Contacts of the helix formed by residues 362 - 380 (chain A) in PDB entry 2H5G
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 THR 362 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A PRO* 1.3 76.4 - - - +
363A VAL* 1.3 61.2 + - - +
364A GLU* 3.5 21.7 + - + +
365A GLN* 3.1 47.8 + - + +
366A GLN* 2.9 27.0 + - - +
540A GLU* 5.3 3.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 363 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A PRO 4.0 0.4 + - - -
362A THR* 1.3 75.4 + - - +
364A GLU* 1.3 77.8 - - - +
366A GLN* 3.4 14.7 + - + +
367A GLY 2.9 22.5 + - - -
502A LEU* 5.2 0.9 - - + -
536A VAL* 4.4 25.8 - - + -
540A GLU* 3.6 36.9 + - + +
551A MSE 3.4 20.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 364 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A THR* 3.6 20.3 + - + +
363A VAL* 1.3 94.8 - - - +
365A GLN* 1.3 58.4 + - + +
367A GLY* 3.4 1.7 + - - -
368A GLU* 3.1 25.6 + - - +
551A MSE 3.9 17.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A PRO* 3.7 15.2 - - + +
362A THR* 3.1 39.4 + - + +
364A GLU* 1.3 73.0 - - + +
366A GLN* 1.3 60.5 + - - +
368A GLU* 3.3 7.2 + - - +
369A MSE 2.9 44.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A PRO* 4.3 23.1 - - + +
362A THR 2.9 13.9 + - - +
363A VAL* 3.6 19.1 + - + +
365A GLN* 1.3 72.7 - - - +
367A GLY* 1.3 60.3 + - - +
369A MSE 3.3 1.6 + - - -
370A ALA* 2.8 32.6 + - - +
502A LEU* 3.9 12.3 - - + -
534A GLN* 3.2 34.0 + - - +
535A LEU 2.8 30.2 + - - +
536A VAL* 3.7 23.0 - - - +
537A ASN 4.5 2.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A VAL 2.9 11.1 + - - -
364A GLU 3.4 1.8 + - - -
365A GLN 3.3 0.2 - - - -
366A GLN* 1.3 76.4 - - - +
368A GLU* 1.3 55.2 + - - +
370A ALA* 3.4 3.5 + - - +
371A ARG* 3.0 29.3 + - - +
475A VAL* 4.6 4.4 - - - +
502A LEU* 4.1 7.8 - - - +
551A MSE 3.7 38.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A GLU 3.1 13.2 + - - +
365A GLN* 3.7 10.3 - - - +
366A GLN 3.3 0.2 - - - -
367A GLY* 1.3 76.0 - - - +
369A MSE 1.3 57.4 + - + +
371A ARG* 3.4 6.8 + - - +
372A SER* 3.0 31.5 + - - +
551A MSE 4.8 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A PRO* 4.7 23.1 - - + -
365A GLN* 2.9 29.5 + - + +
366A GLN* 3.8 4.5 - - - +
368A GLU* 1.3 74.3 - - + +
370A ALA* 1.3 56.5 + - - +
371A ARG 3.2 0.4 - - - -
372A SER* 3.3 7.1 + - - -
373A GLY* 2.8 29.6 + - - -
531A GLU* 3.2 43.9 - - - +
534A GLN* 3.9 25.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 370 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A GLN 2.8 18.4 + - - +
367A GLY 3.7 4.3 - - - +
369A MSE 1.3 76.7 - - - +
371A ARG* 1.3 57.2 + - - +
374A GLY 2.8 23.7 + - - -
475A VAL* 4.1 11.4 - - + -
500A GLY* 3.3 11.4 - - - -
501A LEU 4.0 21.3 - - - +
502A LEU* 3.9 19.1 - - + -
531A GLU 3.5 10.3 + - - -
532A ALA* 4.2 2.0 - - - -
534A GLN* 4.1 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 371 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A GLY 3.0 16.8 + - - +
368A GLU* 3.7 7.9 - - - +
369A MSE 3.2 0.2 - - - -
370A ALA* 1.3 79.1 - - - +
372A SER* 1.3 58.2 + - - +
374A GLY* 3.4 1.0 + - - -
375A ARG* 3.0 42.6 + - + +
474A GLY* 6.2 0.4 - - - -
475A VAL* 3.5 21.3 - - + +
