Contacts of the helix formed by residues 362 - 373 (chain P) in PDB entry 5X22
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 SER 362 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361P LEU* 1.3 76.5 - - - +
363P GLU* 1.3 65.2 + - - +
364P ARG* 3.9 6.7 + - - +
365P GLU* 3.0 30.5 + - - +
366P ALA* 3.1 18.9 + - - +
403P LYS* 5.5 2.8 + - - -
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Residues in contact with GLU 363 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361P LEU 3.9 0.6 + - - -
362P SER* 1.3 74.5 - - - +
364P ARG* 1.3 56.8 + - - +
366P ALA* 4.0 5.3 - - - +
367P MET* 2.9 34.0 + - - +
390P PHE* 5.4 0.2 - - - -
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Residues in contact with ARG 364 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362P SER* 3.2 8.2 + - - +
363P GLU* 1.3 79.5 - - - +
365P GLU* 1.3 58.9 + - - +
368P VAL* 2.9 31.4 + - - +
390P PHE* 3.5 46.0 + - + -
392P VAL* 4.6 16.7 - - - +
396P ARG* 3.1 32.6 - - - +
400P ILE* 3.9 31.0 - - + +
403P LYS* 5.3 5.1 - - - +
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Residues in contact with GLU 365 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361P LEU* 3.4 23.6 - - + +
362P SER* 3.0 41.4 + - - +
364P ARG* 1.3 76.5 - - - +
366P ALA* 1.3 60.7 + - - +
368P VAL* 3.2 9.7 + - - +
369P LEU* 2.9 32.7 + - - +
400P ILE* 4.0 9.6 - - + +
403P LYS* 3.6 23.4 - - - +
404P ALA* 3.5 30.9 - - + +
407P LYS* 3.7 20.6 + - - +
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Residues in contact with ALA 366 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358P LEU* 3.7 35.9 - - + +
361P LEU* 4.4 11.2 - - + +
362P SER 3.1 18.5 + - - +
363P GLU* 4.0 4.9 - - - +
365P GLU* 1.3 78.0 - - - +
367P MET* 1.3 57.7 + - - +
369P LEU* 3.4 3.0 + - - +
370P LYS* 2.9 41.0 + - - +
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Residues in contact with MET 367 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363P GLU 2.9 20.2 + - - +
366P ALA* 1.3 74.0 - - - +
368P VAL* 1.3 59.8 + - - +
370P LYS* 3.8 7.1 - - - +
371P LEU* 2.9 53.6 + - + +
376P ILE* 3.8 40.4 - - + -
389P PHE* 5.1 11.2 - - + -
390P PHE* 3.7 22.7 - - + -
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Residues in contact with VAL 368 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364P ARG 2.9 23.7 + - - +
365P GLU* 3.2 8.9 + - - +
367P MET* 1.3 77.3 - - - +
369P LEU* 1.3 61.0 + - + +
371P LEU* 3.8 1.0 - - - +
372P ARG* 2.9 35.5 + - + +
383P LEU* 6.4 0.2 - - + -
386P VAL* 3.8 8.2 - - + +
390P PHE* 3.7 9.6 - - + -
397P ILE* 3.7 35.0 - - + +
400P ILE* 3.8 12.3 - - + -
401P GLU* 3.8 39.0 - - + +
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Residues in contact with LEU 369 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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773M LEU* 4.1 22.8 - - + +
358P LEU* 4.6 8.5 - - + -
361P LEU* 4.8 0.4 - - + -
365P GLU 2.9 12.1 + - - +
366P ALA 3.9 4.0 - - - +
368P VAL* 1.3 83.4 - - + +
370P LYS* 1.3 60.8 + - + +
372P ARG* 4.4 3.6 - - + -
373P LYS* 2.9 39.0 + - - +
375P LEU* 4.6 0.9 - - - +
401P GLU* 3.7 22.4 - - + +
404P ALA* 3.6 30.3 - - + -
405P LEU* 4.3 17.7 - - + +
408P LEU* 3.6 31.6 - - + -
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Residues in contact with LYS 370 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355P GLU* 3.0 34.1 + - - -
358P LEU* 3.7 29.2 - - + -
366P ALA* 2.9 26.8 + - - +
367P MET* 3.8 10.1 - - - +
369P LEU* 1.3 76.3 - - - +
371P LEU* 1.3 57.2 + - - +
374P GLY* 3.0 6.1 + - - -
375P LEU* 2.8 48.6 + - + -
376P ILE* 3.6 35.4 + - + +
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Residues in contact with LEU 371 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367P MET* 2.9 40.8 + - + +
368P VAL 4.0 2.7 - - - +
370P LYS* 1.3 77.0 - - - +
372P ARG* 1.3 60.8 + - - +
373P LYS 3.4 0.2 - - - -
374P GLY* 3.7 2.2 + - - -
376P ILE* 3.7 30.7 - - + -
379P ARG 3.7 0.3 - - - +
380P GLU* 3.6 3.3 - - - -
381P HIS* 2.9 58.2 + - + +
386P VAL* 4.2 28.7 - - + -
389P PHE* 4.2 22.2 - - + -
390P PHE* 4.4 0.9 - - + -
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Residues in contact with ARG 372 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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772M ARG* 5.6 0.2 + - - -
368P VAL* 2.9 29.0 + - + +
369P LEU* 4.0 6.1 - - + +
371P LEU* 1.3 79.6 - - - +
373P LYS* 1.3 74.1 + - - +
374P GLY 3.5 0.2 - - - -
380P GLU* 3.0 21.2 - - - +
381P HIS 3.0 24.6 + - - -
382P THR* 3.4 5.1 - - - +
383P LEU* 3.1 44.9 - - + +
386P VAL* 4.2 14.4 - - + -
401P GLU* 2.9 30.1 + - + +
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Residues in contact with LYS 373 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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769M PRO* 3.4 22.8 - - - +
772M ARG* 4.1 30.1 - - + +
773M LEU* 3.9 22.2 - - + +
776M SER* 2.6 37.9 + - - +
65N ARG* 5.0 0.9 + - - -
369P LEU* 2.9 22.5 + - - +
372P ARG* 1.3 93.5 - - + +
374P GLY* 1.3 62.7 + - - +
375P LEU* 3.4 17.5 - - + -
380P GLU* 3.9 13.7 - - - +
401P GLU* 5.8 2.5 + - - -
405P LEU* 5.1 4.4 - - - +
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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