Contacts of the helix formed by residues 205 - 217 (chain K) in PDB entry 2ZHX
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 205 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A SER* 3.6 14.3 + - - -
48A ASN* 2.9 28.0 + - - +
51A ARG* 3.5 52.5 - - - +
54A THR* 4.1 17.8 + - - +
100K GLU* 2.9 20.5 + - - -
103K ALA* 3.8 24.9 - - - +
104K ASP* 3.2 36.6 - - - +
203K GLY* 3.0 19.2 - - - +
204K SER* 1.3 74.9 - - - +
206K PRO* 1.3 67.6 - - - +
208K SER* 4.0 5.4 - - - +
209K ARG* 3.0 32.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 206 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100K GLU* 3.7 17.0 - - + -
104K ASP* 3.8 3.6 - - - +
166K ILE* 4.2 15.5 - - + -
168K TRP* 4.7 5.8 - - + +
187K ILE* 3.8 24.8 - - + +
201K PHE* 4.6 8.5 - - + -
204K SER* 3.2 21.1 - - - +
205K ARG* 1.3 89.3 - - - +
207K PHE* 1.3 84.9 + - + +
209K ARG* 4.4 0.7 - - + -
210K ALA* 2.8 34.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 207 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64K ILE* 5.2 0.4 - - + -
97K ILE* 3.6 29.4 - - + -
100K GLU* 4.1 2.5 - - + -
101K TYR* 3.3 45.3 - + + -
104K ASP* 3.0 12.4 + - + +
105K LEU* 4.0 17.0 - - + -
118K TRP* 3.9 21.5 - + - -
166K ILE* 5.0 4.3 - - + -
168K TRP* 4.8 10.3 - + - -
201K PHE* 5.5 0.2 - + - -
206K PRO* 1.3 95.8 - - + +
208K SER* 1.3 61.9 + - - +
210K ALA* 3.6 1.4 - - - +
211K ASN* 3.2 13.7 + - - +
224K TRP* 3.1 60.5 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 208 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ASN* 5.8 1.4 + - - -
104K ASP* 2.9 31.0 + - - -
105K LEU* 4.4 11.1 - - - +
205K ARG* 3.5 9.4 + - - +
207K PHE* 1.3 73.6 - - - +
209K ARG* 1.3 58.5 + - - +
211K ASN* 3.0 11.3 + - - +
212K GLU* 2.8 51.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 209 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ARG* 4.5 4.3 - - - +
77A VAL* 5.9 2.7 - - + -
85A PRO* 4.5 8.9 - - + +
114A ASP* 2.3 44.5 + - - -
116A THR* 3.5 30.6 + - - +
117A PRO* 4.6 4.4 - - - +
120A GLN* 4.4 3.4 + - - -
187K ILE* 3.9 39.4 - - + +
188K GLU 4.4 12.1 + - - +
204K SER* 2.9 27.7 + - - +
205K ARG* 3.0 24.0 + - + +
206K PRO* 3.9 3.4 - - + +
208K SER* 1.3 81.6 + - - +
210K ALA* 1.3 53.1 + - - +
212K GLU* 3.1 18.6 + - - +
213K LEU* 2.7 40.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 210 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62K VAL* 4.5 5.8 - - + -
164K VAL* 3.7 27.7 - - + +
166K ILE* 4.5 10.5 - - + -
187K ILE* 4.5 2.1 - - + +
206K PRO 2.8 23.6 + - - +
207K PHE 3.6 4.9 - - - +
209K ARG* 1.3 70.7 - - - +
211K ASN* 1.3 57.5 + - - +
213K LEU* 3.3 5.5 - - - +
214K LEU* 2.9 33.7 + - - +
224K TRP* 4.4 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 211 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105K LEU* 5.1 4.2 - - - +
207K PHE 3.2 5.8 + - - +
208K SER* 3.0 13.4 + - - +
210K ALA* 1.3 75.6 - - - +
212K GLU* 1.3 67.5 + - + +
214K LEU* 3.0 8.8 + - - +
215K VAL* 2.8 28.5 + - - +
221K PRO* 3.2 15.5 - - + +
222K ILE* 2.5 42.1 + - - +
224K TRP* 3.0 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 212 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A GLY* 4.9 3.5 - - - +
77A VAL* 4.9 8.1 - - - +
84A ALA* 3.8 19.4 - - - +
85A PRO* 4.0 16.7 - - + +
86A ASP* 3.3 29.9 - - - +
208K SER* 2.8 31.5 + - - +
209K ARG* 3.5 23.5 + - - +
211K ASN* 1.3 72.2 - - + +
213K LEU* 1.3 65.6 + - - +
215K VAL* 3.2 7.3 + - - +
216K GLY 2.8 18.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 213 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A PRO* 3.3 32.7 - - + +
86A ASP 5.2 0.7 - - - +
112A ASN* 4.3 7.0 - - - +
114A ASP* 6.1 0.2 - - - +
164K VAL* 3.7 23.3 - - + -
185K VAL* 4.1 32.8 - - + -
187K ILE* 3.7 30.1 - - + -
209K ARG* 2.7 19.2 + - + +
210K ALA* 3.3 9.2 - - - +
212K GLU* 1.3 72.5 - - - +
214K LEU* 1.3 67.1 + - - +
216K GLY* 3.0 11.2 + - - -
217K MET* 3.1 19.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 214 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61K ARG* 3.6 33.7 - - + +
62K VAL* 4.0 10.1 - - + -
162K PRO 4.5 7.2 - - - +
164K VAL* 3.9 11.9 - - + +
210K ALA 2.9 18.2 + - - +
211K ASN* 3.0 8.9 + - - +
213K LEU* 1.3 71.9 - - - +
215K VAL* 1.3 65.9 + - - +
217K MET* 2.7 24.8 + - + +
218K GLY 3.2 0.2 + - - -
219K ALA* 3.1 29.5 + - + +
220K GLU 3.6 25.4 - - - +
221K PRO* 4.1 0.9 - - + -
222K ILE* 3.9 32.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 215 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ASP* 4.8 11.0 - - - +
211K ASN* 2.8 26.8 + - + +
212K GLU* 3.6 8.3 - - - +
214K LEU* 1.3 71.0 - - - +
216K GLY* 1.3 55.1 + - - +
218K GLY* 2.8 23.7 + - - -
219K ALA 3.5 10.7 + - - +
221K PRO* 4.3 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 216 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ASP* 3.9 22.6 - - - +
212K GLU 2.8 14.3 + - - -
213K LEU 3.0 5.4 + - - -
214K LEU 2.9 0.2 + - - -
215K VAL* 1.3 77.2 - - - +
217K MET* 1.3 57.4 + - - +
218K GLY 3.3 3.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 217 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162K PRO* 3.7 34.0 - - + +
163K LEU 4.4 2.5 - - - +
164K VAL* 3.8 21.1 - - + -
183K ASN* 3.5 29.2 - - + +
185K VAL* 4.0 22.9 - - + -
213K LEU* 3.1 31.2 + - + +
214K LEU* 2.7 14.8 + - + +
216K GLY* 1.3 71.2 - - - -
218K GLY* 1.3 59.1 + - - -
219K ALA 3.3 1.0 + - - -
----------------------------------------------------------
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