Contacts of the strand formed by residues 160 - 167 (chain A) in PDB entry 3RBQ
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 ARG 160 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A PRO* 3.5 34.7 - - - +
66A LEU* 3.9 21.4 - - - +
158A ASN* 4.0 14.3 - - - +
159A PHE* 1.3 77.6 - - - +
161A MET* 1.3 62.0 + - - +
162A ILE* 4.1 8.7 - - + +
176A ASP* 2.7 39.9 + - - +
177A PHE 3.4 15.0 - - - +
178A HIS* 3.5 27.0 - - - +
179A PHE* 4.2 4.9 - - - -
219A PHE 3.8 0.7 - - - +
220A TYR* 3.4 2.9 - - - +
221A PHE* 2.8 44.4 + - + +
224A ASP* 4.5 6.2 + - - -
210D HIS* 6.3 0.8 - - - -
213D GLU* 5.6 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A ARG* 1.3 72.5 - - - +
162A ILE* 1.3 73.0 + - - +
163A GLU* 3.5 36.8 - - + +
175A PHE 3.5 1.9 - - - +
176A ASP* 3.3 3.5 - - - +
177A PHE* 2.7 76.5 + - + +
179A PHE* 4.0 10.3 - - + -
192A HIS* 4.0 12.3 - - + +
194A TYR* 3.7 12.8 - - - +
218A SER* 4.2 0.4 - - - -
219A PHE 3.3 11.4 - - - +
220A TYR* 3.4 43.7 - - + -
502G ALA* 5.6 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A PRO* 3.8 13.9 - - + -
65A VAL* 3.7 26.9 - - + -
66A LEU* 3.7 33.7 - - + -
160A ARG* 4.1 10.1 - - - +
161A MET* 1.3 78.1 - - - +
163A GLU* 1.3 60.6 + - - +
164A ARG* 4.0 11.9 - - + -
174A SER* 3.6 20.9 - - - +
175A PHE 3.3 4.0 - - - +
176A ASP* 3.8 20.0 - - - +
219A PHE* 2.9 41.6 + - - +
221A PHE* 3.8 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A MET* 3.5 27.4 - - + +
162A ILE* 1.3 75.9 - - - +
164A ARG* 1.3 63.3 + - - +
165A HIS* 3.0 28.0 + - + +
174A SER* 3.4 1.2 - - - -
175A PHE* 2.8 47.6 + - + +
194A TYR* 2.7 28.9 + - - -
216A SER* 4.5 4.0 - - - -
217A ASP 3.2 6.7 - - - +
218A SER* 2.4 29.4 + - - +
500G DAO 3.3 12.3 - - - +
501G GLY 3.0 12.2 + - - -
502G ALA 4.7 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A VAL 3.2 23.7 + - - -
66A LEU* 3.1 30.1 + - - +
67A GLY 3.7 2.4 - - - -
68A LEU* 2.8 25.6 + - - +
69A GLN* 4.5 0.8 - - - +
162A ILE* 4.0 8.3 - - + +
163A GLU* 1.3 75.2 - - - +
165A HIS* 1.3 61.2 + - - +
166A TYR* 3.0 39.3 + - + +
171A LEU* 3.8 12.9 - - + +
173A LYS 3.6 4.0 - - - -
174A SER* 2.9 49.2 + - - +
216A SER* 3.0 5.4 - - - -
217A ASP* 2.8 37.4 + - + +
219A PHE* 4.2 17.7 - - + -
97C ASP 2.8 21.2 + - - -
98C SER* 5.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A GLU* 3.0 30.1 + - + +
164A ARG* 1.3 78.4 - - - +
166A TYR* 1.4 55.7 + - - +
171A LEU* 3.5 5.5 - - - +
172A LEU* 2.7 36.0 + - + -
173A LYS 2.9 13.3 + - - +
175A PHE* 3.7 26.4 - + - -
214A THR* 5.3 3.7 - - + +
215A GLN 3.6 4.7 - - - +
216A SER* 3.7 7.7 - - - -
234A TYR* 3.2 34.9 + + - -
236A TYR* 5.8 0.4 + - - -
500G DAO 3.7 51.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A LEU* 3.3 11.0 + - - +
69A GLN 3.4 12.1 - - - -
70A ARG* 3.3 32.9 + - - -
71A ILE* 3.8 33.7 - - + -
164A ARG* 3.0 56.2 + - + +
165A HIS* 1.4 74.6 - - - +
167A PHE* 1.3 59.9 + - - +
168A ARG 4.0 0.2 - - - -
169A ASN* 4.1 17.0 - - - +
170A GLN 3.2 7.9 - - - +
171A LEU* 3.5 32.8 - - + -
172A LEU* 3.9 5.6 - - - -
213A GLU 3.8 1.2 - - - +
214A THR* 3.3 3.8 - - - +
215A GLN* 2.9 33.2 + - + +
217A ASP* 4.5 4.2 + - - -
219A PHE* 5.7 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A TYR* 1.3 72.6 - - - +
168A ARG* 1.3 95.5 + - + +
169A ASN 3.3 0.2 - - - -
170A GLN* 2.8 35.7 + - - +
172A LEU* 3.7 17.5 - - + +
203A LEU* 3.8 18.2 - - + -
206A GLU* 3.7 40.2 - - + -
207A MET* 3.6 29.8 - - + -
210A HIS* 4.0 11.4 - + + -
213A GLU* 3.7 25.8 - - + -
214A THR* 3.3 19.5 - - - +
----------------------------------------------------------
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