Contacts of the helix formed by residues 529 - 544 (chain A) in PDB entry 2IUK
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 529 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524A SER 4.1 7.0 - - - +
525A HIS 2.5 22.7 + - - +
527A LEU 2.9 1.1 + - - -
528A ASN* 1.3 83.9 - - - +
530A HIS* 1.3 79.8 + - - +
531A ALA 3.6 0.7 - - - -
532A VAL 3.8 0.3 + - - -
533A MET* 3.3 26.9 + - - +
711A THR* 4.0 9.4 - - - +
715A LEU* 3.6 21.3 - - + -
716A HIS* 3.8 32.4 - - + +
719A VAL* 4.4 2.9 - - + -
862A ILE* 3.4 16.1 - - - +
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Residues in contact with HIS 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A HIS* 3.1 22.5 + + - -
526A TRP* 3.0 31.6 + + + +
529A THR* 1.3 93.6 + - - +
531A ALA* 1.3 63.6 + - - +
533A MET* 4.0 1.7 - - - +
534A GLU 3.6 9.7 + - - -
561A THR* 4.3 1.2 - - - +
564A ILE* 3.3 23.1 - - + +
565A ASN* 2.9 41.8 + - - +
716A HIS* 3.5 1.8 + - - -
862A ILE* 3.4 14.2 - - + +
864A ILE* 3.0 23.6 - - - -
901A FE 2.3 24.3 - - - -
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Residues in contact with ALA 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A TYR* 3.8 23.6 + - - +
238A TYR* 4.5 2.7 - - - +
239A PRO* 3.3 23.1 - - + +
526A TRP* 2.9 36.7 + - - +
527A LEU* 4.0 11.0 - - + -
530A HIS* 1.3 76.1 - - - +
532A VAL* 1.3 57.4 + - - +
534A GLU* 3.9 2.3 + - - +
535A PRO* 3.2 22.2 - - - +
565A ASN* 4.6 2.0 - - - +
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Residues in contact with VAL 532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A PRO* 4.3 5.2 - - + -
527A LEU* 3.2 30.3 + - + +
528A ASN 4.2 12.8 - - - +
529A THR 4.4 2.0 - - - +
530A HIS 3.4 0.4 - - - -
531A ALA* 1.3 75.6 - - - +
533A MET* 1.3 60.9 + - - +
535A PRO* 3.6 1.6 - - - +
536A PHE* 3.3 12.4 - - + -
597A TYR* 4.3 2.9 - - + -
600A TRP* 3.4 51.6 - - + +
602A PHE* 6.2 0.2 - - + -
605A GLN* 4.5 2.0 - - + +
683A HIS* 3.1 34.4 - - - +
711A THR* 4.9 7.4 - - + -
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Residues in contact with MET 533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529A THR 3.3 13.8 + - - +
530A HIS 4.0 2.0 - - - +
532A VAL* 1.3 76.4 - - + +
534A GLU* 1.3 66.8 + - - +
535A PRO* 3.2 2.7 - - - -
536A PHE* 3.0 25.1 + - - +
537A ALA* 3.0 11.1 + - + -
557A HIS 4.1 12.1 - - - +
558A TYR* 3.3 38.8 - - + -
561A THR* 4.5 7.4 - - + -
708A ILE* 3.7 35.0 - - + +
711A THR* 4.1 13.9 - - + -
712A ALA* 4.3 4.5 - - + -
862A ILE* 3.4 26.9 - - + -
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Residues in contact with GLU 534 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A TYR* 4.5 4.8 + - - +
240A LEU 4.9 0.7 - - - +
241A ARG* 4.0 13.8 - - - +
242A VAL* 3.0 37.6 + - - +
530A HIS 3.6 4.2 + - - +
531A ALA* 4.2 3.1 - - - +
533A MET* 1.3 77.4 - - - +
535A PRO* 1.3 60.8 - - + +
537A ALA* 3.6 7.9 - - - +
538A ILE* 3.0 43.2 + - + +
561A THR* 4.8 3.6 - - + +
562A ILE* 3.6 24.7 - - + +
565A ASN* 2.9 42.0 + - - +
569A ARG* 4.7 4.5 + - - -
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Residues in contact with PRO 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A TYR* 3.6 17.1 + - + -
239A PRO* 3.8 7.4 - - + -
240A LEU 3.6 17.3 - - - +
531A ALA 3.2 15.7 - - - +
532A VAL 3.6 2.0 - - - +
533A MET 3.4 3.1 - - - -
534A GLU* 1.3 87.1 - - + +
536A PHE* 1.3 59.7 + - + +
538A ILE* 3.7 0.8 + - + -
539A ALA* 3.1 26.2 + - - +
678A ALA* 4.4 3.0 - - - +
682A GLY* 3.6 22.9 - - - +
683A HIS* 3.5 34.3 - - + +
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Residues in contact with PHE 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A VAL* 3.3 29.4 - - + -
533A MET* 3.0 23.6 + - - +
535A PRO* 1.3 71.4 - - - +
537A ALA* 1.3 64.0 + - - +
539A ALA* 3.6 5.9 - - - +
540A THR* 2.8 31.5 + - - +
558A TYR* 3.7 17.7 - - + +
600A TRP* 4.6 1.3 - + - -
602A PHE* 3.6 33.4 - + - -
674A TRP* 5.1 3.6 - + - +
675A TRP* 3.9 24.7 - + - -
678A ALA* 3.7 21.8 - - + -
683A HIS* 3.9 18.6 - + - -
692A TRP* 4.8 4.9 - + - -
708A ILE* 4.2 22.7 - - + -
