Contacts of the helix formed by residues 171 - 187 (chain A) in PDB entry 4DUB
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 HIS 171 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A TYR* 3.0 29.7 + + - -
161A ARG 4.7 1.8 - - - -
162A PHE* 3.8 40.6 - + + +
164A SER* 5.6 0.2 + - - -
167A ARG* 3.5 33.6 - - - +
170A PRO* 1.3 73.8 - - - +
172A PRO* 1.3 82.7 - - + +
173A PHE* 3.0 37.0 + - + +
174A ILE* 2.9 20.2 + - + +
175A THR 3.1 7.8 + - - -
215A LEU* 3.9 12.3 - - + -
134B ASN* 5.4 0.9 - - - -
137B GLU* 5.1 3.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ARG* 4.6 6.7 - - - +
170A PRO 3.4 5.5 - - - +
171A HIS* 1.3 98.5 - - + +
173A PHE* 1.3 61.4 + - - +
175A THR* 3.5 8.5 + - - -
176A SER* 3.0 27.2 + - - -
211A VAL* 3.8 10.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A LEU* 6.0 0.2 - - + -
158A PHE* 5.7 0.2 - + - -
162A PHE* 3.7 19.3 - + + -
171A HIS* 3.0 19.0 + - + +
172A PRO* 1.3 77.8 - - - +
174A ILE* 1.3 58.6 + - + +
176A SER* 3.3 2.3 + - - -
177A MET* 2.7 52.7 + - + +
211A VAL* 4.0 11.8 - - + +
212A MET* 3.6 47.6 - - + +
215A LEU* 3.8 25.8 - - + -
216A VAL* 3.7 21.1 - - + -
259A ILE* 4.5 8.1 - - + -
262A LEU* 3.7 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A LEU* 3.7 37.2 - - + -
162A PHE* 3.5 48.7 - - + -
164A SER* 3.5 16.8 - - - +
170A PRO* 3.6 22.7 - - + -
171A HIS* 2.9 14.7 + - + +
173A PHE* 1.3 82.0 - - + +
175A THR* 1.3 65.5 + - - +
177A MET* 3.1 5.5 + - + +
178A VAL* 2.9 35.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A GLN* 5.8 0.3 - - - +
170A PRO* 3.7 32.1 + - - +
171A HIS 3.1 5.9 + - - -
172A PRO* 3.8 11.4 - - - +
174A ILE* 1.3 75.5 - - - +
176A SER* 1.3 57.8 + - - +
178A VAL* 3.9 4.6 - - - +
179A ARG* 2.9 61.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A PRO 3.0 17.5 + - - -
173A PHE 3.8 3.4 - - - -
175A THR* 1.3 76.3 - - - +
177A MET* 1.3 57.1 + - - +
179A ARG* 3.4 5.8 + - - +
180A ALA* 2.8 30.3 + - - +
207A GLU* 5.6 0.2 + - - -
208A ASP* 2.8 49.5 + - - +
211A VAL* 3.5 22.1 - - - +
212A MET* 4.5 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A PHE* 4.9 1.5 - - + -
150A LEU* 3.5 31.6 - - + -
173A PHE* 2.7 36.4 + - + +
174A ILE* 3.8 5.2 - - - +
176A SER* 1.3 74.2 - - - +
178A VAL* 1.4 63.3 + - + +
180A ALA* 3.2 2.3 + - - +
181A LEU* 2.8 31.7 + - + +
212A MET* 3.6 24.4 - - - +
259A ILE* 4.6 2.0 - - - +
262A LEU* 3.7 11.7 - - - +
263A ALA* 3.5 37.0 - - + -
266A HIS* 3.7 22.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A THR* 6.0 2.2 - - + -
150A LEU* 5.3 2.5 - - + -
174A ILE* 2.9 36.6 + - + +
175A THR* 3.9 4.7 - - - +
177A MET* 1.4 76.1 - - + +
179A ARG* 1.3 59.6 + - - +
181A LEU* 3.4 10.2 + - + +
182A ASP* 3.0 29.3 + - + +
266A HIS* 4.8 15.9 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
175A THR* 2.9 42.4 + - + +