551A MSE 5.6 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 372 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A GLU* 3.0 20.8 + - - +
369A MSE 3.3 6.4 + - - -
371A ARG* 1.3 78.5 - - - +
373A GLY* 1.3 58.0 + - - +
375A ARG* 3.3 9.6 + - - +
376A MSE 3.0 39.3 + - - +
531A GLU* 3.6 13.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 373 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A MSE 2.8 22.7 + - - -
372A SER* 1.3 71.4 + - - +
374A GLY* 1.3 57.2 + - - +
376A MSE 3.5 10.8 + - - +
377A LEU* 2.9 32.4 + - - +
529A VAL* 4.2 6.2 - - - +
531A GLU* 4.3 5.8 + - - -
532A ALA* 3.7 22.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 374 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A ALA 2.8 21.9 + - - -
371A ARG* 3.7 1.6 - - - -
372A SER 3.3 0.2 - - - -
373A GLY* 1.3 73.6 - - - +
375A ARG* 1.3 56.1 + - - +
377A LEU* 3.1 5.0 + - - +
378A ALA* 3.0 24.6 + - - +
474A GLY 5.2 1.1 - - - -
498A GLY 3.2 12.8 - - - +
499A ASN 3.9 5.4 - - - -
500A GLY* 3.7 23.6 - - - -
532A ALA* 4.1 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 375 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A ARG* 3.0 34.9 + - + +
372A SER* 3.3 8.7 + - - +
374A GLY* 1.3 75.3 - - - +
376A MSE 1.3 60.6 + - - +
378A ALA* 3.4 8.3 + - - +
379A THR* 3.2 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 376 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A SER* 3.0 28.9 + - - +
373A GLY* 3.7 7.4 - - - +
374A GLY 3.3 0.2 - - - -
375A ARG* 1.3 73.1 - - - +
377A LEU* 1.3 65.0 + - - +
379A THR* 3.0 24.3 + - - +
380A LEU* 3.2 17.2 + - + +
527A HIS 5.3 1.3 - - - +
528A GLY 3.9 12.8 - - - +
529A VAL* 3.7 23.6 - - + -
531A GLU* 5.7 4.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 377 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A GLY 2.9 13.4 + - - +
374A GLY 3.3 6.7 - - - +
376A MSE 1.3 74.7 - - - +
378A ALA* 1.3 60.4 + - - +
379A THR 3.3 0.7 + - - -
380A LEU* 3.3 19.8 + - + +
385A ARG* 2.9 30.3 + - + -
388A ILE* 4.2 9.0 - - + -
495A ILE* 4.0 42.4 - - + +
498A GLY* 4.4 7.2 - - - -
499A ASN 3.5 21.5 - - - +
524A LEU* 4.4 1.8 - - + -
529A VAL* 4.0 23.0 - - + +
532A ALA* 3.5 27.8 - - + -
533A VAL* 5.9 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 378 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A GLY 3.0 12.7 + - - +
375A ARG* 3.7 11.2 - - - +
376A MSE 3.3 0.2 - - - -
377A LEU* 1.3 76.6 - - - +
379A THR* 1.3 60.8 + - + +
380A LEU 3.8 1.4 - - - +
385A ARG* 3.3 16.1 + - - +
451A VAL* 4.7 10.6 - - + +
472A PRO* 3.9 30.3 - - + -
498A GLY* 3.9 7.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 379 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A ARG 3.2 13.9 + - - +
376A MSE 3.0 22.1 + - - +
378A ALA* 1.3 77.2 - - + +
380A LEU* 1.3 67.5 + - - +
381A GLU* 3.9 3.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 380 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A MSE 3.2 17.3 + - + +
377A LEU* 3.3 27.3 + - + +
378A ALA 3.8 1.7 - - - +
379A THR* 1.3 83.9 + - - +
381A GLU* 1.3 64.6 + - - +
382A PRO* 3.8 1.6 - - - +
384A GLN* 3.8 24.9 - - + +
385A ARG* 2.9 23.9 + - + +
388A ILE* 4.0 18.8 - - + -
527A HIS* 3.8 37.5 - - + +
529A VAL* 4.3 6.7 - - + -
----------------------------------------------------------
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