYS* 2.9 35.1 + - + +
777A VAL* 5.5 3.6 - - + -
806A PRO* 3.8 23.8 - - + -
953A ARG* 3.5 55.6 - - - +
955A TYR* 3.9 23.1 - - + +
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Residues in contact with GLU 532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A PHE* 3.8 14.1 - - + -
517A THR* 3.8 20.2 - - + +
528A MET* 3.2 16.3 + - + +
529A GLY 3.4 6.3 + - - +
531A ILE* 1.3 79.2 - - - +
533A PHE* 1.3 63.8 + - - +
535A LYS* 3.0 46.7 + - - +
536A VAL* 3.2 17.8 + - - +
953A ARG* 4.9 5.0 + - - -
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Residues in contact with PHE 533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A LEU* 4.2 24.2 - - + -
509A MET* 4.0 15.7 - - - -
510A ALA* 3.9 29.6 - - + +
513A PHE* 3.5 36.4 - + + -
529A GLY 3.2 10.6 + - - +
530A ASN* 3.3 18.6 - - - +
532A GLU* 1.3 77.2 - - - +
534A MET* 1.3 81.4 + - - +
536A VAL* 3.2 2.8 + - - +
537A VAL* 2.9 60.0 + - + +
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Residues in contact with MET 534 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A ASN* 2.9 25.0 + - - +
531A ILE* 3.0 9.2 + - - +
533A PHE* 1.3 96.5 - - + +
535A LYS* 1.3 59.5 + - - +
537A VAL* 3.4 9.6 - - + +
538A THR* 2.7 36.9 + - - +
776A GLY* 5.5 3.8 - - - -
777A VAL* 3.4 34.8 - - + +
955A TYR* 3.6 24.5 - - + -
956A PHE* 4.5 24.0 - - + +
957A MET* 6.5 0.4 - - + -
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Residues in contact with LYS 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A ILE* 2.9 21.2 + - + +
532A GLU* 3.0 44.5 + - - +
534A MET* 1.3 77.1 - - - +
536A VAL* 1.3 65.2 + - + +
538A THR* 3.7 6.2 + - - -
539A SER* 3.8 14.9 + - - -
591A HIS* 5.6 1.2 - - - -
950A GLU 5.3 1.6 + - - -
953A ARG* 4.0 35.7 - - + +
954A TYR 3.9 16.2 - - - +
955A TYR* 3.8 15.0 - - + -
1982A GOL 4.7 5.5 + - - +
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Residues in contact with VAL 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A MET* 4.6 9.9 - - + -
513A PHE* 3.4 43.3 - - + -
532A GLU 3.2 6.1 + - - +
533A PHE 3.7 1.3 - - - +
535A LYS* 1.3 76.5 - - + +
537A VAL* 1.3 70.3 + - - +
538A THR 3.1 0.7 + - - -
539A SER* 3.2 7.5 + - - -
540A ALA* 3.1 22.7 + - + +
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Residues in contact with VAL 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A LEU* 5.9 1.3 - - + -
509A MET* 3.7 20.6 - - + -
533A PHE* 2.9 62.5 + - + +
534A MET* 3.4 22.0 - - + +
536A VAL* 1.3 72.6 - - + +
538A THR* 1.3 68.7 + - - +
540A ALA* 3.1 8.8 + - - +
541A VAL* 3.1 32.3 + - + +
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Residues in contact with THR 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534A MET* 2.7 25.2 + - - +
535A LYS 3.9 5.2 - - - -
536A VAL 3.1 0.2 + - - -
537A VAL* 1.3 81.2 - - - +
539A SER* 1.3 62.5 + - - +
541A VAL* 3.3 12.1 - - - +
543A LEU* 3.2 54.0 + - + +
954A TYR* 3.7 18.4 - - + +
955A TYR* 3.6 3.2 - - - +
956A PHE* 2.9 37.9 + - + +
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Residues in contact with SER 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535A LYS 3.8 8.8 + - - -
536A VAL* 3.2 7.9 + - - -
538A THR* 1.3 79.6 - - - +
540A ALA* 1.3 63.0 + - - +
541A VAL 3.2 0.4 + - - -
542A GLY* 3.5 10.0 + - - +
543A LEU 4.3 7.1 + - - -
590A ASP* 3.8 40.0 + - - +
591A HIS* 3.6 28.9 + - - -
593A ARG* 5.0 0.5 + - - -
713A HIS* 4.7 7.8 - - - -
954A TYR* 5.4 0.2 - - - -
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Residues in contact with ALA 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A TYR* 4.2 9.5 - - + -
211A ASP* 4.9 6.4 - - - +
509A MET* 5.9 3.8 - - + -
536A VAL* 3.1 19.1 + - + +
537A VAL* 3.1 13.4 + - - +
539A SER* 1.3 78.4 - - - +
541A VAL* 1.3 63.4 + - + +
542A GLY 3.8 0.3 + - - -
590A ASP* 5.8 0.2 - - - -
713A HIS* 5.5 3.7 - - - -
718A ARG* 5.9 0.9 + - - -
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Residues in contact with VAL 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A PHE* 3.6 33.5 - - + -
207A THR 5.3 0.2 - - - -
208A TYR* 3.9 39.0 + - + +
211A ASP* 5.4 3.1 - - - -
212A GLY 4.8 2.6 - - - +
214A SER* 4.9 3.5 + - - -
493A VAL* 4.4 10.3 - - + -
537A VAL* 3.1 17.5 + - + +
538A THR* 3.3 14.4 - - - +
540A ALA* 1.3 83.7 - - + +
542A GLY* 1.3 56.9 + - - +
543A LEU* 3.5 25.7 + - + -
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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
------------------------------------------------------------
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