Contacts of the helix formed by residues 434 - 447 (chain A) in PDB entry 1IK2
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 ARG 434 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265A THR* 4.8 12.1 + - - +
267A LEU* 5.8 2.6 - - - +
268A LEU* 5.3 6.4 - - - +
429A LYS* 3.4 36.4 - - + +
430A ALA 2.9 12.5 + - - -
432A TYR 2.8 4.9 + - - -
433A GLU* 1.3 75.4 - - - +
435A MET* 1.3 50.6 + - - +
436A PHE 2.9 1.5 + - - -
437A ASN* 2.7 64.3 + - + +
438A TRP 3.0 1.8 + - - -
621A PHE* 6.0 2.0 - - + -
627A ALA* 4.8 10.3 - - + +
631A ILE* 2.9 51.9 + - - +
632A GLU* 4.5 13.7 + - - +
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Residues in contact with MET 435 (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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230A PHE* 4.8 21.5 - - + -
283A TYR* 6.4 1.8 - - - -
352A LEU* 4.4 30.1 - - + -
353A THR* 5.2 3.8 - - - +
388A MET* 6.2 1.3 - - + -
428A ALA 4.1 20.6 - - - +
429A LYS* 4.2 11.5 - - + +
430A ALA* 4.6 4.1 - - + +
432A TYR* 2.7 29.0 + - + +
434A ARG* 1.3 66.2 - - - +
436A PHE* 1.3 64.0 + - - +
438A TRP* 3.2 18.3 - - + +
439A MET* 3.2 31.1 + - + +
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Residues in contact with PHE 436 (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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227A LEU* 3.8 26.5 - - + -
230A PHE* 3.7 27.6 - - + +
231A GLY* 3.7 16.8 - - - -
244A PHE* 3.6 24.2 - + + -
265A THR* 3.8 31.4 - - + -
268A LEU* 4.0 25.4 - - + -
283A TYR* 4.9 3.8 - - + +
429A LYS* 4.0 18.0 - - - +
434A ARG 2.9 2.6 + - - -
435A MET* 1.3 78.2 - - - +
437A ASN* 1.3 69.8 + - + +
439A MET* 3.0 27.2 + - + +
440A VAL* 3.3 21.6 + - + +
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Residues in contact with ASN 437 (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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264A GLU* 5.5 0.9 - - - -
265A THR* 3.3 28.7 + - - +
429A LYS* 5.2 0.4 - - - +
433A GLU 5.3 0.8 + - - -
434A ARG* 2.7 48.9 + - + +
436A PHE* 1.3 81.9 - - + +
438A TRP* 1.4 50.4 + - - +
440A VAL* 3.0 11.2 + - - +
441A THR* 2.7 55.1 + - - -
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Residues in contact with TRP 438 (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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341A PHE* 3.9 22.2 - + - -
345A GLU* 4.0 34.8 - - + -
352A LEU* 4.8 10.1 - - + -
432A TYR* 3.8 30.1 - + + +
433A GLU* 3.2 52.4 + - + +
434A ARG 3.0 5.1 + - - -
435A MET* 3.2 28.9 - - + +
437A ASN* 1.4 75.4 - - - +
439A MET* 1.3 85.8 + - + +
441A THR* 2.9 17.9 + - - -
442A ARG* 2.9 41.5 + - + +
617A LEU* 5.0 16.2 - - + +
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Residues in contact with MET 439 (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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226A ALA 4.6 2.7 - - - +
227A LEU* 5.3 4.5 - - + -
230A PHE* 3.6 51.8 - - + -
336A PHE* 3.5 35.0 - - + -
341A PHE* 4.7 5.4 - - + -
345A GLU 5.7 1.3 - - - +
435A MET* 3.3 19.3 - - + +
436A PHE* 3.0 14.1 + - + +
438A TRP* 1.3 106.7 - - + +
440A VAL* 1.3 64.5 + - + +
442A ARG* 3.4 3.3 + - - +
443A ILE* 3.1 30.1 + - + +
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Residues in contact with VAL 440 (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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227A LEU* 3.8 22.2 - - + +
263A ILE* 4.0 30.3 - - + +
265A THR* 4.2 9.6 - - - +
436A PHE* 3.5 42.4 - - + +
