Contacts of the strand formed by residues 167 - 172 (chain D) in PDB entry 3EXF
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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D ILE* 3.3 4.8 + - - +
113D VAL* 3.3 14.7 - - + +
114D PHE* 2.9 24.6 + - - -
143D LYS* 3.1 19.3 - - + +
145D VAL* 4.6 7.0 - - + -
160D ALA* 3.6 27.4 - - + +
163D ASP* 4.0 25.1 - - + +
165D ASN 3.2 18.2 + - - +
166D PRO* 1.3 75.7 - - - +
168D VAL* 1.3 68.8 + - - +
169D VAL* 4.0 10.5 - - + -
195D ILE* 4.4 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 168 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D PHE* 3.8 15.0 - - + -
93D VAL* 4.3 17.0 - - + -
114D PHE* 3.3 32.8 - - + -
136D TYR* 4.0 18.8 - - + -
142D LEU* 4.5 12.1 - - + -
143D LYS 2.9 6.3 + - - -
144D VAL* 3.6 11.9 - - + -
145D VAL* 3.0 27.5 + - - +
167D VAL* 1.3 73.4 - - - +
169D VAL* 1.3 62.4 + - - +
170D LEU* 3.8 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 169 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D PHE* 3.5 4.4 - - - -
113D VAL* 4.3 11.4 - - + -
114D PHE 2.6 10.1 + - - -
115D ARG* 3.4 13.0 - - + -
116D GLY 3.3 20.4 + - - -
145D VAL* 3.7 19.7 - - + -
147D PRO* 4.2 15.5 - - + -
156D LEU* 5.8 0.4 - - + -
157D ILE* 3.8 28.0 - - + -
160D ALA* 4.2 13.7 - - + -
167D VAL* 4.0 13.5 - - + -
168D VAL* 1.3 75.8 - - - +
170D LEU* 1.3 59.6 + - - +
171D GLU* 3.2 22.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 170 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D PHE* 4.0 20.4 - - + -
116D GLY 4.1 1.8 - - - -
118D ASN* 3.7 30.3 - - - +
132D PHE* 4.2 2.5 - - + +
133D ALA* 3.5 37.7 - - + +
136D TYR* 4.3 8.1 - - + -
144D VAL* 3.9 19.3 - - + -
145D VAL 3.1 14.6 + - - +
146D SER* 3.5 18.3 + - - +
147D PRO* 3.3 19.6 - - - +
168D VAL* 3.8 22.0 - - + -
169D VAL* 1.3 69.5 - - - +
171D GLU* 1.3 65.7 + - - +
212D HIS* 6.4 0.2 - - + -
213D SER* 5.0 2.1 + - - -
241D ILE* 4.9 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 171 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D VAL* 6.4 0.2 - - + -
9D ILE* 3.6 26.4 - - + +
115D ARG* 2.5 45.3 + - - +
116D GLY* 2.8 27.9 + - - +
117D PRO* 3.9 0.7 - - - -
118D ASN* 3.0 24.1 + - - +
147D PRO* 4.6 10.5 - - + -
157D ILE* 4.8 1.1 - - + +
169D VAL* 3.8 21.9 - - + +
170D LEU* 1.3 76.7 - - - +
172D ASN* 1.3 64.3 + - - +
176D TYR* 2.3 39.2 + - + +
213D SER* 4.9 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 172 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D VAL* 6.0 1.6 - - - +
117D PRO* 4.7 0.4 - - - -
118D ASN 4.4 10.5 + - - -
119D GLY* 5.6 2.4 - - - -
120D ALA 4.6 7.6 + - - +
147D PRO 5.3 3.3 + - - +
171D GLU* 1.3 78.7 + - - +
173D GLU* 1.3 67.5 + - - +
174D LEU* 3.1 17.8 + - - +
175D MET* 3.2 28.9 + - + +
176D TYR* 3.3 20.4 + - - -
213D SER* 2.8 29.2 + - - +
214D ARG* 3.4 28.7 - - - +
215D PRO* 5.2 1.0 - - - +
----------------------------------------------------------
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