Contacts of the helix formed by residues 370 - 382 (chain A) in PDB entry 3UGM
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 370 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A ASN* 3.6 1.2 - - - +
369A ILE* 1.3 82.7 - - - +
371A GLY* 1.3 64.8 + - - +
372A LYS* 3.3 2.0 - - - +
373A GLN* 2.5 23.3 + - - +
374A ALA* 3.1 8.2 + - - -
402A HIS 5.1 1.1 + - - -
403A GLY* 4.6 8.1 - - - -
404A GLY 4.9 3.6 - - - +
405A GLY 5.8 1.1 - - - -
2B C 4.1 10.1 - - - -
3B A 3.2 25.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 371 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A ALA* 5.0 7.0 - - - -
365A ILE 4.0 7.9 - - - +
366A ALA* 3.4 27.6 - - - -
368A ASN* 3.1 7.9 + - - +
369A ILE 3.0 8.1 + - - -
370A GLY* 1.3 70.9 - - - +
372A LYS* 1.3 62.5 + - - -
374A ALA* 2.9 15.6 + - - +
375A LEU* 2.9 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 372 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A GLN* 3.1 49.6 + - + +
340A ALA* 4.6 6.5 - - - +
343A THR* 3.1 43.0 + - + +
370A GLY 2.7 2.6 + - - +
371A GLY* 1.3 67.8 - - - +
373A GLN* 1.3 60.9 + - - +
374A ALA 2.8 5.4 + - - -
375A LEU* 2.8 6.9 + - - +
376A GLU* 2.6 52.0 + - - +
1B G 5.2 0.6 + - - -
2B C 3.5 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 373 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A GLY 2.5 14.9 + - - +
372A LYS* 1.3 74.5 - - - +
374A ALA* 1.3 56.3 + - - -
376A GLU* 3.6 23.2 + - - +
377A THR* 2.5 29.2 + - - -
406A LYS* 3.5 35.3 + - + +
2B C 2.5 43.9 + - - +
3B A 3.4 21.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 374 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A ILE* 3.3 31.2 - - + +
368A ASN* 6.1 0.7 - - + -
370A GLY 3.1 6.7 + - - +
371A GLY* 2.9 13.9 + - - +
372A LYS 2.8 0.8 + - - -
373A GLN* 1.3 75.3 - - - +
375A LEU* 1.3 68.0 + - - +
377A THR* 3.0 3.5 + - - -
378A VAL* 2.9 26.0 + - - +
400A ALA* 4.0 15.7 - - + +
402A HIS 5.3 2.5 - - - +
405A GLY* 4.6 8.0 - - - +
406A LYS 4.6 6.5 - - - +
409A LEU* 5.6 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 375 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A ALA 4.4 3.4 - - - +
343A THR* 3.3 39.9 - - - +
344A MET* 3.8 13.2 - - + -
347A LEU* 4.2 17.8 - - + +
348A LEU 6.0 0.2 - - - +
351A LEU* 4.1 26.1 - - + +
362A VAL* 4.5 8.5 - - + +
365A ILE* 3.6 27.4 - - + -
366A ALA* 4.2 17.0 - - + +
371A GLY 2.9 12.1 + - - +
372A LYS* 2.8 12.2 + - - +
374A ALA* 1.3 76.2 - - - +
376A GLU* 1.3 63.9 + - - +
378A VAL* 3.3 14.7 + - - +
379A GLN* 3.6 3.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 376 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A THR* 4.7 7.3 - - + +
347A LEU* 4.5 11.8 - - + +
372A LYS* 2.6 46.5 + - + +
373A GLN* 3.6 27.4 + - - +
375A LEU* 1.3 75.4 - - - +
377A THR* 1.3 64.6 + - - +
378A VAL 3.2 1.6 + - - -
379A GLN* 3.4 2.8 + - - +
380A ARG* 3.3 51.2 + - + +
406A LYS* 5.6 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 377 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A GLN 2.5 23.7 + - - -
374A ALA 3.0 3.9 + - - -
376A GLU* 1.3 73.9 - - - +
378A VAL* 1.3 67.8 + - - +
380A ARG* 4.3 10.1 - - + -
381A LEU* 3.1 30.5 + - + +
406A LYS* 2.8 39.4 - - + +
409A LEU* 4.2 16.2 - - + +
410A GLU* 4.2 19.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 378 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A LEU* 4.1 15.5 - - + -
357A LEU* 4.4 9.4 - - + -
365A ILE* 4.1 21.5 - - + -
374A ALA 2.9 22.5 + - - +
375A LEU* 3.4 9.9 - - + +
376A GLU 3.1 0.4 - - - -
377A THR* 1.3 75.8 - - - +
379A GLN* 1.3 53.0 + - - +
381A LEU 2.8 6.8 + - - -
382A LEU* 2.4 68.3 + - + +
396A VAL 5.5 1.6 - - - +
397A VAL* 6.2 1.3 - - - -
400A ALA* 4.3 15.3 - - + -
409A LEU* 5.2 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 379 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A LEU* 3.2 38.4 - - + +
350A VAL* 4.2 21.6 - - + +
351A LEU* 4.4 7.2 - - + +
355A HIS* 4.8 11.6 - - + +
375A LEU 3.6 3.3 + - - +
376A GLU 3.4 6.1 + - - +
378A VAL* 1.3 82.1 - - - +
380A ARG* 1.3 85.0 + - - +
381A LEU 3.2 0.5 + - - -
382A LEU* 4.7 3.1 - - - +
383A PRO* 3.9 14.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 380 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A LEU* 5.8 1.8 - - - +
376A GLU* 3.3 44.3 + - - +
377A THR* 4.2 11.9 - - + +
378A VAL 3.3 0.6 - - - -
379A GLN* 1.3 100.0 + - - +
381A LEU* 1.3 63.1 + - + +
384A VAL* 3.4 18.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 381 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A THR* 3.1 22.6 + - + +
378A VAL* 2.8 4.1 + - - -
380A ARG* 1.3 82.6 - - + +
382A LEU* 1.3 64.8 + - - +
383A PRO* 3.5 2.9 - - - -
384A VAL* 3.7 26.1 + - + -
385A LEU* 3.5 33.4 - - + +
391A LEU* 5.8 0.2 - - - +
396A VAL* 6.0 0.3 - - - +
409A LEU* 4.5 14.4 - - + +
410A GLU* 4.4 22.4 - - + -
413A GLN* 3.8 31.6 - - + +
414A ARG* 5.7 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 382 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A LEU* 5.5 0.2 - - + -
355A HIS* 3.5 41.7 - - + +
357A LEU* 3.8 15.3 - - + -
378A VAL* 2.4 52.4 + - + +
379A GLN 4.6 0.9 - - - +
381A LEU* 1.3 73.0 - - - +
383A PRO* 1.4 69.0 - - + +
385A LEU* 4.3 1.9 + - - +
386A CYS* 3.5 24.8 + - - -
391A LEU* 4.6 3.5 - - - +
393A PRO* 4.9 11.7 - - + +
396A VAL* 4.2 24.7 - - + -
409A LEU* 6.1 1.8 - - - -
----------------------------------------------------------
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