Contacts of the helix formed by residues 532 - 545 (chain A) in PDB entry 3IAY
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 MET 532 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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528A MET 3.1 8.2 + - - -
529A GLU* 3.2 10.7 + - - +
530A LYS 3.2 11.3 - - - +
531A LEU* 1.3 78.1 - - - +
533A ALA* 1.3 58.8 + - - +
534A LEU 3.3 2.7 - - - -
535A VAL* 3.8 20.6 - - + -
536A ASN* 2.9 52.9 + - - +
689A LYS* 6.0 1.6 - - - +
692A VAL* 3.4 25.1 - - + -
693A LEU* 3.9 28.7 - - + -
696A ARG* 4.8 2.2 - - - +
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Residues in contact with ALA 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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462A LEU* 4.0 9.8 - - + +
464A LEU* 4.3 7.9 - - + -
467A PHE* 3.5 44.5 - - + -
528A MET* 3.0 23.8 + - + +
531A LEU* 3.1 2.3 + - + -
532A MET* 1.3 76.2 - - - +
534A LEU* 1.3 57.8 + - - +
536A ASN* 4.5 0.2 - - - +
537A TYR* 3.1 36.4 + - - +
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Residues in contact with LEU 534 (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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267A MET* 4.5 10.8 - - + -
315A LEU* 4.6 8.1 - - + -
317A ILE* 3.9 25.6 - - + -
349A ALA* 4.0 20.2 - - + -
397A VAL* 4.6 16.2 - - + -
460A LEU* 5.2 0.4 - - + -
462A LEU* 4.1 8.9 - - + +
528A MET* 4.1 26.3 + - + +
532A MET 3.3 0.2 - - - -
533A ALA* 1.3 77.0 - - - +
535A VAL* 1.3 62.0 + - + +
538A THR* 2.7 44.9 + - - +
548A PHE* 4.0 23.8 - - + -
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Residues in contact with VAL 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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529A GLU* 5.6 5.6 - - - +
532A MET* 3.3 23.2 + - + +
534A LEU* 1.3 81.9 - - + +
536A ASN* 1.3 67.1 + - - +
538A THR* 3.5 6.3 + - - -
539A GLU* 3.1 24.5 + - + +
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Residues in contact with ASN 536 (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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467A PHE* 5.6 4.2 - - + -
531A LEU 4.0 6.7 + - - -
532A MET* 2.9 52.5 + - - +
533A ALA* 4.5 1.8 - - - +
535A VAL* 1.3 82.9 - - - +
537A TYR* 1.3 67.0 + - + +
539A GLU* 3.3 10.8 + - - +
540A MET* 3.0 26.5 + - - +
692A VAL* 4.2 4.6 + - - +
696A ARG* 3.7 39.6 + - + +
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Residues in contact with TYR 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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462A LEU* 5.4 1.6 - - + -
467A PHE* 3.6 28.2 - + - -
470A ARG* 4.2 7.4 - - - +
471A GLU* 2.7 36.8 + - - +
533A ALA 3.1 18.2 + - - +
536A ASN* 1.3 80.7 - - + +
538A THR* 1.3 59.4 + - - +
540A MET* 3.2 11.1 + - + -
541A ALA* 2.9 28.2 + - - +
548A PHE* 3.5 27.8 - + + -
551A LEU* 3.2 38.7 + - + +
552A LEU* 3.5 40.7 - - + +
699A ALA* 6.1 1.1 - - + -
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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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116A GLN* 4.3 1.1 + - - +
267A MET* 3.7 37.3 - - + +
312A THR* 4.2 16.6 - - + +
534A LEU* 2.7 30.7 + - - +
535A VAL* 3.5 8.2 - - - +
537A TYR* 1.3 76.5 - - - +
539A GLU* 1.3 63.0 + - - +
541A ALA* 3.3 1.7 + - - +
542A ARG* 3.0 59.1 + - - +
548A PHE* 4.1 1.6 - - - -
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Residues in contact with GLU 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 VAL 3.1 13.7 + - - +
