Contacts of the helix formed by residues 195 - 207 (chain I) in PDB entry 1SXG
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 195 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148I ILE* 3.7 35.7 - - + +
150I SER* 6.2 1.8 - - - +
161I TYR* 4.0 10.8 - - + -
162I GLU* 3.4 41.2 - - + +
191I ILE* 3.3 12.3 + - + +
193I HIS 3.5 0.6 - - - -
194I ALA* 1.3 98.8 - - + +
196I LYS* 1.3 64.1 + - - +
197I VAL 3.6 0.7 - - - -
198I LYS* 3.5 1.2 + - - +
199I GLY 2.8 23.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 196 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161I TYR* 4.4 13.5 - - - +
165I ALA* 3.4 17.0 - - + +
182I PHE* 4.0 16.4 - - + -
191I ILE* 2.9 42.0 + - + +
192I ASN* 3.5 26.0 - - - +
195I LYS* 1.3 70.2 - - - +
197I VAL* 1.3 68.2 + - - +
199I GLY* 2.8 12.8 + - - -
200I TYR* 2.8 11.3 + - - +
221I TYR* 5.8 3.0 - - - -
244I PHE* 5.1 1.6 - - + -
246I GLY* 3.2 35.0 + - - +
247I THR* 5.2 1.2 + - - -
274I PHE* 4.1 32.4 - - + -
275I ASP* 5.2 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 197 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182I PHE* 3.9 21.3 - - + -
184I SER* 5.7 0.4 - - - +
187I LEU* 5.7 8.3 - - + -
192I ASN 2.9 22.2 + - - +
193I HIS* 3.0 28.9 - - + +
196I LYS* 1.3 73.0 - - - +
198I LYS* 1.3 58.9 + - + +
200I TYR* 2.8 8.3 + - + +
201I LYS* 2.6 61.4 + - + +
216I ILE* 4.4 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 198 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162I GLU* 3.9 8.7 - - + +
193I HIS* 3.2 20.9 - - - +
194I ALA* 3.7 30.3 + - - +
195I LYS 3.5 8.0 + - - +
196I LYS 3.2 0.4 - - - -
197I VAL* 1.3 84.2 - - + +
199I GLY* 1.3 57.3 + - - +
201I LYS* 3.9 23.1 - - + +
202I ARG* 3.0 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 199 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162I GLU* 3.4 34.3 - - - +
165I ALA* 4.0 0.2 - - - -
166I PHE* 3.2 26.7 - - - +
195I LYS 2.8 7.7 + - - -
196I LYS 2.8 8.9 + - - -
198I LYS* 1.3 76.0 - - - +
200I TYR* 1.3 62.3 + - - +
202I ARG 4.0 0.2 - - - -
203I ALA* 3.4 12.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 200 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165I ALA* 4.3 0.9 - - - +
169I VAL* 4.0 22.0 - - + +
180I ILE* 2.5 35.2 + - + -
181I ALA* 3.6 14.2 - - - -
182I PHE* 3.7 29.4 - + + -
196I LYS 2.8 9.8 + - - +
197I VAL* 2.8 12.3 + - + +
199I GLY* 1.3 76.0 - - - +
201I LYS* 1.3 76.4 + - + +
202I ARG 3.3 0.2 + - - -
203I ALA* 3.4 2.9 + - - +
204I LEU* 3.0 50.6 + - + +
211I VAL* 4.9 3.1 - - + -
212I ARG 4.8 1.2 + - - -
215I TYR* 3.7 18.9 - - - +
216I ILE* 3.8 26.9 - - + -
244I PHE* 4.7 11.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 201 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197I VAL* 2.6 42.9 + - + +
198I LYS* 4.0 23.7 - - - +
200I TYR* 1.3 80.5 - - + +
202I ARG* 1.3 56.0 + - - +
204I LEU* 3.3 4.0 + - - +
205I THR* 2.9 36.7 + - + +
211I VAL* 3.6 35.0 - - + -
216I ILE* 4.4 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 202 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162I GLU* 2.7 43.7 + - - -
163I GLN* 3.2 19.8 + - - +
166I PHE* 2.9 42.2 - - + +
198I LYS 3.0 18.9 + - - +
199I GLY 4.1 1.1 - - - +
200I TYR 3.2 0.2 - - - -
201I LYS* 1.3 73.6 - - - +
203I ALA* 1.3 67.4 + - - +
204I LEU 2.9 1.2 + - - -
205I THR* 3.1 6.4 + - - -
206I GLU* 3.0 55.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 203 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166I PHE* 3.2 39.4 - - + +
169I VAL* 3.3 38.4 - - + -
170I GLN* 4.1 8.6 + - + +
173I ILE* 3.1 19.8 - - - +
199I GLY 3.4 3.3 + - - +
200I TYR 3.4 0.2 + - - -
202I ARG* 1.3 79.0 - - - +
204I LEU* 1.3 61.9 + - - +
206I GLU* 4.5 0.7 - - - +
207I SER* 3.8 10.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 204 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169I VAL* 4.0 20.2 - - + -
173I ILE* 4.6 0.2 - - + -
178I LYS 5.0 3.1 - - - +
180I ILE* 4.1 23.6 - - + +
200I TYR* 3.0 52.0 + - + +
201I LYS* 3.6 4.9 - - - +
202I ARG 2.9 1.6 + - - -
203I ALA* 1.3 76.5 - - - +
205I THR* 1.3 64.1 + - - +
207I SER 3.5 1.2 + - - -
209I LEU* 3.1 56.4 + - + +
210I PRO 4.1 15.3 - - - +
211I VAL* 4.3 12.6 - - + -
212I ARG* 5.3 0.9 - - - +
215I TYR* 5.8 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 205 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201I LYS* 2.9 22.3 + - + +
202I ARG* 3.4 7.1 + - - -
204I LEU* 1.3 67.2 - - - +
206I GLU* 1.3 61.0 + - - +
207I SER 3.1 2.2 - - - -
208I GLY* 2.6 28.2 + - - -
209I LEU 3.6 11.2 - - - +
210I PRO* 5.6 0.2 - - + -
211I VAL* 3.4 29.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 206 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166I PHE* 3.6 20.4 - - + -
170I GLN* 5.8 2.5 - - - +
202I ARG* 3.0 49.0 + - + +
203I ALA 4.5 3.1 - - - +
205I THR* 1.3 78.5 + - - +
207I SER* 1.3 57.4 + - - +
208I GLY* 3.1 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 207 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170I GLN* 5.2 5.8 - - - -
173I ILE* 3.3 26.9 - - - +
203I ALA 3.8 11.1 + - - -
204I LEU 3.5 1.2 + - - -
205I THR 3.1 1.0 + - - -
206I GLU* 1.3 76.4 - - - +
208I GLY* 1.3 54.7 + - - +
209I LEU* 2.9 31.4 + - - +
----------------------------------------------------------
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