Contacts of the helix formed by residues 440 - 457 (chain A) in PDB entry 2X96
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 VAL 440 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228A TYR* 3.7 15.7 + - + -
231A ILE* 4.1 11.9 - - + -
264A ALA 4.2 1.5 - - - +
265A GLN 3.6 13.0 - - - +
266A GLN* 4.1 0.2 - - - -
267A TRP* 3.3 68.0 - - + +
435A ALA 3.1 9.9 + - - +
436A LEU* 3.5 22.0 - - - +
439A ILE* 1.3 77.1 - - - +
441A PHE* 1.3 60.3 + - - +
443A PRO* 3.4 15.2 - - - +
444A PHE* 4.1 6.6 + - - +
477A SER* 5.0 0.7 + - - -
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Residues in contact with PHE 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A GLN* 3.3 24.7 - - + +
266A GLN* 4.3 7.4 - - + -
437A ASP 3.3 21.3 + - - +
438A LYS 4.0 1.1 - - - +
439A ILE 3.1 0.8 - - - -
440A VAL* 1.3 78.1 - - - +
442A LEU* 1.3 60.1 + - + +
443A PRO 3.6 0.2 - - - -
444A PHE* 3.2 13.0 + + - +
445A ALA* 2.9 37.4 + - + -
504A TYR* 3.4 32.3 - + - -
507A TYR* 3.6 32.8 - - + -
511A PHE* 3.4 39.5 - + + -
1615A RX3 3.6 22.4 - + + -
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Residues in contact with LEU 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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221A PHE* 4.2 11.9 - - + -
224A ILE* 3.8 35.4 - - + -
438A LYS 3.4 16.2 - - - +
439A ILE* 3.0 11.7 + - - +
441A PHE* 1.3 77.7 - - + +
443A PRO* 1.4 70.1 - - + +
445A ALA* 3.4 0.7 + - - +
446A PHE* 3.1 23.4 + - - +
508A LEU* 3.8 28.7 - - + +
511A PHE* 3.6 35.2 - - + -
512A ILE* 4.7 7.2 - - + -
582A ILE* 4.2 13.2 - - + -
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Residues in contact with PRO 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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221A PHE* 3.7 25.5 - - + -
228A TYR* 3.8 33.7 - - + -
439A ILE 3.4 7.6 - - - +
440A VAL 3.4 13.7 - - - +
442A LEU* 1.4 93.6 - - + +
444A PHE* 1.3 61.8 + - - +
446A PHE* 3.3 4.4 + - + +
447A THR* 3.1 28.3 + - - +
476A TYR* 3.4 24.2 - - + +
477A SER* 3.5 9.4 - - - +
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Residues in contact with PHE 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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263A TRP* 3.5 27.1 - - + -
264A ALA 4.9 1.1 - - - +
265A GLN* 3.5 41.3 - - + -
440A VAL 4.3 4.7 - - - +
441A PHE* 3.2 21.0 + + - +
443A PRO* 1.3 81.4 - - - +
445A ALA* 1.3 65.4 + - - +
447A THR* 2.6 23.5 + - - -
448A MET* 3.2 38.5 + - + +
473A ARG* 3.3 32.1 - - - +
477A SER* 3.5 2.3 + - - +
495A LYS* 4.0 8.7 - - + -
504A TYR* 3.3 30.5 - + - -
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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 PHE* 2.9 42.7 + - + +
442A LEU 3.9 3.6 - - - +
444A PHE* 1.3 69.8 - - - +
446A PHE* 1.3 67.7 + - - +
448A MET* 3.4 14.2 + - - +
449A ASP* 3.8 5.5 + - - +
504A TYR* 3.7 29.4 - - + +
505A LEU* 5.1 1.2 + - - +
508A LEU* 4.0 23.0 - - + +
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Residues in contact with PHE 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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214A GLU* 4.6 2.2 - - - -
217A LEU* 4.0 22.9 - - + -
218A GLU* 3.8 25.6 - - + -
221A PHE* 3.9 38.8 - + + -
442A LEU 3.1 17.6 + - - +
443A PRO* 3.7 6.7 - - + +
445A ALA* 1.3 76.3 - - - +
447A THR* 1.3 58.8 + - + +
449A ASP* 3.4 2.3 + - - +
450A LYS* 2.9 61.0 + - + +
453A TRP* 4.3 11.7 - + - -
476A TYR* 4.9 2.7 - + + -
505A LEU* 4.2 16.8 - - + -
508A LEU* 3.4 25.9 - - + +
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Residues in contact with THR 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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443A PRO 3.1 12.2 + - - +
444A PHE 2.6 19.1 + - - -
446A PHE* 1.3 75.5 - - - +
448A MET* 1.3 72.1 + - - +
450A LYS* 4.1 7.0 - - + -
451A TYR* 2.9 27.2 + - - +
469A PHE* 5.5 0.3 - - - -
472A LEU* 3.6 27.2 - - + +
473A ARG* 3.1 24.3 + - - +
476A TYR* 3.5 35.0 - - + -
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Residues in contact with MET 448 (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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444A PHE* 3.2 48.8 + - + +
445A ALA 3.7 7.2 - - - +
446A PHE 3.3 0.4 - - - -
447A THR* 1.3 93.9 + - - +
449A ASP* 1.3 59.9 + - - +
451A TYR* 3.8 4.2 - - - +
452A ARG* 3.4 32.1 + - - +
469A PHE* 3.7 25.4 - - + -
473A ARG* 3.8 7.6 - - - -
495A LYS* 4.1 11.7 - - - -
498A ILE* 3.9 25.7 - - + +
504A TYR* 3.7 34.8 - - + -
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Residues in contact with ASP 449 (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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204A TRP* 3.8 11.7 - - - -
