Contacts of the helix formed by residues 389 - 403 (chain A) in PDB entry 3QN3
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 ARG 389 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A SER* 3.0 29.5 + - - -
16A ARG* 4.8 3.6 - - - +
201A LEU* 4.0 9.0 + - + +
202A GLY 3.0 18.5 + - - -
203A ASP* 3.3 21.2 + - - +
205A GLY* 3.5 27.6 - - - +
388A ALA* 1.3 78.3 - - - +
390A GLY* 1.3 60.3 - - - +
391A GLU* 2.8 33.2 + - - +
392A ARG* 2.9 7.9 + - + -
393A THR* 2.9 26.0 + - - -
15B SER* 2.9 15.6 + - - -
201B LEU* 3.7 25.1 - - - +
388B ALA* 4.7 0.2 - - - +
389B ARG* 3.7 36.6 - - + +
391B GLU* 3.7 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A GLU* 4.9 1.1 - - - -
389A ARG* 1.3 72.4 - - - +
391A GLU* 1.3 56.0 + - - +
392A ARG 3.0 0.2 - - - -
393A THR* 3.3 11.8 + - - -
394A ALA* 2.9 33.8 + - - +
15B SER* 4.1 3.2 - - - -
365B SER* 5.4 0.7 - - - -
366B GLU* 4.6 10.2 - - - +
390B GLY* 4.5 1.6 - - - -
391B GLU* 2.9 36.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 391 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A SER* 3.2 28.4 + - - +
203A ASP 3.4 0.5 - - - +
364A GLU* 3.6 4.5 - - + +
365A SER 3.3 30.1 - - - +
366A GLU* 4.4 0.7 - - - +
389A ARG* 2.8 40.0 + - - +
390A GLY* 1.3 70.2 - - - +
392A ARG* 1.3 92.4 + - - +
394A ALA* 4.7 0.2 - - - -
395A LYS* 2.8 34.0 + - - +
389B ARG* 3.8 0.5 - - - -
390B GLY* 2.8 24.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A SER* 3.5 8.3 + - - -
203A ASP 3.0 21.1 + - - -
204A GLU* 3.8 16.7 - - - +
360A HIS* 2.9 28.4 + - - -
361A ARG 2.8 23.0 + - - -
362A SER 2.7 26.5 + - - -
364A GLU* 3.3 9.4 - - - +
384A THR* 3.3 24.5 - - - +
385A GLY* 4.0 5.2 - - - -
386A ALA 3.5 15.0 - - - +
388A ALA 3.5 15.3 - - - +
389A ARG* 2.9 5.5 + - + +
391A GLU* 1.3 106.8 + - - +
393A THR* 1.3 64.5 - - - +
394A ALA 3.2 1.3 - - - -
395A LYS* 3.1 19.3 + - - +
396A TYR* 3.4 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 393 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A LEU* 3.9 9.0 - - - +
388A ALA* 3.8 25.1 - - - +
389A ARG 2.9 13.3 + - - +
390A GLY* 3.3 20.3 - - - -
392A ARG* 1.3 73.9 - - - +
394A ALA* 1.3 57.5 + - - +
396A TYR* 3.9 8.4 - - + +
397A ASN* 2.9 36.0 + - - +
13B LEU* 4.2 24.0 + - + -
14B ASP 3.5 24.6 + - - +
15B SER* 4.3 1.9 - - - -
365B SER* 5.9 0.7 - - - -
366B GLU* 4.5 4.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 394 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A GLU* 3.7 26.7 - - - +
368A ALA* 3.7 6.9 - - + +
390A GLY 2.9 21.1 + - - +
391A GLU 4.7 0.7 - - - -
392A ARG 3.2 0.2 - - - -
393A THR* 1.3 75.7 + - - +
395A LYS* 1.3 64.1 + - + +
397A ASN* 3.7 1.6 - - - +
398A ARG* 2.9 28.9 + - - +
366B GLU* 3.6 29.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 395 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A GLU* 2.8 26.1 + - - -
365A SER 2.8 15.0 + - - -
366A GLU 4.7 0.2 - - - -
367A ASP 2.8 27.7 + - - +
368A ALA* 4.1 14.6 - - - -
370A ILE* 3.9 26.7 - - + -
371A ALA* 3.7 10.4 - - + +
382A ILE* 5.1 2.0 - - + -
384A THR* 3.4 30.5 - - + +
391A GLU 2.8 28.7 + - - +
392A ARG 3.1 8.5 + - - +
394A ALA* 1.3 76.6 - - + +
396A TYR* 1.3 59.3 + - - +
398A ARG 3.3 0.5 + - - -
399A LEU* 2.9 34.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 396 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A PRO* 3.9 21.5 - - + +
145A MET 4.8 0.2 + - - -