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Residues in contact with ALA 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A TYR* 4.8 0.2 - - - -
267A GLU* 5.2 1.6 - - - +
533A MET* 3.0 12.6 + - + +
534A GLU* 3.6 14.6 - - - +
535A PRO 3.3 0.2 - - - -
536A PHE* 1.3 79.4 - - - +
538A ILE* 1.3 57.3 + - - +
540A THR* 3.9 1.9 + - - -
541A ASN* 2.8 31.4 + - - +
558A TYR* 3.9 35.3 - - + +
561A THR* 5.6 4.3 - - - -
562A ILE* 4.2 18.3 - - + +
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Residues in contact with ILE 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A TYR* 3.9 13.4 - - + +
211A ASP* 3.7 29.6 - - - +
212A TYR* 3.7 37.0 - - + -
241A ARG* 3.6 33.9 - - - -
242A VAL* 3.7 15.7 - - + +
534A GLU* 3.0 19.8 + - + +
535A PRO* 3.9 0.7 - - + +
537A ALA* 1.3 76.2 - - - +
539A ALA* 1.3 60.5 + - - +
541A ASN* 3.4 4.0 + - - +
542A ARG* 3.0 30.7 + - + +
562A ILE* 4.2 7.2 - - + -
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Residues in contact with ALA 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A TYR* 3.4 13.6 + - - +
535A PRO 3.1 20.2 + - - +
536A PHE* 3.3 8.7 + - - +
538A ILE* 1.3 75.7 - - - +
540A THR* 1.3 55.3 + - - +
542A ARG* 3.4 1.2 + - - +
543A HIS* 3.0 30.0 + - - +
674A TRP* 3.4 26.9 - - + +
677A GLU* 4.0 7.6 - - - +
678A ALA* 4.1 17.3 - - + -
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Residues in contact with THR 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 PHE 2.8 11.5 + - - -
537A ALA 3.9 1.8 - - - -
539A ALA* 1.3 75.2 - - - +
541A ASN* 1.3 57.0 + - - +
544A LEU* 3.2 39.9 + - + +
550A ILE 4.9 1.8 - - - +
551A TYR* 3.8 28.4 - - + +
554A LEU* 4.6 1.3 - - + +
555A TYR* 4.4 3.8 - - + -
558A TYR* 3.0 39.0 + - + -
674A TRP* 2.8 25.2 + - - -
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Residues in contact with ASN 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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192A PHE* 4.5 4.7 - - - -
195A LEU* 3.3 29.3 - - - +
210A TYR* 3.5 46.5 + - + -
267A GLU* 4.3 3.8 - - - +
537A ALA 2.8 18.5 - - - +
538A ILE 3.4 4.5 + - - +
539A ALA 3.3 0.2 - - - -
540A THR* 1.3 79.3 - - - +
542A ARG* 1.3 60.8 + - - +
543A HIS 3.5 0.2 - - - -
544A LEU 4.9 1.4 - - - +
551A TYR* 4.5 7.8 + - - -
555A TYR* 2.8 45.9 + - - -
558A TYR* 4.9 1.0 - - - -
562A ILE* 5.4 0.2 - - - +
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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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192A PHE* 3.9 9.3 - - - -
195A LEU* 4.6 4.0 - - - -
196A ARG* 2.8 88.6 + - + +
197A GLY 5.1 0.4 + - - -
199A GLY 5.5 0.2 - - - +
210A TYR* 2.8 22.6 + - + +
211A ASP* 3.0 32.8 + - - +
212A TYR* 3.9 11.3 - - - -
538A ILE* 3.0 26.6 + - + +
539A ALA 3.4 1.1 + - - +
541A ASN* 1.3 79.0 - - - +
543A HIS* 1.3 64.9 + - + +
544A LEU 4.0 0.2 - - - -
677A GLU* 3.2 34.1 + - - +
681A LYS* 4.1 12.9 - - - +
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Residues in contact with HIS 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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192A PHE* 3.4 11.6 - - - -
196A ARG* 3.5 32.0 + - - -
539A ALA 3.0 12.6 + - - +
542A ARG* 1.3 81.2 - - + +
544A LEU* 1.3 58.9 + - - +
670A GLU* 3.2 26.9 - - - +
673A ALA* 3.4 32.5 + - + +
674A TRP* 3.5 19.3 - - - +
677A GLU* 3.2 38.5 + - + +
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Residues in contact with LEU 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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192A PHE* 3.2 6.4 - - - -
540A THR* 3.2 25.4 + - + +
541A ASN 4.9 1.2 - - - +
543A HIS* 1.3 74.8 - - - +
545A SER* 1.3 65.7 + - - +
548A HIS* 3.8 16.4 - - + +
550A ILE* 3.8 35.9 - - + +
551A TYR* 3.5 18.1 - - + +
670A GLU* 3.2 36.1 - - + +
671A LEU* 4.1 5.6 - - - -
674A TRP* 3.3 40.8 - - + +
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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
------------------------------------------------------------
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