Contacts of the helix formed by residues 369 - 379 (chain G) in PDB entry 6K71
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 369 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337G GLY* 3.3 14.4 - - - -
360G VAL* 5.1 4.9 - - - -
361G VAL 4.9 4.0 - - - -
362G ASP* 3.9 9.6 - - - +
367G LEU 3.5 4.4 + - - -
368G GLU* 1.3 71.1 - - - +
370G ARG* 1.3 59.7 + - - +
371G HIS 3.4 1.6 - - - -
372G THR* 2.4 26.4 + - - -
373G LEU* 2.8 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 370 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C VAL 4.4 0.8 + - - -
295C LEU* 3.6 30.4 - - - +
296C PRO* 6.3 0.2 - - - +
299C GLU* 5.7 1.4 + - - +
302C ILE* 6.3 1.3 - - - +
362G ASP* 3.5 14.6 + - - -
367G LEU* 3.2 61.6 + - + +
368G GLU* 3.5 4.4 - - + +
369G GLY* 1.3 86.7 - - - +
371G HIS* 1.3 58.3 + - - +
373G LEU* 3.7 18.2 - - - +
374G ARG* 2.9 67.7 + - - +
385G TYR* 3.8 17.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 371 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338G CYS* 5.1 18.0 - - - +
339G SER 4.0 20.0 + - - +
340G SER* 4.4 11.0 - - - -
343G SER* 5.7 3.3 + - - -
369G GLY 3.4 0.4 - - - -
370G ARG* 1.3 77.1 - - - +
372G THR* 1.3 59.2 + - + +
374G ARG* 4.1 3.2 - - + +
375G SER* 2.9 43.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 372 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335G VAL* 5.0 3.8 - - + -
337G GLY* 2.9 40.4 + - - -
338G CYS* 3.8 8.7 - - - +
339G SER 4.1 9.2 - - - +
342G VAL* 4.6 7.0 - - + -
343G SER* 3.9 26.8 - - - +
346G LEU* 6.4 0.4 - - - -
360G VAL* 4.1 9.6 - - - +
369G GLY* 2.4 27.1 + - - -
371G HIS* 1.3 79.0 - - + +
373G LEU* 1.3 55.3 + - - +
375G SER* 3.2 1.6 + - - -
376G LEU* 2.9 37.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 373 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C ILE* 3.7 30.1 - - + -
306C VAL* 5.9 6.7 - - + -
360G VAL* 3.8 34.7 - - + +
369G GLY* 2.8 31.8 + - - +
370G ARG* 3.7 30.7 - - - +
372G THR* 1.3 73.1 + - - +
374G ARG* 1.3 79.1 + - + +
376G LEU* 3.3 6.4 + - - +
377G VAL* 3.0 34.5 + - + +
383G ALA* 5.1 8.5 - - + -
385G TYR* 4.2 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 374 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C GLU* 2.4 35.5 + - - +
300C GLY* 4.2 4.6 - - - +
301C ASP* 4.9 8.7 + - - +
302C ILE* 4.4 16.6 - - + +
370G ARG* 2.9 59.8 + - - +
371G HIS* 4.2 2.9 - - + +
373G LEU* 1.3 85.2 - - + +
375G SER* 1.3 58.2 + - - +
377G VAL 3.4 0.3 + - - -
378G HIS* 2.9 52.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 375 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343G SER* 4.9 7.5 + - - -
347G GLN* 2.3 47.5 + - - -
371G HIS* 2.9 32.3 + - - -
372G THR* 3.2 4.2 + - - -
374G ARG* 1.3 77.6 - - - +
376G LEU* 1.3 56.6 + - - +
378G HIS* 3.9 5.6 - - - +
379G ALA* 2.9 19.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 376 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335G VAL* 5.3 0.2 - - + -
343G SER* 5.3 4.5 - - - +
346G LEU* 3.9 35.2 - - + -
347G GLN* 4.3 6.7 - - + +
358G VAL* 4.0 25.4 - - + -
360G VAL* 4.1 19.1 - - + -
372G THR* 2.9 24.4 + - - +
373G LEU* 3.6 5.4 - - - +
375G SER* 1.3 75.4 - - - +
377G VAL* 1.3 55.2 + - + +
379G ALA* 3.1 6.1 + - - +
380G GLY 2.6 30.1 + - - -
381G VAL* 2.8 44.3 + - + +
383G ALA* 5.0 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 377 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C ASP 5.1 4.3 - - - +
302C ILE* 3.7 28.7 - - + -
305C LYS* 4.6 32.3 - - + +
306C VAL* 5.7 2.5 - - + -
373G LEU* 3.0 18.4 + - + +
374G ARG 4.1 1.3 - - - +
376G LEU* 1.3 75.3 - - - +
378G HIS* 1.3 65.8 + - + +
380G GLY* 2.9 18.7 + - - +
381G VAL 4.0 16.6 - - - +
383G ALA* 4.3 15.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 378 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C ASP* 3.3 33.8 + - - -
302C ILE* 5.5 0.8 - - - +
374G ARG* 2.9 40.2 + - + +
375G SER* 4.2 5.3 - - - +
377G VAL* 1.3 86.9 - - + +
379G ALA* 1.3 58.3 + - - +
380G GLY* 4.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 379 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347G GLN* 3.7 29.6 - - + +
350G TRP* 3.6 18.4 + - + -
351G THR* 5.2 6.5 - - + +
375G SER 2.9 21.6 + - - +
376G LEU* 3.1 6.0 + - - +
378G HIS* 1.3 74.5 - - - +
380G GLY* 1.3 58.4 + - - +
381G VAL* 3.7 5.2 - - + -
----------------------------------------------------------
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