Contacts of the helix formed by residues 439 - 455 (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 439 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A GLY* 5.8 2.4 + - - -
408A ALA* 4.9 7.0 - - - +
433A ILE 4.6 1.7 - - - +
434A ALA* 4.0 18.4 - - - -
436A HIS* 3.2 15.2 + - - -
437A ASP 3.2 1.4 - - - -
438A GLY* 1.3 75.6 - - - +
440A LYS* 1.3 68.6 + - - +
442A ALA* 2.9 24.1 + - - +
443A LEU* 3.2 11.5 + - - +
4B T 4.3 1.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 440 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A GLN* 3.2 61.6 + - + +
408A ALA* 4.7 3.2 - - - +
410A GLU* 5.6 1.6 - - - +
411A THR* 3.4 22.9 + - - +
439A GLY* 1.3 76.8 - - - +
441A GLN* 1.3 77.2 + - - +
443A LEU* 3.0 5.6 + - - +
444A GLU* 2.7 62.5 + - + +
4B T 3.6 9.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 441 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A GLY 4.7 2.0 - - - +
439A GLY 3.4 0.6 - - - -
440A LYS* 1.3 94.6 - - - +
442A ALA* 1.3 64.0 + - - +
444A GLU* 3.9 14.6 - - + +
445A THR* 2.7 28.8 + - - -
474A LYS* 2.8 53.2 + - + +
4B T 2.6 47.1 + - - +
5B C 4.1 16.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 442 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A ILE* 3.6 24.7 - - + +
436A HIS* 6.6 0.2 - - + -
438A GLY 3.9 9.1 + - - +
439A GLY* 2.9 15.0 + - - +
441A GLN* 1.3 81.5 - - - +
443A LEU* 1.3 63.4 + - - +
445A THR* 3.2 2.4 + - - -
446A VAL* 3.2 25.6 + - - +
468A ALA* 4.0 19.1 - - - +
470A ASN 5.8 0.7 - - - +
473A GLY* 5.2 2.2 - - - +
474A LYS* 4.6 12.5 - - - +
477A LEU* 4.2 3.2 - - - +
5B C 5.7 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 443 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A ALA* 4.5 1.6 - - - +
411A THR* 3.6 39.3 - - + +
412A VAL* 4.1 9.6 - - + -
415A LEU* 5.4 6.1 - - + -
419A LEU* 4.6 10.2 - - + +
430A VAL* 3.4 30.3 - - + +
433A ILE* 3.4 32.3 - - + +
434A ALA* 3.9 20.6 - - + -
439A GLY 3.2 8.7 + - - +
440A LYS 3.0 6.5 + - - +
442A ALA* 1.3 79.8 - - - +
444A GLU* 1.3 63.3 + - - +
446A VAL* 2.9 23.0 + - + +
447A GLN* 3.3 7.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 444 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A THR* 4.0 17.2 - - + +
415A LEU* 4.8 11.0 - - + +
440A LYS* 2.7 53.1 + - + +
441A GLN* 4.2 11.7 - - + +
443A LEU* 1.3 72.9 - - - +
445A THR* 1.3 59.3 + - - +
446A VAL 3.1 0.2 - - - -
447A GLN* 3.5 14.2 - - - +
448A ARG* 3.1 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 445 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A GLN* 2.7 24.8 + - - -
442A ALA 3.2 0.2 + - - -
444A GLU* 1.3 74.4 - - - +
446A VAL* 1.3 60.4 + - - +
448A ARG* 3.6 37.3 + - - +
449A LEU* 2.8 51.4 + - + +
474A LYS* 3.5 24.3 - - + +
477A LEU* 3.6 26.1 - - + +
478A GLU 4.4 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 446 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A LEU* 4.0 18.8 - - + -
423A HIS* 4.9 2.5 - - + -
425A LEU* 5.4 3.4 - - + -
433A ILE* 3.8 30.5 - - + -
442A ALA 3.2 16.1 + - - +
443A LEU* 2.9 12.8 + - - +
445A THR* 1.3 76.5 - - - +
447A GLN* 1.3 65.9 + - - +
448A ARG 3.0 0.5 + - - -
450A LEU* 2.5 60.1 + - + +
464A VAL* 5.2 5.2 - - + -
465A VAL* 6.1 0.4 - - + -
468A ALA* 3.9 13.7 - - + -
