Contacts of the strand formed by residues 203 - 211 (chain A) in PDB entry 1HYH
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 203 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A ASN* 3.1 10.1 - - - -
195A LEU* 2.8 60.2 + - + -
196A GLY* 4.4 2.5 - - - -
201A SER 3.7 12.3 - - - +
202A GLN* 1.3 75.8 - - - +
204A VAL* 1.3 72.0 + - - +
205A ALA* 4.5 2.0 - - + -
231A GLU* 4.2 7.0 - - - +
303A LEU* 5.2 0.4 - - + -
307A GLU* 3.4 44.4 - - + -
310A LYS* 3.7 39.3 - - + +
311A LEU* 3.6 39.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A MET* 4.0 18.6 - - + -
193A TYR 4.3 1.3 - - - +
194A ASN* 3.4 28.0 - - - +
202A GLN* 5.8 0.7 - - - +
203A PHE* 1.3 80.8 - - - +
205A ALA* 1.3 60.0 + - - +
206A TRP* 3.2 62.9 + - + +
209A VAL* 4.0 7.9 - - + -
231A GLU* 3.3 30.4 + - + +
234A ALA* 5.1 3.4 - - + -
307A GLU* 4.7 1.6 - - - +
310A LYS* 5.0 3.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A TYR* 2.9 18.5 + - + +
195A LEU* 3.8 26.7 - - + -
203A PHE* 3.7 5.3 + - + -
204A VAL* 1.3 69.1 - - - +
206A TRP* 1.3 59.0 + - - +
207A SER 3.0 2.5 - - - -
208A THR* 2.7 47.4 + - + +
209A VAL* 3.6 2.9 + - - +
303A LEU* 4.3 1.1 - - + -
307A GLU* 3.4 21.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A MET* 4.5 3.8 - - + -
179A VAL* 4.1 17.0 - - + -
204A VAL* 3.2 35.5 + - + +
205A ALA* 1.3 70.5 - - - +
207A SER* 1.3 61.2 + - - +
209A VAL* 3.3 26.1 + - + +
215A PRO* 5.8 0.9 - - - +
216A ILE* 3.5 32.5 - - + +
217A VAL* 3.8 28.2 + - + +
227A LEU* 3.3 43.3 + - + +
230A ILE* 3.7 25.8 - - + -
231A GLU* 3.2 35.3 + - + -
307A GLU* 3.2 5.4 + - - +
310A LYS* 6.2 1.3 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
205A ALA 2.9 0.8 + - - -
206A TRP* 1.3 77.8 - - - +
208A THR* 1.3 68.7 + - - +
209A VAL 4.5 2.4 - - - +
210A ARG* 5.5 2.3 - - - +
215A PRO* 5.2 7.3 - - - +
217A VAL* 4.7 8.4 - - - +
302A ASP 4.0 12.9 + - - -
303A LEU* 4.4 0.2 - - - -
304A THR* 4.0 14.8 - - - -
307A GLU* 2.5 34.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A SER* 3.8 2.3 + - - -
192A GLY* 3.3 14.8 + - - -
193A TYR* 3.0 38.2 + - + -
205A ALA* 2.7 33.7 + - + +
207A SER* 1.3 82.2 - - - +
209A VAL* 1.3 63.4 + - - +
210A ARG* 3.6 10.6 + - - +
301A LEU* 4.5 11.7 - - + -
302A ASP 5.6 1.6 - - - +
303A LEU* 4.3 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A MET* 3.9 24.9 - - + -
179A VAL* 4.8 0.7 - - + -
190A VAL* 4.2 15.7 - - + -
191A SER 3.0 14.8 - - - +
192A GLY* 4.1 2.9 - - - -
193A TYR 4.6 0.2 - - - +
204A VAL* 4.0 4.3 - - + -
205A ALA 3.7 14.4 - - - +
206A TRP* 3.3 25.5 + - + +
207A SER 4.5 1.0 - - - +
208A THR* 1.3 78.1 - - - +
210A ARG* 1.3 67.1 + - - +
211A VAL* 5.0 0.9 - - + -
215A PRO* 3.6 3.6 - - - +
216A ILE* 3.1 52.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A SER 4.1 2.6 - - - +
190A VAL* 3.9 1.6 - - - -
191A SER* 3.1 41.8 + - - +
207A SER 5.5 2.2 - - - +
208A THR 3.8 8.1 - - - +
209A VAL* 1.3 79.3 - - - +
211A VAL* 1.3 67.9 + - - +
212A MET 4.3 0.2 - - - -
213A GLY* 2.6 40.6 + - - +
214A GLN* 3.3 13.9 - - - +
215A PRO* 3.9 19.5 - - + +
216A ILE 4.2 0.9 - - - +
193B TYR* 5.6 3.6 + - - -
210B ARG* 4.8 22.9 - - - +
301B LEU* 5.8 1.4 - - - +
302B ASP* 4.6 5.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A VAL* 3.5 28.9 - - + -
183A PHE* 3.9 19.5 - - + -
185A LEU* 4.0 14.1 - - + -
189A SER 4.9 1.8 - - - -
190A VAL* 3.8 20.0 - - + -
209A VAL* 5.0 0.7 - - + -
210A ARG* 1.3 78.2 - - - +
212A MET* 1.3 72.8 + - + +
213A GLY 3.3 2.0 - - - -
214A GLN* 2.8 25.4 + - - +
216A ILE* 4.3 12.8 - - + -
219A LEU* 3.9 25.0 - - + +
----------------------------------------------------------
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