Contacts of the strand formed by residues 207 - 214 (chain A) in PDB entry 1P9W
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 VAL 207 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ILE* 3.8 27.4 - - + -
198A ILE 3.7 1.7 - - - +
199A SER* 3.8 3.2 + - - -
200A LEU* 2.8 36.7 + - + +
202A ILE* 4.0 22.2 - - + -
206A ALA* 1.3 80.3 - - - +
208A ASP* 1.3 65.7 + - - +
209A VAL* 3.4 8.2 + - + +
226A LEU* 3.7 31.2 - - + -
227A LEU 3.8 13.0 - - - +
228A ASP* 5.6 2.9 - - - +
229A LYS* 5.2 1.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ARG* 3.0 44.2 + - - -
198A ILE 3.6 5.9 - - - +
199A SER* 4.7 5.3 + - - -
206A ALA 4.4 0.4 + - - -
207A VAL* 1.3 69.1 - - - +
209A VAL* 1.3 60.6 + - - +
210A ARG* 3.1 32.0 + - - -
226A LEU* 3.5 1.6 + - - -
227A LEU* 2.7 50.4 + - + +
228A ASP 5.2 2.0 - - - +
229A LYS* 3.9 25.1 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
131A LEU* 4.5 6.1 - - + -
197A ARG* 3.6 1.7 - - - -
198A ILE* 2.8 71.4 + - + +
200A LEU* 4.5 11.7 - - + -
207A VAL* 4.0 8.5 - - + +
208A ASP* 1.3 76.0 - - - +
210A ARG* 1.3 60.3 + - - +
211A VAL* 3.8 9.8 + - + -
224A MSE 3.7 35.7 - - + -
225A ARG 4.4 0.4 - - - +
226A LEU* 3.8 25.6 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
196A GLY 3.8 10.8 - - - +
197A ARG* 3.8 28.6 - - + +
208A ASP* 3.1 25.2 + - - -
209A VAL* 1.3 72.1 - - - +
211A VAL* 1.3 62.1 + - - +
212A SER* 4.2 4.7 + - - +
223A VAL* 3.5 2.6 - - - +
224A MSE 3.4 1.7 - - - -
225A ARG* 2.7 49.1 + - + +
226A LEU 4.1 1.4 - - - +
227A LEU* 3.6 24.4 - - + +
701A ANP 5.5 19.2 + - - -
----------------------------------------------------------
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* 3.6 26.7 - - + -
183A ALA* 3.7 31.6 - - + -
185A LEU* 4.2 10.3 - - + -
194A GLN 4.0 0.3 - - - +
195A ASP* 3.5 2.8 - - - +
196A GLY 2.8 37.3 + - - +
198A ILE* 3.8 22.2 - - + -
209A VAL* 3.9 12.6 - - + +
210A ARG* 1.3 76.0 - - - +
212A SER* 1.3 62.5 + - - +
213A THR* 4.5 8.3 - - + -
222A VAL* 4.9 0.9 - - + -
223A VAL 3.3 8.1 - - - +
224A MSE 4.0 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A GLN 3.4 3.8 - - - -
195A ASP* 3.0 21.3 + - - +
210A ARG* 4.9 5.4 + - - +
211A VAL* 1.3 75.2 + - - +
213A THR* 1.3 64.9 + - - +
221A ARG 3.9 0.3 - - - +
222A VAL* 3.4 3.5 - - - +
223A VAL* 3.0 45.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A VAL 5.8 0.2 - - - +
179A VAL* 5.5 1.1 - - + -
180A LYS* 4.1 19.7 - - + -
185A LEU* 4.8 4.5 - - + -
192A VAL 4.8 0.2 + - - -
193A PRO* 3.4 5.9 - - - +
194A GLN* 2.9 45.1 + - - +
195A ASP* 5.3 0.3 - - - +
211A VAL* 4.5 12.6 - - + -
212A SER* 1.3 80.7 - - - +
214A MSE 1.3 68.7 + - - +
220A GLU* 3.6 19.6 + - - -
221A ARG 3.2 8.5 - - - -
222A VAL* 3.6 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A PRO* 4.6 11.4 - - + -
213A THR* 1.3 82.8 + - - +
215A PRO* 1.3 88.7 - - + +
216A SER* 3.4 8.4 + - - +
220A GLU* 2.9 8.9 + - - +
221A ARG* 2.9 57.5 + - + +
----------------------------------------------------------
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