536A ASN* 3.4 11.3 - - - +
537A TYR 3.3 0.2 - - - -
538A THR* 1.3 74.2 - - - +
540A MET* 1.3 59.8 + - - +
542A ARG* 3.1 10.5 + - + +
543A VAL* 2.8 46.4 + - + +
673A ALA* 4.7 10.7 - - - +
676A ARG* 5.3 5.4 + - - -
696A ARG* 3.0 49.0 + - - +
700A LEU* 4.3 17.1 - - + +
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Residues in contact with MET 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 ASN 3.0 14.0 + - - +
537A TYR* 3.2 15.9 + - + +
539A GLU* 1.3 75.4 - - - +
541A ALA* 1.3 62.1 + - - +
543A VAL* 4.6 2.7 - - - -
544A THR* 2.8 42.3 + - - +
551A LEU* 3.8 27.4 - - + -
559A LYS* 3.6 18.6 - - - +
699A ALA* 3.9 29.2 - - + +
700A LEU* 4.1 22.4 - - + -
703A SER* 3.5 26.7 - - - +
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Residues in contact with ALA 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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266A GLY* 3.3 19.4 + - - -
267A MET* 4.1 10.8 - - + -
537A TYR 2.9 16.3 + - - +
538A THR 3.6 4.7 - - - +
540A MET* 1.3 77.1 - - - +
542A ARG* 1.3 56.9 + - - +
544A THR* 4.3 2.7 - - - -
545A GLY* 2.9 29.1 + - - -
546A VAL* 3.2 26.9 + - - +
548A PHE* 4.1 11.7 - - - +
551A LEU* 4.0 3.5 - - + +
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Residues in contact with ARG 542 (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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116A GLN* 3.6 10.3 - - - +
265A VAL* 3.6 23.9 - - + +
266A GLY 3.2 17.7 - - - +
267A MET 3.0 23.4 + - - +
268A SER* 4.9 0.2 - - - +
269A TRP* 4.1 9.1 - - - +
305A ALA* 3.7 28.4 - - + +
309A TRP 4.4 0.4 + - - -
310A SER* 2.7 33.8 + - - +
311A HIS 2.9 23.2 + - - -
312A THR* 3.8 6.2 - - - +
538A THR* 3.0 34.8 + - + +
539A GLU* 3.5 8.7 - - + +
541A ALA* 1.3 79.4 - - - +
543A VAL* 1.3 64.9 + - + +
544A THR 3.6 0.2 + - - -
545A GLY 3.6 1.4 + - - -
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Residues in contact with VAL 543 (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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539A GLU* 2.8 39.6 + - + +
540A MET* 4.0 4.7 - - - +
542A ARG* 1.3 76.5 - - + +
544A THR* 1.3 61.6 + - + +
563A GLN* 4.2 8.0 - - - +
669A GLU* 5.1 9.9 - - + +
670A LEU* 3.7 30.1 - - + -
673A ALA* 4.4 23.1 - - + -
676A ARG* 5.4 3.8 - - - +
700A LEU* 4.8 7.0 - - + -
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Residues in contact with THR 544 (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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540A MET* 2.8 33.4 + - - +
543A VAL* 1.3 84.3 - - + +
545A GLY* 1.3 59.2 + - - +
546A VAL* 3.5 19.9 - - - +
559A LYS* 3.8 32.8 - - - +
562A SER* 2.8 21.0 + - - -
563A GLN* 3.4 41.3 + - - +
566A ARG* 4.3 2.7 + - - -
670A LEU* 4.5 5.6 - - + -
703A SER* 5.1 1.8 - - - +
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Residues in contact with GLY 545 (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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256A LEU* 4.3 1.0 - - - +
259A MET* 4.2 0.7 - - - +
265A VAL* 3.8 20.2 - - - -
266A GLY 4.0 5.1 + - - -
541A ALA 2.9 14.0 + - - -
542A ARG 3.6 0.4 + - - -
543A VAL 3.4 2.6 - - - -
544A THR* 1.3 78.4 - - - +
546A VAL* 1.3 60.7 + - - +
547A PRO* 4.1 3.8 - - - +
562A SER* 3.4 8.9 + - - -
566A ARG* 2.7 31.9 + - - -
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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