Contacts of the helix formed by residues 389 - 403 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C SER* 2.9 30.3 + - - -
16C ARG* 4.8 3.0 - - - +
201C LEU* 4.2 20.1 + - + +
202C GLY 2.9 20.6 + - - -
203C ASP* 3.2 27.1 + - - +
205C GLY* 3.5 27.1 - - - +
388C ALA* 1.3 76.6 - - - +
390C GLY* 1.3 55.5 + - - +
391C GLU* 2.8 31.8 + - - +
392C ARG* 2.8 25.9 + - + -
393C THR* 2.9 12.9 + - - -
15D SER* 2.9 17.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 390 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366C GLU* 5.0 3.5 - - - -
389C ARG* 1.3 70.1 - - - +
391C GLU* 1.3 57.8 + - - +
393C THR* 3.2 12.5 + - - -
394C ALA* 2.8 32.4 + - - +
15D SER* 3.9 16.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 391 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C SER* 3.2 34.1 + - - +
203C ASP 3.2 0.2 - - - +
364C GLU* 3.5 10.1 - - + +
365C SER* 3.3 29.2 - - - +
366C GLU* 4.6 1.8 - - - +
384C THR* 4.8 0.2 + - - -
389C ARG* 2.8 42.0 + - - +
390C GLY* 1.3 77.0 + - - +
392C ARG* 1.3 90.9 + - - +
394C ALA* 4.8 0.4 - - - -
395C LYS* 2.9 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 392 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C SER* 3.6 7.9 + - - -
203C ASP 3.0 22.0 + - - -
204C GLU* 3.7 17.2 - - - +
360C HIS* 2.8 33.5 + - - -
361C ARG 2.9 17.6 + - - -
362C SER 2.7 26.5 + - - -
364C GLU* 3.5 8.4 - - - +
384C THR* 3.3 25.1 - - - +
385C GLY* 4.0 4.3 - - - -
386C ALA 3.6 15.9 - - - +
388C ALA 3.4 17.3 - - - +
389C ARG* 2.8 5.4 + - + +
391C GLU* 1.3 105.4 + - - +
393C THR* 1.3 59.7 + - - +
394C ALA 3.2 1.1 - - - -
395C LYS* 2.9 26.3 + - - +
396C TYR* 3.5 12.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 393 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387C LEU* 4.0 7.2 - - - +
388C ALA* 3.8 25.6 - - - +
389C ARG 2.9 11.3 + - - +
390C GLY* 3.2 21.3 + - - -
392C ARG* 1.3 75.0 - - - +
394C ALA* 1.3 58.9 + - - +
396C TYR* 3.2 8.7 + - + +
397C ASN* 2.8 37.9 + - - +
13D LEU* 4.2 25.1 + - + -
14D ASP 3.6 26.0 + - - +
15D SER* 4.2 1.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 394 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366C GLU* 3.6 31.2 - - + +
368C ALA* 3.5 12.5 - - + +
390C GLY 2.8 20.6 + - - +
391C GLU 4.8 0.4 - - - -
392C ARG 3.2 0.2 - - - -
393C THR* 1.3 75.8 + - - +
395C LYS* 1.3 63.8 + - + +
397C ASN* 3.9 9.2 - - - +
398C ARG* 3.1 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 395 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364C GLU* 2.7 32.1 + - - -
365C SER 3.0 15.2 + - - -
367C ASP 3.0 19.2 + - - +
368C ALA* 4.1 12.8 - - + -
370C ILE* 3.8 30.3 - - + -
371C ALA* 3.7 7.6 - - + +
382C ILE* 5.1 1.8 - - + -
384C THR* 3.4 29.8 - - + +
391C GLU 2.9 27.3 + - - +
392C ARG 2.9 8.8 + - - +
394C ALA* 1.3 77.8 - - + +
396C TYR* 1.3 68.1 + - - +
398C ARG* 3.3 3.5 + - - +
399C LEU* 3.0 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 396 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C PRO* 4.0 22.0 - - + +
145C MET 4.8 0.2 + - - -
146C CYS* 3.5 12.6 - - - -
174C PHE* 4.2 10.4 - + - -
178C LEU* 3.6 29.4 - - + -
384C THR* 3.6 28.2 + - + +
385C GLY 2.6 24.6 + - - -
386C ALA 3.6 13.9 - - - -
387C LEU* 3.5 25.1 - - + -
