Contacts of the strand formed by residues 209 - 213 (chain A) in PDB entry 1W7L
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 209 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LEU* 4.0 29.8 - - + -
176A LYS* 3.1 23.2 + - - +
177A ALA* 3.1 8.9 - - + +
178A LEU 3.0 24.3 + - - -
203A CYS* 4.8 0.2 - - - -
207A ASP 5.8 0.7 - - - +
208A VAL* 1.3 76.1 - - - +
210A CYS* 1.3 71.1 + - - +
211A ILE* 4.4 7.9 - - + -
238A ARG* 3.3 15.7 - - + +
240A LEU* 4.5 10.1 - - + -
265A ILE* 4.2 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A LEU* 3.5 14.4 - - - -
180A LEU* 3.9 25.4 - - - -
199A VAL* 4.4 1.6 - - - -
203A CYS* 4.2 9.2 - - - -
208A VAL 3.8 1.6 + - - -
209A VAL* 1.3 72.8 - - - +
211A ILE* 1.3 65.0 + - - +
212A THR* 3.5 4.3 + - - -
229A ILE* 3.9 31.2 - - - -
235A MET* 4.1 21.3 - - + -
238A ARG 2.8 11.4 + - - +
239A THR* 3.3 7.0 - - - +
240A LEU 2.9 25.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A LEU* 4.1 15.7 - - + -
107A ALA* 4.3 25.6 - - + +
108A PHE* 4.5 24.0 - - + -
111A LEU* 4.7 8.3 - - + -
112A VAL* 5.5 2.0 - - + -
177A ALA* 3.9 26.2 - - + -
178A LEU 2.9 11.4 + - - +
179A VAL* 3.4 12.5 - - + +
180A LEU 2.8 27.0 + - - +
209A VAL* 4.4 10.1 - - + -
210A CYS* 1.3 71.8 - - - +
212A THR* 1.3 62.4 + - - +
213A ASP 3.9 0.5 + - - -
240A LEU* 3.7 10.3 - - + +
242A ILE* 3.9 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A LEU* 3.3 20.9 + - - +
182A THR* 4.9 1.9 - - - +
210A CYS* 3.5 6.3 + - - -
211A ILE* 1.3 75.1 - - - +
213A ASP* 1.3 61.2 + - - +
214A GLU* 3.2 29.0 + - - +
229A ILE* 4.0 14.3 - - + +
230A ALA 5.4 0.2 - - - +
239A THR* 3.7 11.2 - - + -
240A LEU 2.8 21.7 + - - +
241A THR* 3.4 21.5 - - + +
242A ILE* 2.8 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A LEU* 3.7 18.9 - - + +
128A TYR* 2.6 33.3 + - + +
179A VAL* 5.2 0.4 - - + -
180A LEU 2.7 11.6 + - - +
181A ASN* 2.8 31.3 + - - +
182A THR 3.1 13.5 + - - +
211A ILE 3.9 1.7 + - - +
212A THR* 1.3 68.9 - - - +
214A GLU* 1.3 61.0 + - - +
215A VAL* 3.3 23.7 + - - +
242A ILE* 4.3 8.3 - - - -
1247A PLP 2.6 26.3 + - - -
----------------------------------------------------------
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