Contacts of the strand formed by residues 162 - 171 (chain A) in PDB entry 2ATW
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 ARG 162 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ALA* 3.8 24.1 - - - +
117A GLY 3.3 14.8 - - - +
118A VAL* 4.2 15.5 - - + +
160A GLY 3.4 3.3 + - - +
161A ASN* 1.3 74.7 - - - +
163A LEU* 1.3 66.3 + - - +
164A ARG* 3.5 33.5 - - - +
249A GLU* 4.7 5.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A VAL 4.0 0.2 - - - +
116A ALA* 3.6 2.4 - - - +
117A GLY 3.0 39.7 + - - +
119A ILE* 3.9 32.8 - - + -
133A VAL* 4.0 15.9 - - + -
146A ILE* 4.4 2.5 - - + -
155A GLU* 5.8 0.4 - - - -
156A SER 5.7 0.9 - - - +
157A TYR* 4.1 20.6 - - + -
161A ASN* 5.3 1.8 - - + -
162A ARG* 1.3 77.9 - - - +
164A ARG* 1.3 64.0 + - - +
165A CYS* 3.9 15.7 + - - -
183A ARG* 3.8 29.4 - - + +
249A GLU* 3.3 13.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ILE* 3.8 18.4 - - + -
115A VAL 3.3 11.0 - - - +
116A ALA* 4.4 12.8 - - + +
162A ARG* 3.5 27.9 - - - +
163A LEU* 1.3 76.9 - - - +
165A CYS* 1.3 61.4 + - - +
183A ARG* 2.9 26.5 + - - -
188A LEU* 4.0 6.8 - - + +
192A LEU* 3.6 25.6 - - + +
195A LEU* 3.9 17.3 - - - +
196A GLU* 5.2 10.2 + - - -
249A GLU* 2.6 52.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ILE* 3.4 4.3 - - - +
115A VAL* 2.9 37.4 + - + +
133A VAL* 5.3 1.3 - - - -
146A ILE* 3.9 24.0 - - - -
163A LEU* 3.9 15.2 + - - -
164A ARG* 1.3 79.8 - - - +
166A TYR* 1.3 62.3 + - - +
181A LEU* 3.9 34.5 - - + -
182A SER 3.6 8.7 - - - +
183A ARG* 3.9 15.7 - - - -
188A LEU* 4.2 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A GLY* 3.4 41.3 + - - -
113A GLU 3.5 10.3 - - - -
114A ILE* 4.6 1.6 - - + +
165A CYS* 1.3 74.3 - - - +
167A VAL* 1.3 66.8 + - - +
168A VAL* 3.4 11.8 + - + -
181A LEU* 3.6 1.2 - - - -
182A SER* 2.8 38.9 + - - +
185A HIS* 3.7 41.0 + + + -
187A ASN* 3.2 40.9 + - + -
188A LEU* 4.2 20.1 - - + +
191A LYS* 4.3 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A THR* 4.0 7.0 - - + -
110A ARG 3.5 24.2 - - - +
111A GLU* 3.5 3.5 - - - +
112A GLY* 2.6 29.5 + - - +
113A GLU* 2.9 21.9 + - + +
115A VAL* 3.8 26.5 - - + -
166A TYR* 1.3 75.4 - - - +
168A VAL* 1.3 60.8 + - - +
169A GLY 3.7 11.0 - - - +
170A VAL* 3.7 24.0 - - + -
179A ILE* 4.2 6.3 - - + -
180A THR 3.7 5.8 - - - +
181A LEU* 3.9 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A GLU* 4.5 10.4 - - - +
150A GLU* 4.4 14.4 - - - +
166A TYR* 3.4 16.1 + - + -
167A VAL* 1.3 76.1 - - - +
169A GLY* 1.3 56.0 + - - +
180A THR* 2.9 33.8 + - + +
181A LEU 4.3 0.9 - - - +
182A SER* 3.8 30.1 - - - -
185A HIS* 4.0 14.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A GLU* 4.7 6.1 - - - -
167A VAL* 3.5 5.1 - - - +
168A VAL* 1.3 80.3 - - - +
170A VAL* 1.3 66.4 + - - +
171A THR* 4.2 4.7 - - - -
178A LEU 4.1 1.8 - - - -
179A ILE* 3.3 4.5 - - - -
180A THR* 2.6 42.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A PHE 4.5 12.3 - - - +
109A THR* 3.6 36.6 - - + +
110A ARG* 3.9 9.9 - - - -
111A GLU* 3.9 12.9 + - + +
167A VAL* 3.7 19.5 - - + -
169A GLY* 1.3 78.8 - - - +
171A THR* 1.3 67.9 + - - +
177A PRO* 5.1 8.5 - - + -
178A LEU 3.3 6.3 - - - +
179A ILE* 4.5 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A GLY* 5.1 3.1 - - - -
170A VAL* 1.3 85.9 - - - +
172A ARG* 1.3 72.1 + - - +
177A PRO* 4.7 2.9 - - - -
178A LEU* 2.8 48.6 + - - +
----------------------------------------------------------
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