Contacts of the helix formed by residues 368 - 383 (chain B) in PDB entry 3K5N
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 GLY 368 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B LEU* 3.1 17.3 - - - +
365B ARG* 4.5 8.5 - - - +
367B GLY* 1.3 72.5 - - - -
369B SER* 1.3 65.5 + - - +
370B VAL 3.3 1.8 - - - -
371B ALA* 3.7 16.6 - - - -
372B ALA* 3.0 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 369 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B GLY 3.5 4.4 + - - -
368B GLY* 1.3 73.3 - - - +
370B VAL* 1.3 68.7 + - - +
372B ALA* 3.1 5.9 + - - +
373B PHE* 2.9 23.2 + - - +
498B ALA* 4.8 15.8 - - - +
499B PHE* 6.0 0.3 - - - -
502B VAL* 3.9 19.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 370 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B GLY* 4.3 0.2 - - - -
369B SER* 1.3 78.1 - - - +
371B ALA* 1.3 65.9 + - - +
373B PHE* 3.2 2.6 + - - +
374B GLY* 2.9 21.3 + - - -
502B VAL* 4.2 16.8 - - + +
505B THR* 4.6 7.4 - - - +
507B ALA* 3.7 31.0 - - + +
508B CYS* 3.9 29.4 - - + -
509B ARG* 5.4 2.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 371 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B MET* 5.6 0.5 - - - +
361B LEU* 4.2 10.0 - - + +
365B ARG* 3.4 29.8 - - - +
368B GLY* 3.4 16.0 - - - +
370B VAL* 1.3 83.8 - - - +
372B ALA* 1.3 55.7 + - - +
374B GLY* 3.6 2.4 + - - -
375B HIS* 3.2 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 372 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B ASN* 3.6 39.7 - - + +
361B LEU* 4.0 5.6 - - + -
368B GLY 3.0 15.9 + - - +
369B SER* 3.6 5.4 - - - +
371B ALA* 1.3 74.3 - - - +
373B PHE* 1.3 71.1 + - - +
374B GLY 2.9 1.3 - - - -
375B HIS* 2.6 13.3 + - - +
376B LEU* 3.0 19.5 + - + +
499B PHE* 6.2 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 373 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B SER 2.9 13.1 + - - +
370B VAL 3.6 7.0 - - - +
372B ALA* 1.3 78.0 - - - +
374B GLY* 1.3 58.5 + - - +
376B LEU* 3.2 2.3 + - - +
377B TYR* 2.8 57.0 + + + +
435B PRO* 4.4 6.1 - - + -
466B LEU* 3.3 33.4 - - + -
499B PHE* 3.7 35.6 - + + -
502B VAL* 4.0 20.2 - - + -
503B LEU* 3.8 25.6 - - + -
508B CYS* 4.4 7.0 - - - -
510B PHE* 3.4 35.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 374 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B MET* 4.3 3.6 - - - -
370B VAL 2.9 13.1 + - - -
371B ALA 3.8 4.9 - - - -
372B ALA 2.9 1.0 - - - -
373B PHE* 1.3 84.3 - - - +
375B HIS* 1.3 61.5 + - - +
377B TYR* 4.6 0.7 - - - -
378B PHE* 3.0 45.7 + - - -
509B ARG* 5.7 2.2 - - - -
510B PHE* 4.8 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 375 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ARG* 5.1 3.1 - - - -
112B GLU* 4.3 10.1 + - + +
115B LEU* 4.1 8.3 - - + -
116B MET* 3.4 50.3 - - + +
119B PHE* 6.2 0.7 - - - -
120B ILE 3.2 24.2 + - - -
121B THR* 5.3 1.3 - - - -
359B ASN 4.0 9.9 - - - +
360B GLY* 3.9 27.6 + - - -
361B LEU* 5.3 3.4 - - + +
371B ALA 3.2 13.2 + - - +
372B ALA* 2.6 13.8 + - - +
374B GLY* 1.3 71.8 - - - +
376B LEU* 1.3 69.9 + - + +
379B PRO* 3.2 23.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 376 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B PHE* 5.5 0.3 - - - -
358B VAL* 4.2 19.7 - - + +
359B ASN* 3.9 13.7 - - - +
372B ALA* 3.0 18.0 + - + +
373B PHE 3.9 3.8 - - - +