392C ARG 3.5 19.9 + - - -
393C THR* 3.2 14.2 + - + +
395C LYS* 1.3 76.2 - - - +
397C ASN* 1.3 62.1 + - - +
399C LEU* 3.1 11.8 + - + +
400C LEU* 3.0 26.4 + - - +
13D LEU* 4.3 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 397 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393C THR* 2.8 25.5 + - - +
394C ALA* 3.9 7.5 - - - +
396C TYR* 1.3 76.6 - - - +
398C ARG* 1.3 61.9 + - - +
400C LEU* 3.1 12.8 + - - +
401C GLU* 3.1 27.2 + - + +
12D VAL* 3.5 29.7 - - + +
13D LEU* 2.9 47.1 + - - +
22D LYS* 6.2 2.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 398 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C PRO* 3.8 24.2 - - - +
129C LEU* 4.3 3.2 - - - +
130C TYR* 4.1 4.4 - - - -
368C ALA* 3.7 16.6 - - + -
371C ALA* 3.8 12.6 - - + -
372C ASP* 2.8 44.0 + - - +
394C ALA 3.1 19.7 + - - +
395C LYS 3.3 5.6 + - - +
397C ASN* 1.3 75.4 - - - +
399C LEU* 1.3 56.9 + - - +
401C GLU* 3.0 42.3 + - - +
402C ILE* 2.9 39.4 + - + +
405C GLU* 5.8 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 399 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C LEU* 4.0 7.9 - - + +
142C PRO* 3.9 24.2 - - + -
174C PHE* 3.6 35.0 - - + -
371C ALA* 3.8 20.2 - - + +
375C VAL* 3.8 29.4 - - + -
382C ILE* 4.2 20.6 - - + -
384C THR* 5.5 0.2 - - + -
395C LYS* 3.0 21.2 + - + +
396C TYR* 3.1 12.5 + - + +
398C ARG* 1.3 76.5 - - - +
400C LEU* 1.3 56.0 + - - +
402C ILE* 3.4 5.6 + - + +
403C GLU* 3.0 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 400 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C PHE* 3.8 7.9 - - + -
175C LYS* 3.8 24.5 - - + -
178C LEU* 3.6 31.6 - - + -
396C TYR 3.0 16.9 + - - +
397C ASN* 3.1 14.6 + - - +
399C LEU* 1.3 76.3 - - - +
401C GLU* 1.3 60.1 + - - +
403C GLU* 3.5 30.3 - - - +
404C PHE* 3.3 24.0 - - + -
10D TYR* 5.5 1.3 - - + -
11D GLU 3.6 24.7 - - - +
12D VAL* 4.1 17.7 - - + -
13D LEU* 4.9 2.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 401 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397C ASN* 3.1 17.1 + - - +
398C ARG* 3.0 43.4 + - - +
400C LEU* 1.3 75.3 - - - +
402C ILE* 1.3 67.1 + - - +
403C GLU 3.1 1.2 + - - -
404C PHE* 3.2 25.6 + - - +
405C GLU* 4.1 7.4 + - - +
10D TYR* 2.5 38.3 + - + +
12D VAL* 5.5 0.2 - - + -
22D LYS* 2.6 30.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 402 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C TYR* 3.8 46.2 - - + +
141C LEU* 4.0 17.0 - - + -
371C ALA 4.3 1.6 - - - +
372C ASP* 3.9 26.9 - - - +
375C VAL* 4.1 23.6 - - + -
398C ARG* 2.9 38.9 + - + +
399C LEU* 3.4 8.0 + - + +
401C GLU* 1.3 77.9 - - - +
403C GLU* 1.3 56.2 + - - +
405C GLU* 2.9 24.1 + - - +
406C SER* 3.0 15.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 403 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C LEU* 3.7 13.7 - - + +
173C SER* 4.0 7.8 - - - -
174C PHE* 3.3 17.4 + - - +
175C LYS* 3.0 45.9 + - - +
399C LEU 3.0 16.8 + - - +
400C LEU* 3.5 21.6 - - - +
401C GLU 3.1 0.8 - - - -
402C ILE* 1.3 76.1 - - - +
404C PHE* 1.3 62.3 + - + +
405C GLU 3.2 0.9 + - - -
406C SER 3.5 11.1 - - - -
407C ASP* 3.5 28.2 - - + +
----------------------------------------------------------
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