Contacts of the strand formed by residues 162 - 171 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C ALA* 3.8 23.1 - - - +
117C GLY 3.2 14.6 - - - +
118C VAL* 4.3 11.5 - - + +
160C GLY 3.4 3.7 + - - +
161C ASN* 1.3 74.8 - - - +
163C LEU* 1.3 67.3 + - - +
164C ARG* 3.3 33.3 - - - +
249C GLU* 4.7 4.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 163 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C VAL 4.1 0.2 - - - +
116C ALA* 3.5 2.7 - - - -
117C GLY 3.1 36.7 + - - +
119C ILE* 4.1 19.3 - - + -
133C VAL* 4.0 21.1 - - + -
146C ILE* 4.5 2.9 - - + -
156C SER 5.6 0.9 - - - +
157C TYR* 4.0 26.9 - - + -
161C ASN* 4.4 1.8 - - + +
162C ARG* 1.3 79.6 - - - +
164C ARG* 1.3 63.1 + - - +
165C CYS* 4.0 15.4 + - - -
183C ARG* 3.7 33.0 - - + +
249C GLU* 3.3 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 164 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C ILE* 4.2 13.0 - - + -
115C VAL 3.2 14.4 - - - +
116C ALA* 3.8 17.1 - - + +
162C ARG* 3.3 28.1 - - - +
163C LEU* 1.3 74.7 - - - +
165C CYS* 1.3 60.3 + - - +
183C ARG* 2.9 27.5 + - - -
188C LEU* 3.8 5.8 - - + +
192C LEU* 3.6 23.9 - - + +
195C LEU* 3.9 22.4 - - - +
196C GLU* 5.1 9.8 + - - -
245C ASN 5.7 0.4 + - - -
249C GLU* 2.6 52.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 165 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C ILE* 3.4 5.0 - - - +
115C VAL* 2.8 36.6 + - + +
133C VAL* 4.7 2.5 - - - -
135C ILE* 6.0 0.4 - - - -
146C ILE* 4.0 23.6 - - - -
163C LEU* 4.0 23.8 - - - -
164C ARG* 1.3 79.1 - - - +
166C TYR* 1.3 60.9 - - - +
181C LEU* 3.9 32.3 - - + -
182C SER 3.5 10.5 - - - +
183C ARG* 4.3 5.8 - - - -
188C LEU* 3.9 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 166 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C GLY* 3.4 35.6 + - - -
113C GLU 3.6 11.0 - - - -
114C ILE* 4.7 1.6 - - + +
165C CYS* 1.3 73.9 - - - +
167C VAL* 1.3 75.2 + - - +
168C VAL* 3.3 8.6 + - + -
181C LEU* 3.6 1.3 - - - -
182C SER* 2.8 38.8 + - - +
185C HIS* 3.7 36.8 - + + -
187C ASN* 2.9 49.8 + - + -
188C LEU* 4.0 18.6 - - + +
191C LYS* 4.3 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 167 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C THR* 3.9 11.0 - - + -
110C ARG 3.4 25.6 - - - +
111C GLU* 3.5 9.6 - - - +
112C GLY* 2.9 27.6 + - - +
113C GLU 2.9 22.3 + - - +
115C VAL* 3.8 31.0 - - + -
166C TYR* 1.3 75.7 - - - +
168C VAL* 1.3 59.6 + - - +
169C GLY 3.7 8.5 - - - +
170C VAL* 3.6 22.2 - - + -
179C ILE* 4.5 2.5 - - + -
180C THR 3.8 5.8 - - - +
181C LEU* 4.2 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 168 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C GLU* 4.0 14.9 - - - +
150C GLU* 4.5 15.3 - - - +
166C TYR* 3.3 16.5 + - + -
167C VAL* 1.3 75.1 - - - +
169C GLY* 1.3 57.4 + - - +
180C THR* 2.9 38.8 + - + +
181C LEU 4.5 6.5 - - - +
182C SER* 3.7 23.6 - - - -
185C HIS* 4.0 14.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 169 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C GLU* 3.8 9.4 - - - +
167C VAL* 3.4 4.5 - - - +
168C VAL* 1.3 80.7 - - - +
170C VAL* 1.3 66.1 + - - +
171C THR* 5.1 4.3 - - - -
178C LEU 4.1 1.6 - - - -
179C ILE* 3.1 6.2 - - - +
180C THR* 2.7 41.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 170 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C PHE* 3.8 35.0 - - + -
109C THR* 3.6 35.0 - - + +
110C ARG* 4.0 0.4 - - - -
111C GLU* 3.7 25.2 + - + +
167C VAL* 3.6 20.4 - - + -
169C GLY* 1.3 79.7 - - - +
171C THR* 1.3 65.8 + - - +
177C PRO* 4.3 9.4 - - + -
178C LEU 3.5 3.1 - - - -
179C ILE* 4.5 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 171 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C PHE* 4.3 1.6 - - - -
111C GLU* 5.4 3.1 - - - +
169C GLY* 5.1 2.5 - - - -
170C VAL* 1.3 84.8 - - - +
172C ARG* 1.3 66.2 + - - +
177C PRO* 3.1 5.6 - - - +
178C LEU* 2.8 60.6 + - + +
----------------------------------------------------------
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