Contacts of the strand formed by residues 204 - 212 (chain A) in PDB entry 6K0X
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 GLU 204 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLU* 5.9 0.2 - - - +
28A ASP* 5.2 1.0 + - - +
125A TYR* 2.8 40.6 + - - -
126A VAL* 5.1 4.2 - - - +
174A ILE* 4.0 22.6 - - + +
176A GLU* 5.2 5.4 - - - +
200A GLN* 3.3 7.2 + - - -
201A ALA* 2.8 55.0 + - + +
202A GLY 3.4 0.2 - - - -
203A GLN* 1.3 82.5 - - - +
205A THR* 1.3 59.8 + - - +
206A LEU* 3.8 12.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A ILE* 3.3 4.3 - - - +
175A LYS* 3.1 42.9 + - + +
176A GLU* 5.3 1.2 + - - -
198A SER* 5.5 5.6 - - - -
199A ARG 3.7 6.7 - - - +
200A GLN* 2.6 24.8 + - - +
204A GLU* 1.3 69.7 - - - +
206A LEU* 1.3 64.1 + - - +
207A SER* 4.0 4.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLU* 4.2 4.3 - - + +
28A ASP* 3.8 32.8 - - + +
31A LEU* 3.5 16.4 - - + -
125A TYR* 3.7 18.8 - - + +
172A VAL* 4.1 6.1 - - + -
173A THR 3.2 10.1 - - - +
174A ILE* 3.5 23.6 - - + -
198A SER* 3.2 7.3 - - - -
199A ARG* 2.7 41.9 + - + +
201A ALA* 3.5 30.3 - - + -
204A GLU* 4.0 9.2 - - + +
205A THR* 1.3 74.2 - - - +
207A SER* 1.3 61.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU* 4.5 1.1 - - - -
171A LEU 3.6 1.0 - - - +
172A VAL* 3.6 1.4 - - - -
173A THR* 2.8 54.9 + - - -
174A ILE 6.1 0.2 - - - -
179A PRO* 4.8 11.1 - - - +
195A THR* 4.2 6.1 + - - +
197A LEU 3.6 4.9 - - - -
198A SER* 2.9 19.4 + - - -
205A THR* 4.0 5.4 + - - +
206A LEU* 1.3 72.5 + - - +
208A VAL* 1.3 62.2 + - - +
209A LEU* 3.7 15.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU* 3.6 31.4 - - + -
32A LEU* 4.2 25.8 - - + +
35A ALA* 3.9 17.9 - - + -
170A TYR* 3.9 28.7 - - + -
171A LEU 3.3 7.4 - - - +
172A VAL* 4.4 11.7 - - + -
195A THR* 3.6 3.1 - - - +
196A ALA* 2.7 33.7 + - + -
197A LEU 2.8 15.6 + - - +
207A SER* 1.3 71.3 - - - +
209A LEU* 1.3 58.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A PHE 3.6 1.1 - - - +
170A TYR* 3.3 4.9 - - - -
171A LEU* 2.8 36.8 + - + +
173A THR* 4.0 26.9 - - + +
179A PRO* 4.0 25.8 - - + +
182A ILE* 4.0 23.8 - - + -
183A LEU* 4.3 8.3 - - + -
194A THR 3.4 5.2 - - - +
195A THR* 3.6 26.0 - - - +
207A SER* 4.1 13.7 - - - -
208A VAL* 1.3 81.1 - - - +
210A LYS* 1.3 60.7 + - - +
211A PHE* 3.7 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ALA* 5.4 0.6 - - - +
42A GLU* 2.4 43.2 + - - -
168A LEU* 4.2 12.6 - - + -
169A PHE 3.3 5.4 - - - +
170A TYR* 3.6 37.5 + - + +
192A GLN 3.7 0.5 - - - +
193A GLY* 3.4 4.0 - - - -
194A THR* 2.8 50.7 + - + +
196A ALA* 4.2 13.0 - - + -
208A VAL 4.1 0.2 + - - -
209A LEU* 1.3 73.4 - - - +
211A PHE* 1.3 65.5 + - - +
212A THR* 4.4 9.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A LEU* 4.1 2.0 - - - +
167A GLY 3.9 0.3 - - - +
168A LEU* 3.4 5.9 - - - +
169A PHE* 2.7 79.9 + + + +
171A LEU* 4.4 9.0 - - + -
182A ILE* 4.0 12.6 - - + -
183A LEU* 3.7 26.2 - - + -
186A MET* 3.4 42.0 - - + -
191A LEU* 4.4 14.4 - - + -
192A GLN 3.0 8.3 - - - +
193A GLY* 3.6 15.3 - - - -
209A LEU* 3.7 31.0 - - + -
210A LYS* 1.3 74.0 - - - +
212A THR* 1.3 61.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLU* 5.3 0.4 + - - +
163A LEU* 4.8 0.2 - - - -
165A PRO 5.0 1.8 - - - +
166A ARG 4.6 6.5 - - - +
167A GLY 3.4 17.0 - - - +
168A LEU* 3.6 21.1 - - + +
191A LEU* 3.3 9.9 - - - +
192A GLN* 2.8 37.4 + - - +
210A LYS* 4.4 11.6 + - - +
211A PHE* 1.3 75.6 + - - +
213A LYS* 1.3 61.9 + - - +
214A SER* 3.2 31.3 + - - +
----------------------------------------------------------
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