445A ALA 3.8 2.3 + - - +
446A PHE 3.4 5.3 + - - +
448A MET* 1.3 76.2 - - - +
450A LYS* 1.3 56.3 + - - +
451A TYR 3.1 1.6 - - - -
452A ARG* 2.7 35.2 + - - +
453A TRP* 2.7 60.1 + - + +
503A GLU* 3.4 10.4 - - - +
504A TYR* 3.1 12.6 + - - +
505A LEU* 2.8 37.0 + - + +
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Residues in contact with LYS 450 (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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218A GLU* 2.6 30.0 + - - -
446A PHE* 2.9 57.4 + - + +
447A THR* 4.0 6.3 - - - +
449A ASP* 1.3 75.4 - - - +
451A TYR* 1.3 61.9 + - - +
453A TRP* 3.8 17.9 - - + +
454A SER* 3.1 24.6 + - - -
472A LEU* 4.2 14.8 - - + +
476A TYR* 3.2 44.3 + - + +
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Residues in contact with TYR 451 (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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181A PHE* 5.0 3.1 - + - -
447A THR 2.9 19.1 + - - +
448A MET* 3.8 3.8 - - - +
450A LYS* 1.3 77.5 - - - +
452A ARG* 1.3 74.7 + - + +
454A SER* 2.7 23.7 + - - -
455A LEU* 3.2 39.2 + - + +
465A TRP 2.7 30.8 + - - -
466A ASN* 4.6 0.2 - - - -
468A ALA* 4.0 7.6 - - + -
469A PHE* 3.4 47.0 - + + +
472A LEU* 3.6 14.5 - - + +
490A PHE* 3.5 21.0 - - - -
492A ALA* 3.4 24.0 - - + +
498A ILE* 4.8 2.0 - - + -
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Residues in contact with ARG 452 (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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181A PHE* 4.6 14.4 - - + -
184A TYR* 4.6 7.5 + - - -
204A TRP* 3.4 31.4 - - + -
448A MET* 3.4 12.9 + - - +
449A ASP* 2.7 28.8 + - - +
451A TYR* 1.3 88.9 - - + +
453A TRP* 1.3 61.8 + - - +
455A LEU* 3.2 6.6 + - - +
456A PHE* 2.8 43.2 + - + -
497A HIS* 3.2 20.4 + - - +
498A ILE* 3.8 27.3 + - + +
501A ASP* 4.4 3.8 - - - +
502A VAL 2.9 33.7 + - - +
503A GLU 3.8 0.6 - - - -
504A TYR* 3.2 17.6 - - - +
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Residues in contact with TRP 453 (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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201A ALA* 3.5 37.8 + - + +
204A TRP* 3.9 22.9 - + - +
205A LEU* 3.9 13.4 - - + +
214A GLU* 3.9 28.3 - - + -
217A LEU* 5.5 0.2 - - + -
218A GLU* 6.0 0.4 - - - -
446A PHE* 4.3 17.7 - + - -
449A ASP* 2.7 41.0 + - + +
450A LYS* 3.8 20.6 - - + +
452A ARG* 1.3 73.2 - - - +
454A SER* 1.3 55.6 + - - +
456A PHE* 3.2 2.0 + + - +
457A ARG* 2.8 58.2 + - - +
505A LEU* 3.7 43.3 - - + -
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Residues in contact with SER 454 (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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450A LYS 3.1 12.4 + - - -
451A TYR* 2.7 24.5 + - - -
453A TRP* 1.3 78.2 - - - +
455A LEU* 1.3 60.8 + - - +
458A GLY 3.3 2.3 + - - -
459A GLU* 2.9 51.7 + - - +
460A VAL* 3.5 24.1 + - - +
468A ALA* 5.5 0.3 - - - +
472A LEU* 5.0 4.3 - - - +
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Residues in contact with LEU 455 (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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181A PHE* 3.7 31.4 - - + -
185A VAL* 4.0 18.3 - - + +
451A TYR* 3.2 48.7 + - + +
452A ARG* 3.2 6.9 + - + +
454A SER* 1.3 78.0 + - - +
456A PHE* 1.3 66.8 + - + +
458A GLY* 3.1 13.9 + - - -
460A VAL* 4.0 14.1 - - + +
465A TRP* 3.5 54.4 - - + +
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Residues in contact with PHE 456 (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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181A PHE* 5.9 0.7 - + - -
184A TYR* 3.5 33.2 - + - -
185A VAL* 4.4 17.9 - - + -
188A ASN* 3.7 33.0 - - + -
189A THR* 3.8 21.8 + - - +
199A SER* 3.3 15.9 - - - +
200A GLY* 3.6 7.9 - - - +
201A ALA* 3.4 32.5 - - - +
204A TRP* 3.5 36.6 - + - -
452A ARG* 2.8 34.3 + - + +
453A TRP* 3.5 4.5 - - - +
455A LEU* 1.3 74.6 - - + +
457A ARG* 1.3 60.2 + - - +
458A GLY* 3.3 1.2 + - - -
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Residues in contact with ARG 457 (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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198A THR* 5.8 4.9 - - + -
199A SER* 3.3 19.3 - - - +
201A ALA* 3.5 10.5 - - + +
202A GLU* 2.9 27.2 + - - +
205A LEU* 3.7 13.5 - - - +
214A GLU* 2.9 38.2 + - - -
453A TRP* 2.8 41.9 + - - +
454A SER 4.2 0.2 - - - +
456A PHE* 1.3 71.6 - - - +
458A GLY* 1.3 62.0 + - - +
459A GLU* 3.5 36.7 + - + +
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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
------------------------------------------------------------
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