Contacts of the strand formed by residues 173 - 180 (chain A) in PDB entry 2DVL
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 GLY 173 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A ARG* 4.0 9.4 - - - -
170A THR* 2.6 44.7 + - - -
171A GLU 3.4 0.6 + - - -
172A LYS* 1.3 75.6 - - - +
174A ILE* 1.3 67.5 + - - -
175A SER* 3.2 4.0 + - - -
222A GLY* 3.5 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A LYS* 3.8 18.6 - - + +
135A LEU* 3.6 40.4 - - + -
167A MET* 4.3 10.8 - - + -
168A ALA 3.4 10.5 - - - +
169A ARG* 3.8 21.3 - - + +
173A GLY* 1.3 69.4 - - - -
175A SER* 1.3 66.7 + - - +
222A GLY* 3.1 11.8 + - - -
224A GLY 2.9 20.3 + - - -
225A LEU* 3.8 44.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A VAL 3.7 0.3 - - - +
167A MET* 3.5 9.2 - - - +
168A ALA 2.7 32.5 + - - -
170A THR* 3.7 2.1 + - - -
173A GLY 3.2 7.1 + - - -
174A ILE* 1.3 72.6 - - - +
176A ALA* 1.3 60.4 + - - +
177A PHE* 4.0 25.2 - - - -
217A LEU* 4.2 11.9 - - - -
220A GLU 5.3 0.4 - - - -
221A GLU* 3.4 12.6 - - - +
222A GLY 2.7 25.8 + - - -
224A GLY* 3.9 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A MET* 3.6 31.0 - - + -
165A VAL* 4.7 2.0 - - + -
166A VAL 4.0 2.0 - - - -
167A MET* 4.0 7.9 - - - -
175A SER* 1.3 74.7 - - - +
177A PHE* 1.3 62.1 + - - +
217A LEU* 3.4 8.7 - - - +
218A LEU* 2.9 52.4 + - + +
220A GLU 5.8 0.2 + - - -
224A GLY* 3.9 8.2 - - - -
227A TYR* 4.6 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ALA* 3.3 32.1 - - + -
146A PHE* 3.7 42.4 - + + -
148A LEU* 3.7 27.8 - - + -
164A TYR 3.2 3.1 - - - +
165A VAL* 3.3 4.4 - - - +
166A VAL* 2.8 48.8 + - - +
168A ALA* 4.1 10.1 - - + -
170A THR* 4.0 8.5 - - + -
175A SER* 4.0 20.4 - - - -
176A ALA* 1.3 78.7 - - - +
178A LEU* 1.3 64.2 + - - +
179A VAL* 3.7 4.8 + - + -
212A VAL* 4.5 11.0 - - + -
216A ASN 3.7 11.0 - - - -
217A LEU* 4.1 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A LEU* 3.9 23.1 - - + -
104A GLN* 3.6 29.6 - - - +
108A TYR* 3.5 30.5 - - + -
163A LEU* 4.2 15.3 - - + -
164A TYR 3.7 2.5 - - - -
165A VAL* 4.0 24.0 - - + -
177A PHE* 1.3 72.1 - - - +
179A VAL* 1.3 64.7 + - - +
212A VAL* 3.9 4.5 - - - +
216A ASN* 3.0 48.3 + - - +
218A LEU* 4.3 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A LEU* 4.2 10.3 - - + -
163A LEU* 3.7 4.6 - - - +
164A TYR* 2.8 45.6 + - + +
166A VAL* 3.8 24.7 - - + -
177A PHE 4.2 4.3 - - - +
178A LEU* 1.3 80.9 - - - +
180A GLU* 1.3 71.8 + - - +
183A THR* 4.0 14.1 - - + +
186A LEU* 4.0 20.2 - - + -
207A LEU* 5.0 1.8 - - + -
210A VAL* 4.4 12.6 - - + -
212A VAL* 4.0 19.1 - - + -
216A ASN* 4.8 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ARG* 4.7 7.5 + - - -
108A TYR* 3.2 41.4 + - + +
117A TRP* 4.7 4.0 - - - -
162A HIS* 3.3 31.3 + - + +
163A LEU* 4.6 3.4 - - + +
179A VAL* 1.3 79.5 - - - +
181A LYS* 1.3 69.5 + - - +
183A THR* 2.8 31.0 + - - +
186A LEU* 3.8 2.8 - - - +
216A ASN* 4.5 6.5 + - - +
----------------------------------------------------------
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