Contacts of the strand formed by residues 179 - 187 (chain H) in PDB entry 2CK0
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 TYR 179 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148H GLY 2.7 31.7 + - - -
149H TYR* 2.9 50.3 + + + +
150H PHE* 4.0 17.6 - + - -
152H GLU* 3.9 42.0 - - + +
172H ALA* 3.8 14.8 - - + -
173H VAL 3.5 16.6 - - - -
174H LEU* 3.5 42.9 - - + +
178H LEU* 1.3 71.9 - - - +
180H THR* 1.3 57.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 180 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145H LEU* 4.2 14.8 - - + -
146H VAL 3.6 3.1 - - - -
147H LYS* 3.4 39.6 + - + +
148H GLY* 3.9 1.7 + - - -
171H PRO 4.6 0.7 - - - +
172H ALA* 3.4 2.3 - - - -
173H VAL* 3.0 31.3 + - - +
175H GLN* 5.4 2.8 - - - +
178H LEU* 4.9 2.1 + - - +
179H TYR* 1.3 78.8 + - - +
181H LEU* 1.3 65.2 + - - +
159L LEU* 4.0 34.0 - - + +
177L THR* 5.1 8.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 181 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145H LEU* 3.8 5.3 - - - +
146H VAL* 2.7 51.4 + - + +
149H TYR* 3.8 23.8 - - + +
152H GLU* 5.0 3.4 - - - +
154H VAL* 4.7 10.1 - - + +
156H VAL* 3.6 31.0 - - + -
169H THR* 4.2 11.9 - - + -
170H PHE 3.5 21.3 - - - +
171H PRO* 4.9 1.8 - - + -
172H ALA* 3.9 14.4 - - + +
180H THR* 1.3 76.9 - - - +
182H SER* 1.3 72.6 + - - +
159L LEU* 6.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 182 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128H LEU* 5.4 0.2 - - - -
144H CYS 3.4 10.5 - - - -
145H LEU* 4.6 11.4 - - - -
169H THR* 3.7 1.2 - - - -
170H PHE* 3.1 34.7 + - - +
181H LEU* 1.3 80.4 - - - +
183H SER* 1.3 62.5 + - - +
132L VAL* 5.0 3.1 - - - -
134L PHE* 3.7 18.6 - - - -
175L SER* 3.0 30.2 + - - -
177L THR* 5.3 3.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 183 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143H GLY* 3.2 2.3 - - - -
144H CYS* 2.8 36.5 + - - -
146H VAL* 5.8 0.4 - - - -
156H VAL* 3.5 25.8 - - - +
158H TRP* 2.9 30.5 + - - -
167H VAL* 4.0 1.9 - - - +
168H HIS 3.3 7.3 + - - -
169H THR* 3.1 20.9 + - - -
181H LEU* 5.1 0.4 - - - -
182H SER* 1.3 76.1 - - - +
184H SER* 1.3 60.0 + - - +
134L PHE* 4.0 3.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 184 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141H THR* 4.2 5.4 - - - -
142H LEU 3.4 6.7 - - - -
143H GLY* 4.1 0.4 - - - -
158H TRP* 4.4 1.6 - - - -
166H GLY 3.5 0.6 + - - +
167H VAL* 3.1 7.3 - - - +
168H HIS* 2.9 47.8 + - - +
170H PHE* 3.9 2.9 - - - -
183H SER* 1.3 74.6 + - - +
185H VAL* 1.3 62.1 + - - +
186H THR* 5.6 0.7 + - - -
134L PHE* 3.5 32.5 - - - -
136L ASN* 3.2 21.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 185 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140H VAL 3.9 1.0 - - - +
141H THR* 3.4 3.3 - - - -
142H LEU* 2.8 56.5 + - + +
158H TRP* 3.8 35.4 - - + -
163H LEU* 4.0 23.6 - - + -
165H SER 4.5 5.4 - - - +
166H GLY 3.4 4.0 - - - +
167H VAL* 3.6 22.4 - - + -
184H SER* 1.3 74.6 - - - +
186H THR* 1.3 65.0 + - - +
187H VAL* 4.1 10.3 + - + -
197H VAL* 4.4 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 186 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139H MET* 4.0 40.4 - - + +
140H VAL 3.9 8.1 - - - +
141H THR* 3.6 23.0 + - - +
165H SER 4.5 4.2 - - - +
166H GLY* 3.2 28.1 + - - -
168H HIS* 5.6 2.6 + - - -
184H SER* 5.6 0.9 + - - -
185H VAL* 1.3 75.0 - - - +
187H VAL* 1.3 66.7 + - - +
188H PRO* 4.7 0.9 - - - +
136L ASN* 5.4 3.1 + - - -
137L ASN* 5.8 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 187 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139H MET* 3.2 4.7 - - - -
140H VAL* 2.8 38.1 + - + +
142H LEU* 4.4 11.0 - - + -
163H LEU* 3.9 37.7 - - + -
185H VAL* 4.3 6.7 - - + +
186H THR* 1.3 77.6 - - - +
188H PRO* 1.3 76.8 - - + +
191H PRO* 4.5 7.6 - - + +
192H ARG* 4.2 26.9 - - + -
197H VAL* 4.6 6.1 - - + -
----------------------------------------------------------
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