477A LEU* 4.3 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 447 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A LEU* 3.7 42.1 - - + +
418A VAL* 4.1 15.0 - - + -
419A LEU* 4.3 5.2 - - + -
423A HIS* 4.0 17.2 + - - +
443A LEU 3.3 5.2 + - - +
444A GLU* 3.5 17.0 - - - +
446A VAL* 1.3 80.9 - - - +
448A ARG* 1.3 77.0 + - - +
451A PRO* 3.9 11.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 448 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A GLU 3.1 16.5 + - - +
445A THR* 3.6 29.0 + - - +
446A VAL 3.0 0.4 - - - -
447A GLN* 1.3 95.5 - - - +
449A LEU* 1.3 81.8 + - + +
451A PRO* 4.3 1.6 - - - +
452A VAL* 3.2 18.9 - - - +
474A LYS* 4.8 7.9 - - - +
478A GLU* 2.6 40.8 + - - +
481A GLN* 4.4 4.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 449 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A THR* 2.8 39.3 + - + +
446A VAL 3.0 0.2 + - - -
448A ARG* 1.3 97.3 - - + +
450A LEU* 1.3 66.7 + - - +
451A PRO* 3.4 2.2 - - - -
452A VAL* 3.6 16.8 + - + -
453A LEU* 2.9 38.2 + - + +
477A LEU* 3.8 23.6 - - + +
478A GLU 4.1 0.4 - - - +
481A GLN* 3.4 37.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 450 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A HIS* 3.5 40.4 - - + +
425A LEU* 5.3 5.4 - - + -
445A THR 3.8 0.8 + - - -
446A VAL* 2.5 51.2 + - + +
449A LEU* 1.3 71.7 - - - +
451A PRO* 1.3 82.4 - - + +
453A LEU* 3.3 16.2 - - - +
454A CYS* 3.2 24.6 - - - -
461A PRO* 4.8 17.7 - - + +
464A VAL* 4.1 24.7 - - + +
465A VAL* 4.9 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 451 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A HIS* 3.9 16.2 - - + +
447A GLN 3.9 15.7 - - - +
448A ARG 4.3 0.9 - - - +
449A LEU 3.6 1.3 - - - -
450A LEU* 1.3 104.4 - - + +
452A VAL* 1.3 66.1 + - + +
453A LEU 2.5 18.0 + - - -
454A CYS* 3.0 14.9 + - - -
455A GLN* 3.0 19.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 452 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A ARG 3.2 27.6 - - - +
449A LEU* 3.6 22.4 - - + +
451A PRO* 1.3 77.0 - - + +
453A LEU* 1.3 60.0 + - - +
455A GLN* 3.6 22.9 + - - +
456A ALA* 4.3 8.5 + - - +
457A HIS* 5.0 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 453 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A LEU* 2.9 38.3 + - + +
450A LEU 3.3 4.3 - - - +
451A PRO 2.5 5.5 + - - -
452A VAL* 1.3 73.6 - - - +
454A CYS* 1.4 53.2 + - - +
456A ALA 3.1 6.2 - - - -
457A HIS* 2.6 60.6 + - + +
459A LEU* 4.8 7.4 - - + -
464A VAL* 3.8 35.7 - - + -
477A LEU* 4.1 15.9 - - + +
480A VAL* 3.8 26.0 - - + -
481A GLN* 4.2 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 454 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A LEU* 3.2 29.4 - - - -
451A PRO* 3.0 8.2 + - - -
453A LEU* 1.4 68.0 - - - +
455A GLN* 1.3 64.4 + - - +
456A ALA 3.2 0.4 - - - -
457A HIS 2.2 29.2 - - - +
458A GLY* 4.0 4.3 + - - -
459A LEU* 2.8 31.6 - - - +
460A THR* 5.1 0.2 - - - -
461A PRO* 4.8 13.5 - - + -
464A VAL* 4.9 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 455 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A PRO* 3.0 17.7 + - + +
452A VAL* 3.6 30.0 + - - +
454A CYS* 1.3 77.6 - - - +
456A ALA* 1.3 66.3 + - - +
----------------------------------------------------------
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