375B HIS* 1.3 91.4 - - + +
377B TYR* 1.3 65.2 + - - +
378B PHE 3.5 0.3 + - - -
379B PRO* 3.5 13.9 - - - +
380B ARG* 4.2 7.3 + - - +
469B ILE* 3.9 26.4 - - + +
473B ILE* 5.0 9.2 - - + -
495B ILE* 5.5 3.4 - - + -
499B PHE* 4.4 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 377 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B PHE* 5.2 0.9 - + - -
373B PHE* 2.8 49.7 + + + +
374B GLY* 4.1 2.9 - - - +
376B LEU* 1.3 74.3 - - - +
378B PHE* 1.3 60.2 + - + +
380B ARG* 3.5 2.3 + - - +
381B MET* 2.9 47.8 + - + +
434B ASP* 1.8 38.5 + - - -
435B PRO* 3.4 12.0 - - + +
436B VAL* 2.9 18.9 + - + +
465B CYS* 3.5 21.5 - - + -
466B LEU* 3.9 12.8 - - + -
469B ILE* 4.2 12.1 - - + +
510B PHE* 3.7 31.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 378 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B GLU* 3.8 19.1 - - + -
108B VAL* 4.1 18.4 - - + -
113B ARG* 5.4 1.1 - - - -
116B MET* 3.6 27.8 - - + -
117B GLU* 4.6 0.4 - - - +
374B GLY* 3.0 30.9 + - - +
377B TYR* 1.3 78.2 - - - +
379B PRO* 1.3 65.0 - - + +
381B MET* 3.2 6.6 + - + +
382B HIS* 2.3 51.3 + + - +
388B ALA* 3.5 13.0 - - + -
509B ARG* 2.9 34.8 - - - -
510B PHE* 3.7 27.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 379 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B MET* 3.3 26.2 - - + +
117B GLU* 3.8 22.4 - - - +
119B PHE* 3.8 32.3 - - + -
375B HIS 3.2 21.8 - - - +
376B LEU* 3.5 10.1 - - - +
378B PHE* 1.3 88.1 - - + +
380B ARG* 1.3 63.0 + - - +
382B HIS* 3.5 2.1 + - + +
383B ARG* 3.0 32.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 380 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B PHE* 3.8 27.4 - - + -
376B LEU 4.2 6.7 - - - +
377B TYR 4.0 5.6 - - - +
378B PHE 3.2 0.4 - - - -
379B PRO* 1.3 78.8 - - - +
381B MET* 1.3 64.0 + - - +
383B ARG* 3.6 9.4 + - - +
384B ALA* 3.3 18.5 + - - +
464B HIS 5.7 0.2 + - - -
465B CYS* 3.8 24.2 + - + +
468B GLU* 3.7 40.6 + - - +
469B ILE* 3.7 30.0 - - + +
472B ASN* 4.9 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 381 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B PHE* 4.6 7.9 - - - -
105B GLU* 3.2 12.6 - - - +
377B TYR* 2.9 33.9 + - + +
378B PHE* 3.2 15.7 + - + +
380B ARG* 1.3 75.2 - - - +
382B HIS* 1.3 70.2 + - + +
384B ALA* 2.7 28.0 + - - +
385B GLY 3.3 0.3 + - - -
386B TYR* 3.3 14.4 + - + +
387B VAL* 3.3 8.1 - - - -
388B ALA* 2.6 50.7 - - + +
436B VAL* 5.4 2.5 - - + -
465B CYS* 3.9 10.9 - - - -
510B PHE* 4.0 22.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 382 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B PHE* 4.5 10.4 - + - -
70B LEU* 3.7 24.4 - - + +
105B GLU* 3.4 36.6 + - - -
113B ARG* 4.6 3.4 - - - -
117B GLU* 3.2 28.8 + - - +
378B PHE* 2.3 46.3 + - - -
379B PRO 3.9 4.0 - - - +
380B ARG 3.4 0.4 - - - -
381B MET* 1.3 78.7 - - + +
383B ARG* 1.3 56.7 + - + +
384B ALA 2.6 5.4 + - - -
385B GLY* 2.3 31.2 + - - -
386B TYR 3.4 15.5 + - - +
387B VAL* 5.0 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 383 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B GLU* 3.1 41.8 + - - +
119B PHE* 3.6 29.1 - - - -
379B PRO* 3.0 25.0 + - - +
380B ARG* 3.8 7.4 - - - +
382B HIS* 1.3 79.8 - - + +
384B ALA* 1.3 57.5 + - - +
385B GLY 3.2 1.5 + - - -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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