Contacts of the strand formed by residues 214 - 219 (chain A) in PDB entry 1TSR
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 HIS 214 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A MET* 3.3 23.2 - - - +
161A ALA 4.7 1.2 + - - +
172A VAL* 4.5 7.4 - - + +
173A VAL 3.8 17.9 + - - +
174A ARG* 3.9 27.4 + - + -
192A GLN* 3.6 34.2 + - + +
193A HIS* 3.4 29.5 - + + +
194A LEU 5.1 0.4 + - - +
206A LEU 3.5 3.4 - - - -
207A ASP* 3.4 22.2 + - - -
212A PHE 3.6 15.8 + - - -
213A ARG* 1.3 75.9 - - - +
215A SER* 1.3 64.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A ARG* 3.3 34.2 + - - -
159A ALA 3.2 17.7 - - - -
160A MET* 4.2 14.6 - - - +
193A HIS* 3.7 8.5 - - - -
195A ILE 5.8 0.2 - - - -
205A TYR* 3.5 3.5 - - - -
206A LEU* 3.0 39.3 + - - +
213A ARG 5.3 0.3 + - - -
214A HIS* 1.3 78.8 - - - +
216A VAL* 1.3 61.4 + - - +
217A VAL* 4.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A VAL 3.7 1.0 - - - +
158A ARG* 3.3 2.7 - - - -
159A ALA* 2.9 39.1 + - + +
195A ILE* 3.7 36.3 - - + +
197A VAL* 3.6 21.3 - - + +
203A VAL* 3.4 31.2 - - + -
204A GLU 3.3 6.1 - - - +
205A TYR* 3.8 20.6 - - + -
215A SER* 1.3 74.8 - - - +
217A VAL* 1.3 62.9 + - - +
218A VAL* 5.6 0.2 - - - +
234A TYR* 5.2 1.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ARG* 3.7 46.2 - - + +
157A VAL 3.3 18.2 - - - +
158A ARG* 3.3 44.9 - - + +
202A ARG 4.1 0.3 - - - +
203A VAL* 3.4 0.5 - - - +
204A GLU* 2.6 61.8 + - + +
205A TYR* 5.4 0.4 - - - -
206A LEU* 5.5 0.4 - - + -
215A SER* 5.2 1.1 - - - +
216A VAL* 1.3 76.1 - - - +
218A VAL* 1.3 67.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ARG* 3.3 9.0 - - - +
157A VAL* 2.9 34.9 + - + +
197A VAL* 3.8 26.0 - - + -
200A ASN* 3.7 16.4 - - - +
202A ARG 4.5 0.9 - - - -
203A VAL* 3.7 23.3 - - + -
216A VAL 5.5 0.2 - - - -
217A VAL* 1.3 80.7 - - - +
219A PRO* 1.3 82.7 - - + +
232A ILE* 4.0 31.4 - - + -
234A TYR* 5.5 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A GLY 6.2 0.9 - - - -
155A THR 3.7 6.7 - - - +
156A ARG* 4.2 8.1 - - + +
200A ASN* 4.4 6.9 + - - +
202A ARG* 3.1 73.8 - - + +
218A VAL* 1.3 98.4 - - + +
220A TYR* 1.3 65.7 + - - +
221A GLU* 3.5 10.3 + - - +
----------------------------------------------------------
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