Contacts of the helix formed by residues 560 - 572 (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 ASP 560 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267A GLU* 4.2 1.6 - - - -
269A PHE* 3.2 45.1 + - + +
271A HIS* 5.7 4.5 - - - -
279A THR* 5.8 3.1 - - - -
558A TYR 3.3 1.8 + - - -
559A ARG* 1.3 78.3 - - + +
561A THR* 1.3 57.5 + - - +
562A ILE 3.6 1.6 - - - +
563A ASN* 2.9 33.3 - - - +
564A ILE* 2.9 35.2 + - - +
862A ILE 4.0 2.2 - - - -
863A SER* 4.0 20.0 - - - +
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Residues in contact with THR 561 (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 HIS 4.3 7.9 - - - +
533A MET* 4.5 11.7 - - + +
534A GLU* 4.8 6.1 - - + +
537A ALA* 5.6 3.1 - - + -
557A HIS 4.2 1.6 + - - -
558A TYR* 3.5 24.7 + - - -
559A ARG 3.4 0.5 + - - -
560A ASP* 1.3 70.8 - - - +
562A ILE* 1.3 68.1 + - - +
563A ASN 3.1 1.1 - - - -
564A ILE* 3.6 1.1 - - - -
565A ASN* 2.9 48.7 + - - +
862A ILE* 3.0 46.2 + - + +
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Residues in contact with ILE 562 (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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210A TYR* 4.3 15.9 - - + -
242A VAL* 4.1 13.7 - - + -
263A VAL* 3.7 28.2 - - + +
264A PRO* 3.9 12.6 - - + -
267A GLU* 3.6 32.7 + - + +
534A GLU* 3.6 28.1 - - + +
537A ALA* 4.2 20.6 - - + +
538A ILE* 4.2 19.3 - - + +
561A THR* 1.3 79.0 - - - +
563A ASN* 1.3 58.4 + - - +
565A ASN* 3.7 1.6 - - - +
566A GLY* 3.0 23.6 + - - -
569A ARG* 5.2 0.7 + - - -
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Residues in contact with ASN 563 (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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261A VAL* 6.3 0.6 - - - +
263A VAL* 4.1 19.8 - - + +
267A GLU 3.2 23.4 + - - +
268A ASN* 3.2 25.3 + - - +
269A PHE 4.1 1.4 + - - +
279A THR* 4.8 17.5 + - - +
560A ASP* 2.9 31.7 + - - +
561A THR 3.1 1.0 - - - -
562A ILE* 1.3 78.1 - - - +
564A ILE* 1.3 62.7 + - - +
566A GLY* 3.4 2.1 + - - -
567A LEU* 3.4 18.5 + - - +
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Residues in contact with ILE 564 (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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279A THR* 4.9 13.5 - - - +
282A ILE* 5.1 10.5 - - + -
530A HIS* 3.3 33.9 - - + +
560A ASP* 2.9 22.5 + - - +
561A THR* 3.5 11.9 - - - +
563A ASN* 1.3 72.9 - - - +
565A ASN* 1.3 58.1 + - - +
567A LEU* 3.3 6.8 + - + +
568A ALA* 2.8 31.6 + - + +
572A LEU* 6.0 2.9 - - + -
780A LEU* 5.6 0.7 - - + -
862A ILE 3.2 23.3 - - - +
863A SER 3.7 5.2 - - - +
864A ILE* 3.6 41.5 - - + +
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Residues in contact with ASN 565 (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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215A TYR* 5.3 0.4 + - - +
526A TRP* 3.7 13.9 - - + -
530A HIS* 2.9 56.3 + - - +
531A ALA* 4.4 1.8 - - - +
534A GLU* 2.9 35.0 + - - +
561A THR* 2.9 23.7 + - - +
562A ILE 3.7 2.5 - - - +
564A ILE* 1.3 76.5 - - - +
566A GLY* 1.3 49.9 + - - +
568A ALA* 3.2 7.1 + - - +
569A ARG* 2.8 41.2 + - + +
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Residues in contact with GLY 566 (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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261A VAL* 3.4 26.3 - - - +
263A VAL* 4.6 4.5 - - - -
