Contacts of the strand formed by residues 167 - 171 (chain Z) in PDB entry 3EXG
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 167 (chain Z).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112Z ILE* 3.1 9.2 + - - +
113Z VAL* 3.3 4.4 - - + +
114Z PHE* 2.8 34.7 + - - +
143Z LYS* 3.4 29.2 - - + +
145Z VAL* 4.2 9.0 - - + -
160Z ALA* 3.8 37.2 - - + +
163Z ASP* 4.3 13.9 - - + -
165Z ASN 3.6 10.5 - - - +
166Z PRO* 1.3 77.0 - - - +
168Z VAL* 1.3 68.3 + - - +
169Z VAL* 3.8 7.4 - - + -
195Z ILE* 4.3 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 168 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83Z PHE* 3.4 31.0 - - + -
93Z VAL* 4.5 2.9 - - + -
114Z PHE* 3.3 20.6 - - + -
136Z TYR* 4.0 32.5 - - + -
142Z LEU* 4.2 16.2 - - + -
143Z LYS 3.0 9.4 + - - +
144Z VAL* 3.6 6.5 - - + -
145Z VAL* 3.1 27.2 + - - +
167Z VAL* 1.3 73.6 - - - +
169Z VAL* 1.3 60.8 + - - +
170Z LEU* 3.7 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 169 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83Z PHE* 3.7 2.5 - - - -
113Z VAL* 4.0 11.9 - - + -
114Z PHE 2.7 10.1 + - - -
115Z ARG* 3.6 10.6 - - + -
116Z GLY 3.4 19.2 + - - +
145Z VAL* 3.6 25.4 - - + -
147Z PRO* 4.3 12.3 - - + -
153Z ALA 5.9 0.4 - - - +
156Z LEU* 4.8 1.8 - - + +
157Z ILE* 3.9 26.2 - - + +
160Z ALA* 4.0 15.5 - - + -
167Z VAL* 3.8 12.6 - - + -
168Z VAL* 1.3 71.9 - - - +
170Z LEU* 1.3 60.0 + - - +
171Z GLU* 3.3 22.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 170 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83Z PHE* 3.6 34.1 - - + -
116Z GLY 4.1 1.3 - - - -
118Z ASN* 3.8 24.7 - - + +
132Z PHE* 4.3 1.8 - - + +
133Z ALA* 3.6 31.6 - - + +
136Z TYR* 4.8 5.8 - - + -
144Z VAL* 3.5 29.2 - - + -
145Z VAL 2.7 17.4 + - - +
146Z SER* 3.5 19.0 + - - +
147Z PRO* 3.4 21.7 - - - +
168Z VAL* 3.7 14.6 - - + -
169Z VAL* 1.3 66.4 - - - +
171Z GLU* 1.3 67.1 + - - +
212Z HIS* 6.1 0.2 - - + -
213Z SER* 4.4 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 171 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9Z ILE* 3.7 27.0 - - + +
115Z ARG* 2.6 45.8 + - - +
116Z GLY* 2.9 27.4 + - - +
117Z PRO* 3.7 0.7 - - + -
118Z ASN* 2.5 33.8 + - - +
147Z PRO* 4.6 10.8 - - + -
157Z ILE* 4.0 5.0 - - - +
169Z VAL* 3.8 14.8 - - + +
170Z LEU* 1.3 78.5 - - - +
172Z ASN* 1.3 58.9 + - - +
176Z TYR* 2.5 37.3 + - + +
213Z SER* 4.6 1.5 + - - -
----------------------------------------------------------
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