Contacts of the helix formed by residues 278 - 291 (chain D) in PDB entry 2R2N
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 278 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D PRO* 3.8 37.4 - - + +
105D SER* 5.9 0.2 - - - +
107D GLY 4.0 0.8 - - - -
108D GLN* 2.8 24.5 + - + +
109D MET 5.7 0.2 - - - +
110D ASP* 3.7 30.7 - - + +
276D GLY 3.4 0.2 + - - -
277D PRO* 1.3 69.8 - - - +
279D PRO* 1.4 70.6 - - + +
281D ILE* 3.9 0.7 - - - +
282D GLU* 2.7 61.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 279 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D TYR* 3.7 33.2 - - + -
7D ILE* 4.3 3.9 - - + +
104D PRO 3.5 15.9 - - - +
105D SER* 4.4 8.7 - - - +
107D GLY* 4.2 3.1 - - - -
277D PRO* 3.4 12.8 - - + -
278D LYS* 1.4 101.0 - - + +
280D LEU* 1.3 58.1 + - - +
282D GLU* 3.7 7.7 - - + +
283D ARG* 3.3 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 280 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D TYR* 3.7 30.5 - - + +
6D PHE* 4.6 4.5 - - + -
7D ILE* 3.7 32.5 - - + -
127D MET* 3.5 23.3 - - + +
226D LEU* 4.2 18.8 - - + -
256D ILE* 4.0 22.4 - - + -
277D PRO* 3.0 34.3 + - + +
279D PRO* 1.3 76.8 - - - +
281D ILE* 1.3 66.4 + - + +
282D GLU 3.2 1.1 - - - -
283D ARG* 3.0 15.2 + - - +
284D VAL* 3.2 17.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 281 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D ASP* 3.9 24.7 - - + +
111D LEU 4.2 6.1 - - - +
112D CYS* 4.0 10.8 - - - -
124D VAL* 6.1 0.2 - - + -
256D ILE* 5.2 3.6 - - + -
274D LEU* 3.7 42.0 - - + +
275D THR 4.0 1.1 - - - +
276D GLY* 3.5 42.6 - - - +
277D PRO 3.0 6.8 + - - +
278D LYS 3.9 2.7 - - - +
280D LEU* 1.3 75.0 - - + +
282D GLU* 1.3 57.3 + - - +
284D VAL* 3.2 7.1 + - + +
285D ILE* 2.8 52.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 282 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D PRO* 6.0 0.7 - - - +
110D ASP* 5.2 0.8 + - - -
278D LYS* 2.7 56.9 + - + +
279D PRO* 3.7 8.5 - - + +
280D LEU 3.2 0.2 - - - -
281D ILE* 1.3 74.8 - - - +
283D ARG* 1.3 91.1 + - - +
285D ILE* 3.5 10.2 + - - +
286D LEU* 3.2 30.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 283 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D ILE* 3.7 24.0 - - + -
11D SER* 2.8 42.9 + - - +
12D ALA* 3.3 13.9 + - - +
14D ARG* 2.7 37.4 + - - +
16D PRO* 5.7 1.2 - - - +
127D MET* 3.5 16.6 - - - -
279D PRO 3.3 18.3 + - - +
280D LEU 3.0 9.1 + - - +
282D GLU* 1.3 108.4 + - - +
284D VAL* 1.3 56.3 + - - +
286D LEU* 3.4 20.0 + - - +
287D HIS* 3.1 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 284 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D CYS* 4.2 6.7 - - - -
120D GLY* 4.8 2.7 - - - -
123D LYS* 3.9 26.0 - - + +
124D VAL* 4.3 12.1 - - + +
127D MET* 4.7 6.9 - - + -
256D ILE* 6.4 0.2 - - + -
274D LEU* 3.7 34.3 - - + -
280D LEU 3.2 16.8 - - - +
281D ILE* 3.2 12.5 + - + +
283D ARG* 1.3 73.9 - - - +
285D ILE* 1.3 60.5 + - - +
287D HIS* 3.4 7.7 + - - +