562A ILE 3.0 16.9 + - - -
563A ASN 3.9 1.8 - - - -
564A ILE 3.3 0.8 - - - -
565A ASN* 1.3 74.1 - - - +
567A LEU* 1.3 59.2 + - - +
569A ARG* 3.2 25.4 + - - +
570A GLN 3.0 17.0 + - - -
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Residues in contact with LEU 567 (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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261A VAL* 4.1 3.9 - - - +
279A THR* 3.3 26.7 - - - +
282A ILE* 3.5 36.6 - - + -
283A LYS* 3.3 35.2 - - + -
563A ASN* 3.4 9.3 + - - +
564A ILE* 3.3 12.2 + - + +
566A GLY* 1.3 68.8 - - - +
568A ALA* 1.3 63.6 + - - +
570A GLN* 2.9 16.2 + - - +
571A SER* 2.7 52.3 + - - +
572A LEU* 4.4 6.3 - - + -
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Residues in contact with ALA 568 (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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526A TRP* 3.8 26.0 - - + -
564A ILE* 2.8 18.2 + - + +
565A ASN 3.3 9.9 - - - +
567A LEU* 1.3 72.4 - - - +
569A ARG* 1.3 61.4 + - - +
572A LEU* 3.1 35.4 + - + -
573A ILE* 2.8 31.9 + - + -
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Residues in contact with ARG 569 (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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215A TYR* 4.2 22.4 - - + -
217A ASP* 2.8 54.0 + - - +
218A LEU* 3.9 18.5 - - + +
241A ARG* 3.3 41.7 - - - +
242A VAL* 3.7 26.7 + - - +
244A THR* 3.8 10.5 - - - +
246A ARG* 4.0 6.1 - - - +
261A VAL* 4.3 5.7 - - + +
262A TYR 4.0 9.5 + - - -
263A VAL* 5.1 1.0 - - - +
526A TRP* 5.3 2.5 - - + -
534A GLU* 4.7 6.5 + - - -
562A ILE 5.2 0.4 + - - -
565A ASN* 2.8 19.0 + - + +
566A GLY* 3.2 28.9 + - - +
568A ALA* 1.3 71.1 - - - +
570A GLN* 1.3 58.2 + - - +
573A ILE* 4.3 4.2 - - + +
574A ASN* 3.6 16.8 - - - +
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Residues in contact with GLN 570 (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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259A GLY 3.4 9.3 - - - +
260A GLU* 3.3 20.0 - - - +
261A VAL* 3.2 41.2 + - + +
283A LYS* 4.0 13.1 - - - +
566A GLY 3.0 11.3 + - - +
567A LEU* 2.9 29.5 + - - +
569A ARG* 1.3 77.5 - - - +
571A SER* 1.4 63.2 + - - +
574A ASN* 3.2 20.7 + - - +
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Residues in contact with SER 571 (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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282A ILE* 5.0 6.1 - - - -
283A LYS* 4.2 7.0 - - - +
286A SER* 4.0 22.1 + - - -
567A LEU* 2.7 39.2 + - - +
570A GLN* 1.4 82.7 + - - +
572A LEU* 1.3 56.8 + - - +
574A ASN* 3.0 13.7 - - - +
577A GLY* 4.2 1.9 - - - -
578A ILE* 3.9 20.3 + - - +
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Residues in contact with LEU 572 (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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282A ILE* 3.7 31.0 - - + -
526A TRP* 6.1 0.9 - - + -
564A ILE* 5.6 2.9 - - + +
567A LEU* 3.9 6.0 + - + -
568A ALA* 3.1 28.8 + - + +
571A SER* 1.3 76.6 - - - +
573A ILE* 1.4 63.2 + - + +
574A ASN* 3.5 6.5 + - - +
577A GLY* 4.1 1.7 - - - -
578A ILE* 3.6 19.6 + - + -
579A ILE* 3.0 42.7 + - + +
580A GLU* 4.6 1.0 + - - +
776A VAL* 3.9 21.8 - - + -
780A LEU* 4.8 20.6 - - + -
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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