Contacts of the helix formed by residues 530 - 542 (chain A) in PDB entry 3IAD
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 SER 530 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523A MET* 4.0 6.5 - - - +
529A ALA* 1.3 72.9 - - - +
531A VAL* 1.3 63.7 + - - +
532A GLU* 3.6 10.9 + - - +
533A LYS* 3.1 48.3 + - - +
534A SER* 3.1 24.4 + - - -
596A VAL* 4.8 2.9 - - - +
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Residues in contact with VAL 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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499A THR* 3.6 28.9 - - + -
503A MET* 3.7 34.3 - - + -
507A PHE* 4.8 8.5 - - + -
523A MET* 4.8 2.6 - - - +
529A ALA* 3.9 3.1 - - + +
530A SER* 1.3 71.8 - - - +
532A GLU* 1.3 73.2 + - + +
534A SER* 3.3 7.5 + - - -
535A GLN* 3.1 24.4 + - + +
572A TYR* 4.4 12.3 - - + +
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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
----------------------------------------------------------
530A SER* 3.6 9.6 + - - +
531A VAL* 1.3 91.5 + - + +
533A LYS* 1.3 65.0 + - + +
535A GLN* 3.6 1.9 + - - +
536A VAL* 3.4 28.4 + - - +
572A TYR* 4.0 31.3 - - + +
575A THR* 3.6 40.2 - - + +
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Residues in contact with LYS 533 (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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530A SER* 3.1 30.8 + - - +
532A GLU* 1.3 76.9 - - + +
534A SER* 1.3 61.6 + - - +
536A VAL* 3.6 6.7 + - - +
537A GLY* 3.1 19.1 + - - -
596A VAL* 4.1 14.6 - - + +
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Residues in contact with SER 534 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A MET* 2.7 40.5 - - - +
530A SER 3.1 14.7 + - - -
531A VAL* 3.3 6.5 - - - -
532A GLU 3.3 0.2 - - - -
533A LYS* 1.3 77.6 - - - +
535A GLN* 1.3 52.5 + - - +
537A GLY* 3.0 3.6 + - - -
538A PHE* 2.6 36.1 + - - +
596A VAL* 3.5 13.3 - - - +
901A 15X 3.6 27.2 + - - -
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Residues in contact with GLN 535 (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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495A TYR* 2.6 30.5 + - - +
499A THR* 4.0 22.3 - - + +
503A MET* 5.3 0.4 - - - -
531A VAL* 3.1 16.5 + - - +
532A GLU 4.2 3.4 - - - +
534A SER* 1.3 76.5 - - - +
536A VAL* 1.3 60.4 + - - +
538A PHE* 3.3 11.9 + - - +
539A ILE* 2.9 36.5 + - - +
572A TYR* 4.2 20.4 - - + -
901A 15X 2.8 67.2 + - - +
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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
----------------------------------------------------------
532A GLU 3.4 17.6 + - - +
533A LYS* 3.8 6.7 - - - +
534A SER 3.3 0.4 - - - -
535A GLN* 1.3 78.2 - - - +
537A GLY* 1.3 55.7 + - - +
539A ILE* 3.4 4.4 + - - +
540A ASP* 2.9 46.1 + - - +
569A ARG* 3.9 25.1 - - - +
572A TYR* 3.8 6.7 - - + +
573A GLN* 3.5 47.8 - - + +
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Residues in contact with GLY 537 (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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533A LYS 3.1 11.7 + - - -
534A SER 3.0 6.8 + - - -
536A VAL* 1.3 73.0 - - - +
538A PHE* 1.3 65.2 + - - +
540A ASP* 4.6 0.7 - - - -
541A TYR* 3.0 43.9 + - - +
596A VAL* 4.2 11.4 - - - -
600A ILE* 3.7 8.5 - - - +
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Residues in contact with PHE 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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485A LEU* 4.2 12.6 - - + -
488A PRO* 3.8 16.2 - - + -
495A TYR* 4.9 0.2 - - - -
534A SER 2.6 17.6 + - - +
535A GLN* 3.3 27.3 + - - +
537A GLY* 1.3 72.7 - - - +
539A ILE* 1.3 56.5 + - + +
542A ILE* 3.1 22.2 + - + -
543A VAL* 2.9 49.3 + - + -
600A ILE* 4.8 1.8 - - - -
604A PHE* 3.8 24.5 - + - -
901A 15X 3.1 75.9 + + + +
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Residues in contact with ILE 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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488A PRO* 4.2 7.9 - - + -
495A TYR* 3.7 24.0 - - + +
535A GLN* 2.9 23.2 + - + +
536A VAL 3.9 2.9 - - - +
538A PHE* 1.3 76.4 - - + +
540A ASP* 1.3 65.1 + - - +
541A TYR 3.4 0.3 + - - -
543A VAL* 3.8 7.9 - - + -
544A HIS* 2.7 45.3 + - + +
545A PRO* 3.5 0.7 - - - +
565A LEU* 4.0 33.9 - - + +
566A GLU* 6.0 0.2 - - - -
568A ASN 5.0 0.2 - - - +
569A ARG* 3.7 46.4 - - + +
572A TYR* 5.5 1.6 - - + -
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Residues in contact with ASP 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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536A VAL* 2.9 27.9 + - - +
537A GLY* 5.0 0.5 - - - -
539A ILE* 1.3 74.8 - - - +
541A TYR* 1.3 80.2 + - + +
544A HIS* 4.6 4.3 + - - +
545A PRO* 3.3 18.9 - - - +
569A ARG* 2.9 45.1 + - - +
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Residues in contact with TYR 541 (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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442A HIS* 5.1 0.5 + - - -
443A MET* 4.6 11.1 - - - +
537A GLY* 3.0 29.3 + - - +
540A ASP* 1.3 96.2 - - + +
542A ILE* 1.3 64.4 + - + +
545A PRO* 3.6 11.2 - - - +
600A ILE* 4.0 22.4 - - + +
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Residues in contact with ILE 542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A HIS* 3.6 31.9 - - + +
443A MET* 5.0 2.7 - - + -
485A LEU* 4.3 6.7 - - + -
538A PHE* 3.1 22.0 + - + +
540A ASP 3.7 0.4 - - - -
541A TYR* 1.3 81.4 - - - +
543A VAL* 1.3 70.5 + - - +
544A HIS 3.5 1.3 - - - -
545A PRO* 3.4 4.6 - - - +
546A LEU* 3.3 22.2 + - - +
600A ILE* 3.3 33.7 - - + -
604A PHE* 3.1 63.0 - - + -
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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