Contacts of the strand formed by residues 175 - 180 (chain J) in PDB entry 4XX1
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 175 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24J PRO* 3.3 32.1 - - + +
26J ILE* 3.9 13.2 - - + -
164J VAL* 3.6 36.8 - - + +
167J MET* 3.8 20.0 - - + -
168J HIS* 4.7 2.0 - - - +
173J LYS 4.2 4.7 - - - +
174J PRO* 1.3 78.3 - - - +
176J PHE* 1.3 73.1 + - - +
177J LEU* 4.7 0.9 - - + -
201J ARG* 3.9 2.0 - - - +
202J PHE 2.7 15.5 + - - +
203J ILE* 3.0 21.8 - - + +
204J ASP 3.0 13.3 + - - -
205J GLY 3.8 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 176 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23J ARG* 3.7 30.5 - - + +
24J PRO 2.6 16.7 + - - +
25J VAL* 3.3 5.0 - - + +
26J ILE 2.8 26.5 + - - -
175J VAL* 1.3 73.0 - - - +
177J LEU* 1.3 62.2 + - - +
178J ILE 3.7 0.9 + - - -
204J ASP* 3.4 37.2 - - + -
205J GLY* 3.4 33.9 - - - -
207J ILE* 3.5 25.1 - - + -
310J GLU* 4.5 4.9 - - - -
312J TYR* 3.8 27.4 - + - -
393J ILE* 3.9 11.4 - - + -
394J LEU* 3.7 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 177 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26J ILE* 3.8 32.8 - - + -
160J LEU* 5.8 5.8 - - + -
164J VAL* 4.9 5.2 - - + -
175J VAL* 4.7 1.6 - - + -
176J PHE* 1.3 78.0 - - - +
178J ILE* 1.3 62.9 + - - +
187J LEU* 4.2 27.4 - - + -
190J PHE* 5.4 6.7 - - + -
191J LEU* 4.1 26.5 - - + -
203J ILE* 3.7 30.5 - - + -
205J GLY 2.9 12.4 + - - +
206J PHE* 3.3 14.7 - - + -
207J ILE* 2.8 25.7 + - - -
309J VAL* 6.3 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 178 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25J VAL* 3.5 31.4 - - + -
26J ILE 3.1 16.7 + - - +
27J LEU* 4.0 18.8 - - + -
28J VAL* 3.2 16.2 + - - +
124J LEU* 4.7 7.6 - - + -
128J LEU* 4.5 5.2 - - + -
176J PHE 3.7 1.5 + - - +
177J LEU* 1.3 74.6 - - - +
179J GLY* 1.3 70.6 + - - +
187J LEU* 3.7 5.9 - - - +
207J ILE* 3.4 31.2 - - + +
209J LEU* 4.4 12.8 - - + -
390J ILE* 4.2 17.9 - - + -
394J LEU* 4.0 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 179 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28J VAL 3.7 9.6 - - - -
178J ILE* 1.3 76.2 - - - +
180J HIS* 1.3 60.3 + - - -
184J CYS* 3.2 17.7 - - - -
187J LEU* 3.6 12.5 - - - +
207J ILE 2.8 10.1 + - - -
209J LEU* 3.1 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 180 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28J VAL 3.5 7.8 + - - +
29J PRO* 4.9 1.8 - - + -
30J GLY* 3.1 11.5 + - - +
32J LEU* 5.7 6.5 - - + -
120J TYR* 2.8 32.3 + + + +
121J LEU* 5.6 4.9 - - + -
179J GLY* 1.3 74.8 - - - +
181J SER* 1.3 98.4 + - - +
182J LEU 2.9 2.1 + - - -
183J GLY 3.1 10.6 + - - -
184J CYS* 3.3 4.9 - - - +
209J LEU* 3.4 24.9 - - + -
377J HIS* 4.3 24.9 + + - -
378J LEU* 6.0 1.3 - - - -
380J MET* 4.8 4.2 - - + +
381J VAL* 3.7 31.5 - - + +
----------------------------------------------------------
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