Contacts of the strand formed by residues 174 - 181 (chain A) in PDB entry 4JF7
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 TRP 174 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A PHE* 4.0 19.1 - + - -
167A PHE* 3.8 27.1 - + + -
168A SER 3.1 11.2 - - - +
169A LEU* 3.9 8.1 - - + -
173A HIS* 1.3 76.5 - - - +
175A CYS* 1.3 70.0 + - - +
176A TYR* 4.1 2.2 - - + -
196A SER* 3.5 22.4 - - - -
197A MET* 3.3 14.1 - - - +
198A GLY* 2.9 54.5 + - - -
199A ILE* 2.9 30.0 + - - +
200A ILE* 4.0 7.4 - - + -
210A PHE* 3.4 35.9 - + + -
211A ARG 3.5 24.7 - - - -
212A THR* 3.6 18.4 - - - -
231A THR* 4.1 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A PHE* 3.2 7.3 - - - -
168A SER* 2.7 36.6 + - - +
173A HIS* 4.0 2.7 - - - -
174A TRP* 1.3 80.1 - - - +
176A TYR* 1.3 60.4 + - - +
196A SER 3.4 5.8 - - - -
229A ILE* 3.8 19.7 - - + +
230A SER 4.4 1.6 - - - +
231A THR* 3.8 15.3 - - + +
235A GLY 3.5 13.7 - - - -
236A CYS* 2.0 49.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A PHE* 3.8 19.1 - + + -
152A ILE* 3.2 37.8 - - + +
165A PRO* 3.7 25.1 - - + +
166A SER 3.3 13.0 - - - -
167A PHE* 3.8 21.1 - + + -
174A TRP* 4.1 2.7 - - + -
175A CYS* 1.3 77.2 - - - +
177A THR* 1.3 75.2 + - - +
178A HIS* 2.5 41.4 + + - +
194A PHE* 4.3 11.7 - + - -
195A VAL* 3.4 2.9 - - - +
196A SER* 2.8 52.4 + - - +
229A ILE* 4.2 3.1 - - - +
542A ILE* 4.5 4.0 - - + -
555A ILE* 3.7 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ILE 5.3 0.4 - - - +
165A PRO* 3.2 1.7 - - - +
166A SER* 2.8 56.9 + - - +
176A TYR* 1.3 85.4 - - - +
178A HIS* 1.3 62.1 + - - +
193A GLN* 2.7 32.5 + - - +
194A PHE 2.6 21.3 + - - -
195A VAL* 3.7 1.7 - - - +
227A CYS 4.5 4.9 - - - +
229A ILE* 4.0 12.6 - - + -
238A MET* 3.4 21.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A ILE* 3.6 12.5 - - + +
153A PRO* 3.6 38.8 + - + +
162A THR* 3.7 20.2 - - - +
163A ARG 3.6 9.6 - - - +
164A ILE 3.6 9.6 - - - +
165A PRO* 3.9 3.4 - - + -
176A TYR* 2.5 32.9 + + - +
177A THR* 1.3 78.2 + - - +
179A ASN* 1.3 70.8 + - - +
180A VAL* 3.8 13.2 - - + +
193A GLN* 3.3 10.2 - - - +
194A PHE* 2.8 36.5 + + + +
555A ILE* 4.0 9.0 - - + +
149B PRO* 5.5 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A CYS 3.6 0.5 - - - +
162A THR* 3.2 6.6 - - - -
163A ARG* 2.8 45.0 + - + +
164A ILE* 4.1 9.1 + - + -
178A HIS* 1.3 74.6 - - - +
180A VAL* 1.3 60.1 + - - +
181A ILE* 3.7 10.2 - - - +
191A SER* 3.0 25.4 + - - -
192A ASN 3.3 7.4 + - - -
193A GLN* 3.0 23.6 + - - +
224A ARG 3.2 11.9 + - - -
225A LYS* 2.9 33.1 + - - +
226A SER 6.1 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A CYS 3.4 7.0 - - - +
162A THR* 4.6 7.6 - - + -
178A HIS* 3.8 22.9 - - + +
179A ASN* 1.3 76.3 - - - +
181A ILE* 1.3 64.2 + - - +
182A LEU* 4.2 7.2 + - + +
191A SER* 3.4 4.7 - - - -
192A ASN* 2.7 43.1 + - - +
194A PHE* 4.3 7.2 - - + -
217A TYR* 3.6 38.6 - - + +
147B ASN* 4.0 22.9 - - - +
149B PRO* 4.5 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A GLY* 3.7 0.7 - - - -
161A CYS* 2.8 46.4 + - + +
163A ARG* 4.9 9.2 - - + -
179A ASN* 3.7 15.5 - - - +
180A VAL* 1.3 77.4 - - - +
182A LEU* 1.3 65.2 + - - +
183A ASN 3.6 3.3 + - - +
184A GLY 3.1 29.3 + - - +
185A CYS* 4.3 13.5 - - - +
187A ASP* 3.4 35.7 - - + +
188A HIS* 5.1 2.2 - - + -
190A SER 4.3 9.2 - - - +
191A SER* 4.2 4.5 - - - +
225A LYS* 3.8 16.8 - - - +
147B ASN* 4.4 1.2 + - - -
----------------------------------------------------------
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