176A SER* 3.8 8.9 + - - +
178A VAL* 1.3 75.8 - - - +
180A ALA* 1.3 58.4 + - - +
182A ASP* 3.6 10.4 - - - +
183A GLU* 3.0 28.8 + - + +
204A GLN* 3.4 34.8 + - + +
207A GLU* 4.2 5.9 + - - -
208A ASP* 2.9 37.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A PHE* 3.6 26.2 - - + -
176A SER 2.8 21.8 + - - +
177A MET 3.6 4.0 - - - +
179A ARG* 1.3 71.2 - - - +
181A LEU* 1.3 64.4 + - - +
183A GLU 3.4 0.7 + - - -
184A ALA 3.0 18.9 + - - -
205A PHE* 3.6 19.5 - - + -
208A ASP* 4.2 6.9 + - + -
209A ILE 5.5 0.4 - - - +
212A MET* 3.7 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A VAL* 4.5 9.0 - - + -
81A PHE* 3.8 24.6 - - + -
177A MET* 2.8 24.3 + - + +
178A VAL* 3.6 10.5 - - - +
180A ALA* 1.3 72.3 - - - +
182A ASP* 1.3 64.3 + - - +
184A ALA* 3.3 3.6 + - - +
185A MET* 3.0 30.2 + - + +
263A ALA* 3.9 29.8 - - + +
266A HIS* 3.9 20.4 - - + -
267A GLU* 4.1 10.5 - - - +
437A LEU* 4.0 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A VAL* 3.0 20.0 + - + +
179A ARG* 3.6 12.5 - - - +
180A ALA 3.2 0.2 - - - -
181A LEU* 1.3 75.4 - - - +
183A GLU* 1.3 59.0 + - - +
185A MET* 3.4 6.1 + - - +
186A ASN* 2.9 56.5 + - - +
436A THR* 6.0 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ARG* 3.0 18.3 + - + +
180A ALA 3.7 0.2 - - - +
182A ASP* 1.3 74.6 + - - +
184A ALA* 1.4 64.5 + - - +
186A ASN* 3.1 6.4 + - - +
187A LYS* 3.0 40.8 + - - +
190A ARG* 2.8 33.5 + - - -
201A ASN* 3.1 37.6 - - - +
202A LYS* 4.8 1.9 + - - +
205A PHE* 3.5 38.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PHE* 3.6 58.8 - - + +
78A VAL* 4.0 10.3 - - + +
81A PHE* 4.3 3.8 - - + -
180A ALA 3.0 14.7 + - - +
181A LEU 3.3 7.4 + - - +
183A GLU* 1.4 77.6 - - - +
185A MET* 1.4 72.5 - - + +
187A LYS* 3.7 7.3 + - - +
188A LEU* 4.0 3.1 + - - +
205A PHE* 4.5 4.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ALA* 3.9 24.9 - - + +
78A VAL* 3.6 31.0 - - + -
181A LEU* 3.0 21.6 + - + +
182A ASP* 3.8 6.3 - - - +
184A ALA* 1.4 80.9 - - + +
186A ASN* 1.3 66.8 + - - +
188A LEU* 3.1 37.5 + - + +
189A GLN* 4.3 3.6 + - - +
436A THR* 4.2 13.7 - - + +
437A LEU* 3.8 43.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A ASP* 2.9 48.0 + - - +
183A GLU* 3.1 6.5 + - - +
185A MET* 1.3 77.8 - - - +
187A LYS* 1.3 62.5 + - - +
188A LEU 3.1 1.8 + - - -
189A GLN* 3.1 19.3 + - - +
190A ARG* 3.5 30.5 + - - +
201A ASN* 5.7 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PHE* 3.6 46.3 - - + +
80A ASP* 4.4 9.7 + - - -
183A GLU* 3.0 39.9 + - - +
184A ALA* 3.7 7.9 - - - +
185A MET 3.3 0.4 - - - -
186A ASN* 1.3 74.6 - - - +
188A LEU* 1.3 60.2 + - - +
189A GLN 3.3 0.8 + - - -
190A ARG* 3.7 32.8 + - - +
193A PRO* 5.8 3.4 - - + +
202A LYS* 5.7 8.7 - - - +
205A PHE* 3.4 37.0 - - - -
----------------------------------------------------------
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