Contacts of the strand formed by residues 173 - 178 (chain D) in PDB entry 1EFX
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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141D ARG* 3.1 15.3 - - - -
142D GLU* 3.7 10.1 - - - -
172D GLY* 1.3 74.4 - - - -
174D THR* 1.3 59.9 + - - -
175D TYR* 3.4 7.0 - - - -
195D LEU 3.3 1.9 - - - +
196D LEU* 4.2 5.8 - - - +
197D VAL* 2.6 45.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 174 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141D ARG* 3.6 2.8 - - - -
142D GLU* 3.1 47.2 + - + +
173D GLY* 1.3 73.2 - - - -
175D TYR* 1.3 66.0 + - - +
176D ARG* 4.9 6.9 - - + +
194D PRO* 3.4 32.1 - - + -
195D LEU 2.9 7.2 - - - +
196D LEU* 3.9 18.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 175 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D LEU* 3.4 7.9 - - + +
126D LEU* 3.4 28.3 - - + -
139D LEU* 3.9 15.0 - - + -
140D SER 3.2 9.6 - - - +
141D ARG* 3.5 45.2 + - + -
166D LEU* 4.1 27.1 - - + +
171D HIS 4.6 6.6 + - - -
173D GLY* 3.4 19.3 - - - -
174D THR* 1.3 73.5 - - - +
176D ARG* 1.3 68.4 + - - +
194D PRO* 3.3 0.9 - - - +
195D LEU* 2.7 35.1 + - + +
197D VAL* 3.2 34.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 176 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D LEU* 3.5 4.3 - - - -
138D HIS 3.6 1.4 - - - +
139D LEU* 3.6 2.1 - - - -
140D SER* 3.0 33.9 + - - +
142D GLU 6.4 0.7 - - - +
174D THR* 4.9 5.5 - - + +
175D TYR* 1.3 81.3 - - - +
177D CYS* 1.3 58.7 + - - +
178D PHE* 3.9 14.4 - - + -
191D SER* 3.0 38.4 + - - +
192D SER* 3.3 18.9 + - - +
193D ASP* 4.7 0.2 - - - +
194D PRO* 3.4 36.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 177 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D PRO* 4.2 6.8 - - + +
110D LEU* 3.1 33.7 - - - -
128D CYS* 2.0 52.5 - - + -
138D HIS 2.9 4.5 - - - -
139D LEU* 3.9 6.1 - - - -
176D ARG* 1.3 71.1 - - - +
178D PHE* 1.3 74.7 + - - +
190D ASN 3.8 1.2 - - - +
191D SER* 3.6 1.9 - - - -
192D SER* 2.7 38.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 178 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D LEU* 5.2 6.3 - - + -
102D THR* 4.2 16.8 - - + -
108D PRO* 4.4 1.8 - - - -
137D TYR* 3.0 11.4 - - - -
138D HIS* 2.6 44.8 + - + -
140D SER* 4.6 4.5 - - - -
147D GLU* 4.5 9.4 - - - -
176D ARG* 3.9 20.9 - - + -
177D CYS* 1.3 80.8 - - - +
179D GLY* 1.3 59.9 + - - +
188D TRP* 3.2 48.9 - + + -
189D SER* 3.6 24.9 - - - +
191D SER* 3.5 35.4 - - - -
----------------------------------------------------------
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