Contacts of the helix formed by residues 449 - 461 (chain N) in PDB entry 2GLJ
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 LYS 449 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13N TRP* 4.5 3.1 - - + -
25N PHE* 4.0 17.8 - - + +
26N ALA* 3.5 19.1 + - - +
29N ASP* 5.7 1.3 - - + +
30N ARG* 3.0 39.9 - - + +
251N ASP* 2.6 28.1 + - - -
256N ARG* 2.8 30.4 + - - +
257N SER* 3.0 14.5 + - - +
258N MET 3.6 10.5 - - - -
259N VAL* 3.7 14.8 - - + -
447N SER 3.7 1.4 + - - -
448N SER* 1.3 70.8 - - - +
450N ALA* 1.3 64.2 + - - +
452N ILE* 3.1 13.8 + - + +
453N TYR* 2.9 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 450 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12N ALA* 3.5 12.3 - - + -
13N TRP* 3.4 37.9 - - + +
16N TYR* 2.9 33.2 + - + -
25N PHE* 3.9 5.1 - - - -
364N GLY* 4.9 0.9 - - - -
448N SER* 3.1 4.8 + - - +
449N LYS* 1.3 79.3 - - - +
451N ASP* 1.3 58.1 + - - +
453N TYR* 3.4 0.3 + - - +
454N GLU* 2.8 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 451 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362N TYR 4.2 1.8 - - - +
363N LEU* 3.6 4.0 - - - +
364N GLY* 2.5 35.2 + - - -
365N LYS 3.2 0.4 + - - -
366N GLY 2.8 41.9 + - - +
404N GLN* 5.0 0.4 - - - -
435N VAL* 3.5 21.3 - - + +
436N ALA* 4.7 7.0 - - - +
448N SER* 2.8 20.6 + - - +
450N ALA* 1.3 75.7 - - - +
452N ILE* 1.3 66.0 + - - +
454N GLU* 3.6 5.2 - - - +
455N THR* 2.7 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 452 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29N ASP* 4.1 22.4 - - + +
30N ARG* 5.7 3.6 - - - +
33N ASN* 3.8 24.0 - - + +
259N VAL* 4.2 12.6 - - + -
268N ILE* 3.7 21.1 - - + -
272N THR* 3.7 26.2 - - + +
435N VAL* 4.3 5.8 - - + +
447N SER* 3.9 16.6 - - - +
448N SER 2.9 14.6 + - - +
449N LYS* 3.3 21.8 - - + +
451N ASP* 1.3 73.9 - - - +
453N TYR* 1.3 66.7 + - - +
455N THR* 3.2 6.8 + - - -
456N LYS* 3.1 14.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 453 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15N LYS* 5.3 0.4 - - - -
16N TYR* 3.1 42.4 - + - +
21N LEU* 3.1 29.0 - - + +
24N VAL* 4.0 23.0 - - + +
25N PHE* 3.3 41.3 - + + -
29N ASP* 3.6 15.9 + - + +
449N LYS 2.9 12.2 + - - +
450N ALA 3.4 6.5 - - - +
452N ILE* 1.3 75.7 - - - +
454N GLU* 1.3 64.1 + - - +
456N LYS* 2.9 19.0 + - + +
457N ASN* 3.1 43.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 454 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12N ALA* 3.6 10.8 - - + +
15N LYS* 2.8 19.8 + - - -
16N TYR* 2.5 31.1 + - - -
366N GLY* 3.9 13.0 - - - -
367N ILE* 4.8 0.4 - - - -
401N VAL* 3.5 14.9 - - + +
402N ASN* 3.1 57.6 + - + +
450N ALA 2.8 17.5 + - - +
451N ASP* 3.6 3.1 - - - +
453N TYR* 1.3 71.6 - - - +
455N THR* 1.3 52.2 + - - +
457N ASN* 3.1 14.5 + - - +
458N GLY 2.8 31.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 455 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269N CYS* 5.3 0.2 - - - -
272N THR* 3.6 13.0 - - - +
367N ILE* 3.5 31.6 - - + +
434N GLY 5.1 0.7 - - - -
435N VAL* 3.5 26.2 - - + +
451N ASP 2.7 23.8 + - - -
452N ILE 3.4 4.9 - - - -
454N GLU* 1.3 72.2 - - - +
456N LYS* 1.3 65.7 + - - +
458N GLY* 2.9 3.5 + - - -
459N TYR* 2.9 54.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 456 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29N ASP* 4.1 17.0 + - - +
32N LYS* 4.7 3.8 - - - +
272N THR* 3.9 31.2 - - + +
275N GLU* 2.7 42.5 + - + +
276N ALA* 4.0 11.6 - - + +
279N GLU* 3.5 31.7 + - - -
452N ILE 3.1 7.8 + - - +
453N TYR* 2.9 12.0 + - + +
455N THR* 1.3 78.0 - - - +
457N ASN* 1.3 71.7 + - - +
459N TYR* 2.8 8.5 + - - +
460N SER* 2.8 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 457 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15N LYS* 5.4 0.6 - - - +
401N VAL* 3.5 17.7 - - + +
453N TYR* 3.1 60.5 + - - +
454N GLU* 3.4 14.1 + - - +
456N LYS* 1.3 82.6 - - - +
458N GLY* 1.3 54.0 + - - +
460N SER* 2.8 10.5 + - - +
461N ALA* 2.7 37.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 458 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339N LEU* 4.9 3.7 - - - +
367N ILE* 4.7 8.1 - - - -
396N LEU* 3.4 31.2 - - - +
401N VAL* 3.8 4.5 - - - +
454N GLU 2.8 14.1 + - - -
455N THR 2.9 5.5 + - - -
457N ASN* 1.3 79.8 - - - +
459N TYR* 1.3 65.8 + - - +
461N ALA 3.5 12.1 + - - -
462N PHE* 3.8 4.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 459 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102N LEU* 4.1 17.5 - - + +
269N CYS* 3.8 9.6 - - - +
272N THR* 3.1 24.7 - - - -
273N SER* 3.3 36.8 - - - -
276N ALA* 3.7 11.7 - - + -
339N LEU* 4.0 23.6 - - + -
341N SER* 2.7 33.6 + - - -
367N ILE* 3.8 19.1 - - + -
433N CYS* 4.3 6.3 - - + -
434N GLY 4.1 2.3 + - - -
455N THR* 2.9 25.0 + - + +
456N LYS* 2.8 7.8 + - - +
458N GLY* 1.3 74.2 - - - +
460N SER* 1.3 55.8 + - - +
462N PHE* 2.7 40.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 460 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276N ALA* 3.8 22.1 - - - +
279N GLU* 5.6 7.0 - - - -
280N MET* 5.5 4.9 - - - -
456N LYS* 2.8 14.3 + - - +
457N ASN* 2.8 30.8 + - - -
459N TYR* 1.3 73.1 - - - +
461N ALA* 1.3 56.1 + - - +
462N PHE 2.8 6.4 + - - -
463N LEU* 3.1 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 461 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395N ILE* 2.8 29.3 - - + +
396N LEU* 4.3 11.5 - - + +
399N GLU* 3.6 37.2 - - + +
401N VAL* 4.7 1.8 - - + -
457N ASN 2.7 23.9 + - - +
458N GLY 3.7 7.4 - - - +
459N TYR 3.0 0.8 + - - -
460N SER* 1.3 69.9 + - - +
462N PHE* 1.3 56.5 + - - +
463N LEU* 3.5 9.9 - - - -
464N ASN 5.3 0.7 - - - +
----------------------------------------------------------
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