Contacts of the strand formed by residues 179 - 183 (chain A) in PDB entry 5J2Q
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 179 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A LYS* 3.7 25.4 - - + +
177A ASP 3.7 2.0 + - - +
178A ILE* 1.3 72.2 - - - +
180A ILE* 1.3 62.5 + - - +
181A TYR* 3.6 31.9 - - + -
188A TYR* 3.4 6.4 - - + +
189A VAL* 3.3 5.2 - - - +
190A GLY* 2.8 55.9 + - - +
138B GLU* 3.7 18.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A LEU* 4.2 8.3 - - + -
171A PHE* 3.6 36.3 - - + -
172A ARG* 3.1 47.8 + - + +
178A ILE* 3.7 16.3 + - + +
179A VAL* 1.3 77.8 - - - +
181A TYR* 1.3 59.8 + - - +
182A GLN 3.3 0.3 + - - -
187A LEU* 3.9 29.6 - - + -
188A TYR 3.2 6.3 - - - +
189A VAL* 4.3 12.8 - - + -
205A LEU* 4.2 13.9 - - + -
138B GLU* 3.3 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A PRO* 3.8 18.4 - - + -
99A GLY 3.7 9.7 + - - -
100A LEU* 3.5 24.9 - - + -
179A VAL* 3.6 27.6 - - + -
180A ILE* 1.3 69.6 - - - +
182A GLN* 1.3 59.8 + - - +
183A TYR* 3.7 2.3 + - - +
186A ASP 3.6 6.9 - - - +
187A LEU* 3.6 0.5 - - - -
188A TYR* 2.7 49.3 + + + +
229A TRP* 4.1 13.7 + + + -
135B ILE* 4.1 2.6 + - - +
136B ASN* 3.0 48.2 + - - +
137B ASN 4.4 0.2 - - - -
138B GLU* 3.6 36.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A GLN* 4.8 4.0 + - - +
161A GLN* 3.2 18.4 + - - +
164A MET* 3.3 32.2 - - + +
165A THR* 3.2 25.2 + - - -
168A LEU* 3.5 4.1 - - + +
172A ARG* 3.2 37.8 + - - +
180A ILE 3.3 1.0 + - - -
181A TYR* 1.3 70.9 - - - +
183A TYR* 1.3 63.1 + - - +
184A MET 4.4 7.5 + - - +
186A ASP 3.8 4.5 - - - -
187A LEU* 4.0 11.7 - - + -
137B ASN 4.5 4.0 - - - +
138B GLU 2.8 20.0 + - - +
139B THR* 4.2 0.3 - - - +
140B PRO* 3.5 28.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A GLN* 3.5 35.8 - - + +
94A ILE* 3.6 28.3 - - + +
95A PRO* 3.8 19.3 - - + -
181A TYR 3.7 3.0 + - - +
182A GLN* 1.3 73.6 - - - +
184A MET* 1.3 82.4 + - + +
186A ASP* 3.0 27.8 + - + +
229A TRP* 5.7 2.2 - - - +
230A MET* 3.4 31.2 - - + -
137B ASN 5.8 0.2 - - - -
821P C 2.6 44.7 + - + -
901P 6FM 3.5 13.4 - - + +
707T G 3.4 11.1 + - - -
708T G 3.6 3.1 + - - -
----------------------------------------------------------
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