146A CYS* 3.4 12.8 - - - -
174A PHE* 4.2 10.2 - + - -
178A LEU* 3.5 33.0 - - + -
382A ILE* 5.3 0.9 - - + -
384A THR* 3.4 28.9 + - + +
385A GLY 2.5 23.4 + - - -
386A ALA 3.5 21.3 - - - -
387A LEU* 3.7 16.8 - - + -
392A ARG 3.4 21.3 + - - -
393A THR* 3.4 14.2 + - + +
395A LYS* 1.3 75.3 - - - +
397A ASN* 1.3 58.2 + - - +
399A LEU* 3.2 12.1 + - + +
400A LEU* 2.9 31.9 + - - +
13B LEU* 4.4 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 397 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A THR 2.9 22.8 + - - +
394A ALA 3.7 4.5 - - - +
396A TYR* 1.3 73.9 - - - +
398A ARG* 1.3 65.2 + - - +
400A LEU* 3.1 11.3 + - - +
401A GLU* 3.0 28.2 + - + +
12B VAL* 3.5 25.2 - - + +
13B LEU* 2.9 48.0 + - - +
22B LYS* 6.2 2.2 - - + +
36B ILE* 4.5 1.5 - - + +
366B GLU* 3.0 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 398 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A PRO* 3.9 23.2 - - - +
129A LEU* 4.4 3.4 - - - +
130A TYR* 4.2 0.6 - - - -
368A ALA* 3.7 18.6 - - + -
371A ALA* 3.8 12.3 - - + -
372A ASP* 2.8 43.1 + - - +
394A ALA 2.9 17.9 + - - +
395A LYS 3.3 3.3 + - - +
397A ASN* 1.3 76.2 - - - +
399A LEU* 1.3 57.4 + - - +
401A GLU* 3.1 39.8 + - - +
402A ILE* 2.9 43.4 + - + +
405A GLU* 5.5 2.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LEU* 4.2 7.4 - - + +
142A PRO* 4.0 22.7 - - + -
174A PHE* 3.6 35.2 - - + -
371A ALA* 3.7 30.5 - - + +
375A VAL* 3.7 20.4 - - + -
382A ILE* 4.4 20.0 - - + -
384A THR* 5.6 0.4 - - + -
395A LYS 2.9 19.1 + - - +
396A TYR* 3.2 16.6 + - + +
398A ARG* 1.3 76.0 - - - +
400A LEU* 1.3 56.0 - - - +
402A ILE* 3.3 6.0 + - + +
403A GLU* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 400 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A PHE* 3.9 7.9 - - + -
175A LYS* 3.9 23.8 - - + -
178A LEU* 3.7 30.5 - - + -
396A TYR 2.9 17.4 + - - +
397A ASN* 3.1 15.0 + - - +
399A LEU* 1.3 75.5 - - - +
401A GLU* 1.3 59.9 + - + +
403A GLU* 3.5 31.3 - - - +
404A PHE* 3.3 23.3 - - + -
10B TYR* 5.5 2.2 - - + -
11B GLU 3.6 25.8 - - - +
12B VAL* 4.0 18.8 - - + -
13B LEU* 4.8 2.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 401 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A ASN* 3.0 19.6 + - - +
398A ARG* 3.1 42.0 + - - +
400A LEU* 1.3 74.2 - - - +
402A ILE* 1.3 65.9 + - - +
404A PHE* 3.2 25.5 + - - +
405A GLU* 4.2 6.8 + - - +
10B TYR* 2.4 38.9 + - + +
12B VAL* 5.4 0.4 - - + -
22B LYS* 2.6 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 402 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A TYR* 3.8 44.0 - - + -
141A LEU* 4.0 16.2 - - + -
371A ALA 4.4 0.7 - - - +
372A ASP* 4.0 30.5 - - - +
375A VAL* 4.0 22.9 - - + -
398A ARG* 2.9 37.2 + - + +
399A LEU* 3.3 8.9 + - + +
401A GLU* 1.3 75.2 - - - +
403A GLU* 1.3 57.6 + - - +
405A GLU* 2.9 25.2 + - - +
406A SER* 2.9 14.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 403 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LEU* 3.6 15.9 - - + +
173A SER* 4.0 7.3 - - - -
174A PHE* 3.3 19.1 + - + -
175A LYS* 3.0 44.1 + - - +
399A LEU 3.0 16.6 + - - +
400A LEU* 3.5 21.4 - - - +
401A GLU 3.1 0.4 - - - -
402A ILE* 1.3 76.6 - - - +
404A PHE* 1.3 60.5 + - + +
405A GLU 3.4 0.3 + - - -
406A SER 3.4 11.1 - - - -
407A ASP* 3.4 30.0 + - + +
----------------------------------------------------------
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