Contacts of the strand formed by residues 154 - 163 (chain H) in PDB entry 1CBV
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 PHE 154 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H LEU* 4.7 13.9 - - + -
118H THR* 4.8 15.5 - - + -
120H SER* 3.5 37.7 - - - -
122H ALA* 3.7 23.8 - - + -
123H LYS 3.1 26.5 - - - +
124H THR* 3.3 6.8 - - - -
125H THR 3.1 26.5 + - - +
153H TYR* 1.3 74.6 - - - +
155H PRO* 1.3 88.5 - - + +
178H LEU* 6.2 0.4 - - + -
181H GLY 4.6 7.0 - - - -
182H LEU* 3.9 11.0 - - + -
183H TYR* 4.2 23.6 - + - -
207H HIS* 3.3 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 155 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H LEU* 4.0 24.7 - - + -
118H THR* 5.5 2.7 - - + -
124H THR* 4.0 7.9 - - - +
153H TYR* 3.3 15.0 - - - -
154H PHE* 1.3 116.2 - - + +
156H GLU* 1.3 65.7 + - + +
157H SER* 2.6 21.3 + - - +
183H TYR* 4.7 0.9 - - + -
207H HIS* 3.7 6.5 + - - +
209H ALA* 3.8 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 156 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H LEU* 5.3 5.1 - - + +
116H LEU* 3.2 34.0 - - + +
118H THR* 5.0 15.7 + - + +
153H TYR* 3.0 22.5 + - - -
155H PRO* 1.3 82.5 - - + +
157H SER* 1.3 76.1 + - - +
176H ALA* 4.8 4.3 - - - +
183H TYR* 4.1 23.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 157 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153H TYR* 4.7 0.2 - - - -
155H PRO 2.6 8.3 + - - +
156H GLU* 1.3 97.1 + - - +
158H VAL* 1.3 72.3 + - - +
207H HIS* 3.8 7.1 - - - -
208H PRO* 3.5 22.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 158 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127H PRO* 4.8 3.4 - - + -
150H VAL* 4.1 12.8 - - + -
153H TYR* 3.4 46.0 + - + +
157H SER* 1.3 76.9 - - - +
159H THR* 1.3 72.1 + - - +
160H VAL* 4.2 1.3 - - + +
185H MET* 4.5 19.4 - - + +
205H VAL* 3.5 28.9 - - + -
206H ALA 3.3 10.5 - - - +
207H HIS* 3.6 14.6 - - + -
208H PRO* 4.8 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 159 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158H VAL* 1.3 78.8 + - - +
160H VAL* 1.3 58.5 - - - +
161H THR* 3.7 13.6 + - - +
204H SER 2.8 22.7 - - - +
205H VAL* 3.6 0.3 - - - -
206H ALA* 3.4 24.1 + - + +
208H PRO* 5.4 3.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 160 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148H CYS* 4.9 1.8 - - + -
150H VAL* 4.9 6.3 - - + -
158H VAL* 4.2 2.6 - - + -
159H THR* 1.3 74.9 - - - +
161H THR* 1.3 67.9 + - - +
162H TRP* 4.2 7.5 + - - +
171H VAL* 5.4 1.7 - - - +
173H THR* 4.5 21.5 + - + +
185H MET* 4.2 21.8 - - + -
187H SER* 3.7 34.5 + - - +
203H CYS* 4.4 14.4 - - + -
204H SER 3.4 2.0 - - - -
205H VAL* 4.1 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 161 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159H THR* 3.7 15.6 + - - +
160H VAL* 1.3 74.5 - - - +
162H TRP* 1.3 67.2 + - - +
203H CYS* 3.2 4.3 - - - +
204H SER* 2.6 58.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 162 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147H GLY* 3.4 35.9 - - - -
148H CYS* 3.6 18.4 - - + -
160H VAL* 4.2 8.2 + - + +
161H THR* 1.3 83.3 - - - +
163H ASN* 1.3 61.4 + - - +
164H SER* 3.8 5.2 + - - +
171H VAL* 3.7 27.2 - - + +
187H SER* 2.7 34.1 + - - -
188H SER 4.2 0.8 + - - -
189H VAL* 3.7 31.0 - - + -
201H VAL* 3.4 28.0 - - + -
202H THR 3.1 21.1 - - - -
203H CYS* 3.7 21.1 - - + -
204H SER* 5.7 0.4 - - - -
218H LEU* 4.0 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 163 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161H THR 4.3 0.2 - - - -
162H TRP* 1.3 70.0 - - - +
164H SER* 1.3 61.6 + - - +
165H GLY* 4.2 7.3 + - - -
200H THR* 2.6 29.5 + - - +
201H VAL* 3.0 6.4 - - - +
202H THR* 2.6 60.0 + - + +
204H SER* 5.4 3.7 + - - +
----------------------------------------------------------
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