Contacts of the helix formed by residues 165 - 180 (chain A) in PDB entry 4RWN
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 ASN 165 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A LYS 3.6 1.8 + - - -
164A PRO* 1.3 72.4 - - - +
166A PRO* 1.3 72.0 - - - +
167A GLU* 3.1 31.1 + - - +
168A ILE* 2.9 45.0 + - + +
169A TYR* 4.0 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A PRO 3.2 10.3 - - - +
165A ASN* 1.3 90.5 - - - +
167A GLU* 1.3 55.5 + - - +
168A ILE 3.1 0.2 - - - -
169A TYR* 3.1 17.3 + - + +
170A VAL* 2.9 29.5 + - - +
277A ASP* 6.1 0.9 - - - +
279A THR* 6.5 1.8 - - + -
280A ASN* 4.1 29.2 - - + +
283A VAL* 4.0 4.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A ASN* 3.0 26.0 + - - +
166A PRO* 1.3 78.0 - - + +
168A ILE* 1.3 57.4 + - + +
170A VAL* 3.4 21.0 - - - +
171A GLN* 2.9 28.1 + - - +
280A ASN* 3.7 19.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A PHE* 4.0 4.8 - - + -
152A PHE* 6.1 0.2 - - + -
154A ALA* 3.4 44.9 - - + +
155A LEU* 4.4 19.5 - - + +
164A PRO* 4.6 3.4 - - + -
165A ASN* 2.9 37.9 + - + +
167A GLU* 1.3 78.2 - - + +
169A TYR* 1.3 56.8 + - + +
171A GLN* 3.4 10.0 + - - +
172A LEU* 3.0 25.1 + - - +
189A PHE* 4.2 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A PRO* 4.1 15.5 - - + -
166A PRO* 3.1 19.3 + - + +
168A ILE* 1.3 77.2 - - + +
170A VAL* 1.3 61.4 + - - +
172A LEU* 3.5 10.4 - - + +
173A ILE* 2.9 37.5 + - - +
189A PHE* 3.8 23.6 - + - -
192A LEU* 3.2 21.8 - - - +
275A TYR* 3.4 27.0 - - - +
276A TYR* 3.9 22.2 - + + -
283A VAL* 3.9 13.5 - - + -
302A ALA 2.8 30.8 + - - -
304A PRO* 3.6 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A PRO 2.9 19.5 + - - +
167A GLU* 3.2 27.5 + - - +
169A TYR* 1.3 77.1 - - - +
171A GLN* 1.3 63.7 + - - +
173A ILE* 3.3 3.2 + - - +
174A LYS* 3.0 24.2 + - + +
280A ASN* 3.6 32.1 - - - +
282A VAL* 4.1 28.2 - - + +
283A VAL* 4.4 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A THR 5.1 0.8 + - - -
86A SER* 4.1 15.4 - - - -
87A PHE* 3.4 28.5 - - + +
152A PHE* 4.3 10.6 - - - -
167A GLU 2.9 13.1 + - - +
168A ILE* 3.6 10.5 - - - +
170A VAL* 1.3 76.0 - - - +
172A LEU* 1.3 64.9 + - - +
174A LYS* 3.3 9.5 + - + +
175A GLU* 3.0 39.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A PHE* 3.7 30.3 - - + -
168A ILE 3.0 15.1 + - - +
169A TYR* 3.3 23.5 + - + +
171A GLN* 1.3 77.2 - - - +
173A ILE* 1.3 57.4 + - - +
175A GLU* 3.4 1.4 + - - +
176A CYS* 3.0 36.6 + - - -
185A PHE* 3.8 34.8 - - + +
189A PHE* 3.9 17.5 - - + -
303A ASP* 3.4 26.9 - - - +
304A PRO* 4.3 2.9 - - + -
305A THR* 4.2 10.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A TYR 2.9 25.1 + - - +
170A VAL 3.6 3.8 - - - +
172A LEU* 1.3 73.1 - - + +
174A LYS* 1.3 67.7 + - - +
176A CYS* 3.4 1.5 + - - +
177A LYS* 2.9 32.5 + - + +
282A VAL* 3.9 20.4 - - + +
283A VAL* 3.9 22.9 - - + -
285A ARG* 6.1 0.7 - - - +
286A CYS* 3.6 42.8 - - + -
304A PRO* 4.7 8.3 - - + -
305A THR* 4.0 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A VAL* 3.0 16.3 + - + +
171A GLN* 3.3 13.0 + - + +
173A ILE* 1.3 78.0 - - - +
175A GLU* 1.3 61.5 + - + +
177A LYS* 3.8 4.6 - - - +
178A SER* 2.9 32.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A SER* 4.0 4.2 - - - -
87A PHE* 3.8 23.4 + - + -
88A GLU* 3.2 48.1 + - - +
171A GLN* 3.0 33.3 + - + +
172A LEU 3.8 3.6 - - - +
174A LYS* 1.3 80.2 - - + +
176A CYS* 1.3 63.2 + - - +
178A SER* 3.3 8.0 + - - -
179A ARG* 3.1 34.5 + - + +
181A LYS* 5.4 0.2 - - - +
185A PHE* 5.1 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A LEU* 3.0 33.1 + - - +
173A ILE* 3.8 5.4 - - - +
175A GLU* 1.3 77.6 - - - +
177A LYS* 1.3 52.7 + - - +
179A ARG 3.2 0.9 + - - -
180A GLY* 2.7 32.9 + - - -
181A LYS* 2.9 41.3 + - - +
182A GLU* 4.2 6.3 - - + +
183A GLY 4.7 0.4 - - - -
184A GLU 5.0 0.2 - - - -
185A PHE* 3.8 23.1 - - - -
305A THR* 4.1 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ILE* 2.9 24.0 + - + +
174A LYS* 3.8 4.7 - - - +
176A CYS* 1.3 76.2 - - - +
178A SER* 1.3 63.9 + - - +
180A GLY* 3.6 8.7 + - - +
289A GLN* 6.0 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A LYS* 2.9 20.9 + - - -
175A GLU* 3.4 10.5 - - - -
176A CYS 3.2 0.2 - - - -
177A LYS* 1.3 80.8 - - - +
179A ARG* 1.3 76.8 + - - +
180A GLY 3.8 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A GLU* 3.5 42.0 + - - +
91A LEU* 4.1 24.3 - - + +
92A ARG* 4.6 12.3 - - - +
175A GLU* 3.1 22.5 + - + +
178A SER* 1.3 91.6 + - - +
180A GLY* 1.3 62.3 + - - +
181A LYS* 3.3 34.0 + - + +
185A PHE* 6.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A CYS 2.7 14.3 + - - -
177A LYS* 3.6 7.5 + - - -
178A SER 3.4 2.8 + - - -
179A ARG* 1.3 75.0 - - - +
181A LYS* 1.3 63.1 + - - +
182A GLU* 3.8 4.2 + - - +
----------------------------------------------------------
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