288D ILE* 2.9 46.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 285 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D SER* 4.1 22.2 - - - +
78D ALA* 3.8 25.4 - - + +
110D ASP* 4.7 7.0 - - - +
111D LEU 5.0 1.6 - - - +
112D CYS* 3.9 19.5 - - + -
281D ILE* 2.8 43.7 + - + +
282D GLU* 3.8 8.5 - - + +
284D VAL* 1.3 72.0 - - - +
286D LEU* 1.3 56.3 + - + +
288D ILE* 3.1 9.3 + - + +
289D GLN* 2.8 48.1 + - - +
427D GOL 4.9 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 286 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D ARG* 3.6 29.6 - - + +
15D ASN 4.3 2.7 - - - +
16D PRO* 3.7 28.7 - - + -
282D GLU* 3.2 22.7 + - + +
283D ARG* 3.4 47.8 - - - +
284D VAL 3.3 0.2 - - - -
285D ILE* 1.3 79.0 - - + +
287D HIS* 1.3 61.9 + - - +
289D GLN* 3.3 41.9 + - - +
290D VAL* 3.5 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 287 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C CYS* 4.6 0.9 - - - -
126C GLU* 3.0 25.8 + - - -
14D ARG* 3.4 41.9 + - - +
123D LYS* 3.6 34.1 + - + +
126D GLU* 3.1 35.7 + - + +
127D MET* 5.7 0.4 + - - -
283D ARG 3.1 13.2 + - - +
284D VAL* 3.6 9.4 - - - +
286D LEU* 1.3 74.3 - - - +
288D ILE* 1.3 65.6 + - - +
290D VAL* 3.1 14.9 + - + +
291D SER* 3.0 16.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 288 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D SER 3.9 15.5 - - - +
112D CYS* 4.9 4.9 - - + -
113D VAL 4.5 8.1 - - - +
114D THR* 4.1 15.7 - - + -
119D GLN* 3.7 31.4 - - + +
123D LYS* 4.0 9.9 - - + -
284D VAL* 2.9 39.0 + - + +
285D ILE* 3.1 10.3 + - + +
287D HIS* 1.3 72.2 - - - +
289D GLN* 1.3 57.2 - - - +
291D SER* 2.9 15.1 + - - -
292D THR* 3.2 16.1 + - - +
293D LEU 2.9 40.5 + - - +
294D HIS* 4.3 2.9 - - - +
295D PRO* 5.6 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 289 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C GLN* 5.1 0.2 + - - -
144C GLY* 6.0 1.4 - - - -
15D ASN 4.5 2.3 - - - +
16D PRO* 3.0 24.5 + - - +
20D ARG* 3.3 34.8 + - - +
77D SER* 3.2 31.6 + - - +
285D ILE* 2.8 26.6 + - - +
286D LEU* 3.4 28.7 - - - +
287D HIS 3.2 0.6 - - - -
288D ILE* 1.3 73.4 - - - +
290D VAL* 1.3 64.3 + - + +
293D LEU* 3.1 25.0 - - - +
427D GOL 5.6 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 290 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C GLN* 3.4 20.1 - - - +
122C CYS* 3.2 21.2 - - - +
144C GLY* 4.1 7.9 - - - +
147C GLN* 3.8 30.5 - - + +
148C SER* 3.9 26.6 + - - +
14D ARG* 3.6 27.8 - - - +
15D ASN 6.1 0.7 - - - +
286D LEU 3.5 8.7 + - - +
287D HIS* 3.1 15.7 + - + +
289D GLN* 1.3 81.8 - - + +
291D SER* 1.3 57.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 291 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C SER 4.6 0.2 - - - +
118C GLN* 3.3 10.9 - - - +
119C GLN* 3.1 34.6 + - - +
122C CYS* 3.8 21.5 - - - -
123C LYS* 5.6 3.4 - - - -
119D GLN* 4.3 0.9 + - - -
123D LYS* 2.9 31.5 + - - -
287D HIS* 3.0 12.0 + - - -
288D ILE* 2.9 11.2 + - - -
289D GLN 3.4 0.2 - - - -
290D VAL* 1.3 76.6 - - - +
292D THR* 1.3 69.9 + - - -
293D LEU 3.2 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