Contacts of the helix formed by residues 193 - 208 (chain T) in PDB entry 6FF7
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 GLY 193 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162T LEU* 6.1 5.2 - - - -
189T ASN 2.9 17.2 + - - -
190T ILE* 3.5 7.3 - - - -
191T VAL 3.1 0.2 - - - -
192T ARG* 1.3 77.2 - - - +
194T ARG* 1.3 57.2 + - - +
195T GLY 3.2 3.1 - - - -
196T LEU* 3.1 14.9 + - - +
197T LEU* 2.8 30.7 + - - +
382T LEU 5.9 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 194 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190T ILE 2.9 18.6 + - - +
191T VAL* 3.2 15.4 + - - +
192T ARG 3.3 1.4 + - - -
193T GLY* 1.3 77.7 - - - +
195T GLY* 1.3 56.5 + - - +
197T LEU* 3.9 4.8 - - - +
198T SER* 3.0 29.1 + - - -
229T ILE* 4.7 22.4 - - + +
232T LEU* 5.5 7.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 195 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192T ARG 4.9 0.8 + - - -
193T GLY 3.2 0.6 - - - -
194T ARG* 1.3 76.6 - - - +
196T LEU* 1.3 58.8 + - - +
198T SER* 3.3 5.6 + - - -
199T ARG* 2.8 31.9 + - - +
379T GLU 5.5 1.3 - - - -
382T LEU* 4.1 32.1 + - - +
383T ASN* 4.7 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 196 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162T LEU* 5.9 1.6 - - + +
163T LYS* 5.1 18.8 - - + +
166T ILE* 5.3 7.0 - - + -
193T GLY* 3.1 18.4 + - - +
195T GLY* 1.3 76.4 - - - +
197T LEU* 1.3 56.7 + - - +
199T ARG* 3.4 5.2 + - - +
200T SER* 2.9 30.2 + - - -
382T LEU 4.5 5.0 + - - +
383T ASN* 4.7 6.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 197 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166T ILE* 5.0 10.9 - - + +
190T ILE* 5.0 12.3 - - + -
193T GLY 2.8 20.4 + - - +
194T ARG* 3.9 7.4 - - - +
196T LEU* 1.3 70.8 - - - +
198T SER* 1.3 66.9 + - - +
200T SER* 3.3 5.4 + - - -
201T VAL* 3.0 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 198 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194T ARG 3.0 19.0 + - - -
195T GLY* 3.3 6.5 + - - -
197T LEU* 1.3 75.5 - - - +
199T ARG* 1.3 58.4 + - - +
201T VAL* 3.8 4.8 - - - +
202T LEU* 2.9 32.7 + - - +
229T ILE 5.4 1.8 - - - -
232T LEU* 4.9 9.0 - - - -
233T ILE* 4.5 29.6 - - - +
236T ARG* 6.0 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 199 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195T GLY 2.8 19.1 + - - +
196T LEU* 3.7 5.8 - - - +
198T SER* 1.3 77.4 - - - +
200T SER* 1.3 57.3 + - - +
202T LEU* 3.8 4.7 - - - +
203T GLN* 2.8 33.3 + - - +
383T ASN* 5.3 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 200 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166T ILE* 4.9 5.6 - - - -
167T ASN* 4.9 15.7 - - - -
170T ILE* 4.4 17.3 - - - +
196T LEU 2.9 18.5 + - - -
197T LEU* 3.8 6.1 - - - -
198T SER 3.3 0.2 - - - -
199T ARG* 1.3 76.0 - - - +
201T VAL* 1.3 57.2 + - - +
203T GLN* 4.1 3.5 - - - +
204T ALA* 2.9 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 201 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170T ILE* 5.1 4.6 - - - +
197T LEU 3.0 16.8 + - - +
198T SER* 3.8 4.9 - - - +
200T SER* 1.3 78.2 - - - +
202T LEU* 1.3 57.5 + - - +
204T ALA* 3.4 5.8 + - - +
205T GLN* 3.0 31.5 + - - +
215T TYR* 5.2 11.2 - - + +
219T VAL* 6.3 2.9 - - + -
233T ILE* 6.1 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 202 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198T SER 2.9 18.9 + - - +
199T ARG* 3.9 4.9 - - - +
201T VAL* 1.3 77.5 - - - +
203T GLN* 1.3 62.9 + - - +
205T GLN* 4.0 3.6 - - - +
206T SER* 3.1 24.4 + - - -
233T ILE 6.2 0.2 - - - +
236T ARG* 5.9 7.9 - - + -
237T LEU* 6.2 4.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 203 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199T ARG 2.8 22.5 + - - +
200T SER* 4.1 3.6 - - - +
202T LEU* 1.3 72.3 - - - +
204T ALA* 1.3 64.2 + - - +
206T SER* 3.3 6.6 + - - -
207T ALA* 3.0 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 204 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170T ILE* 4.8 18.4 - - + +
200T SER 2.9 20.0 + - - +
201T VAL* 3.7 6.3 - - - +
203T GLN* 1.3 78.0 - - - +
205T GLN* 1.3 51.6 + - - +
207T ALA* 3.2 4.5 + - - +
208T SER* 2.7 41.6 + - - -
215T TYR* 6.3 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 205 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201T VAL 3.0 16.9 + - - +
202T LEU* 4.1 4.3 - - - +
204T ALA* 1.3 74.8 - - - +
206T SER* 1.3 64.5 + - - +
208T SER 4.3 6.7 - - - +
209T PRO* 3.0 28.5 - - + +
211T PHE 6.2 0.2 - - - -
212T THR* 5.2 9.4 - - - +
215T TYR* 4.6 19.2 - - + +
255T THR* 4.5 4.5 - - - +
259T PHE* 5.2 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 206 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202T LEU 3.1 19.2 + - - -
203T GLN* 3.6 7.2 - - - -
204T ALA 3.2 0.2 - - - -
205T GLN* 1.3 79.4 - - - +
207T ALA* 1.3 59.5 + - - +
209T PRO* 4.6 2.4 - - - +
255T THR* 4.5 19.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 207 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203T GLN 3.0 16.1 + - - +
204T ALA* 4.0 3.6 - - - +
206T SER* 1.3 77.4 - - - +
208T SER* 1.3 60.9 + - - +
209T PRO 3.9 0.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 208 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204T ALA* 2.7 21.0 + - - +
205T GLN* 3.3 6.7 + - - -
207T ALA* 1.3 77.5 - - - +
209T PRO* 1.4 54.0 - - - +
210T ILE* 3.0 9.6 - - - +
211T PHE* 2.9 31.9 + - - +
----------------------------------------------------------
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