437A ASN* 3.2 9.2 - - - +
439A MET* 1.3 75.5 - - - +
441A THR* 1.3 52.0 + - - +
443A ILE* 2.9 11.9 + - + +
444A ASN* 2.7 50.2 + - - +
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Residues in contact with THR 441 (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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433A GLU* 5.4 7.1 + - + +
437A ASN* 2.7 35.4 + - - -
438A TRP* 2.9 11.1 + - - -
440A VAL* 1.3 73.5 - - - +
442A ARG* 1.3 59.2 + - + +
444A ASN* 3.3 14.2 + - + +
445A ALA* 3.1 24.6 + - - +
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Residues in contact with ARG 442 (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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340A GLY 3.4 24.9 + - - -
341A PHE* 3.7 28.2 - - + -
342A THR* 5.0 2.2 - - - +
345A GLU* 3.8 23.4 + - - -
433A GLU* 4.8 9.0 - - - +
438A TRP* 2.9 44.3 + - + +
439A MET 3.9 1.6 - - - +
441A THR* 1.3 74.3 - - - +
443A ILE* 1.3 64.5 + - - +
445A ALA* 3.4 14.5 - - - +
446A THR* 3.3 21.1 + - - +
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Residues in contact with ILE 443 (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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223A ALA* 3.8 23.3 - - + -
226A ALA* 3.5 31.4 - - + -
227A LEU* 3.7 17.3 - - + -
263A ILE* 6.0 2.5 - - + -
336A PHE* 4.6 4.0 - - + -
339A LEU* 3.8 25.4 - - + -
341A PHE* 5.0 7.0 - - + -
439A MET 3.1 17.5 + - - +
440A VAL* 2.9 10.4 + - + +
442A ARG* 1.3 78.2 - - - +
444A ASN* 1.3 54.8 + - - +
445A ALA 3.1 0.2 - - - -
446A THR* 3.2 12.1 + - - +
447A LEU* 3.0 47.4 + - + +
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Residues in contact with ASN 444 (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 ALA 4.2 3.7 - - - +
262A ASP* 3.0 21.6 + - + +
263A ILE* 2.8 47.2 + - - +
440A VAL* 2.7 33.2 + - - +
441A THR* 3.3 15.3 + - + +
443A ILE* 1.3 72.6 - - - +
445A ALA* 1.3 63.3 + - - +
447A LEU* 3.4 17.3 + - - +
448A GLU* 3.6 11.4 + - - +
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Residues in contact with ALA 445 (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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441A THR 3.1 12.2 + - - +
442A ARG* 3.4 22.9 - - - +
444A ASN* 1.3 76.1 - - - +
446A THR* 1.3 58.4 + - - +
447A LEU 3.0 0.2 - - - -
448A GLU* 3.0 29.5 + - - +
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Residues in contact with THR 446 (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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216A LEU* 5.1 1.0 - - - +
219A GLN* 3.1 42.9 + - - +
339A LEU* 3.0 31.8 + - + +
340A GLY* 5.0 1.7 - - - -
442A ARG 3.3 10.0 + - - +
443A ILE* 3.2 19.5 - - - +
445A ALA* 1.3 78.3 - - - +
447A LEU* 1.3 61.3 + - + +
448A GLU 3.2 8.8 + - - +
449A THR* 5.2 2.4 - - - +
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Residues in contact with LEU 447 (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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216A LEU* 3.5 18.8 - - + +
219A GLN* 4.0 25.8 - - + +
220A ILE* 3.7 28.5 - - + -
223A ALA* 5.3 1.1 - - + -
260A SER* 3.3 19.9 - - - -
261A ALA* 3.4 30.2 + - + +
262A ASP 4.9 0.4 - - - +
263A ILE* 5.1 12.1 - - + -
339A LEU* 4.7 0.4 - - + -
443A ILE* 3.0 41.3 + - + +
444A ASN* 3.6 12.1 - - - +
445A ALA 3.0 0.6 - - - -
446A THR* 1.3 86.6 - - + +
448A GLU* 1.3 59.0 + - - +
449A THR* 5.0 0.2 - - - -
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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