Contacts of the helix formed by residues 155 - 170 (chain A) in PDB entry 3CTP
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 ASP 155 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A SER* 1.3 69.4 - - - +
156A ASN* 1.3 56.7 + - - +
157A TYR* 3.9 5.4 + - - +
158A ASN* 2.7 44.2 + - - +
159A GLY* 3.0 23.4 + - - -
162A MET* 5.8 0.3 - - - +
312A ILE* 3.5 20.0 - - + +
313A MET 2.8 19.9 + - - +
314A GLU* 4.5 3.8 - - - -
315A VAL* 3.6 19.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A GLU* 4.2 2.8 + - - -
153A SER* 3.1 26.5 + - - -
154A SER* 2.9 20.2 + - - +
155A ASP* 1.3 70.2 - - - +
157A TYR* 1.3 67.3 + - - +
159A GLY* 3.8 0.2 - - - -
160A GLY 3.0 18.0 + - - -
186A ALA* 3.3 37.9 - - - +
189A LEU* 4.0 12.8 - - + +
190A ARG* 2.8 50.3 + - + +
266A PHE* 3.4 11.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ASP* 3.3 5.3 + - - +
156A ASN* 1.3 78.2 - - - +
158A ASN* 1.3 82.4 + - - +
160A GLY 3.1 2.9 + - - -
161A ARG* 3.1 27.1 + - + +
189A LEU* 3.5 34.0 - - + +
192A LYS* 3.8 12.1 - - + -
193A GLY* 3.4 32.9 - - - -
196A ASP* 2.5 39.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ASP* 2.7 35.0 + - - +
157A TYR* 1.3 98.8 - - - +
159A GLY* 1.3 58.2 + - - +
161A ARG* 3.2 9.6 + - + +
162A MET* 2.9 44.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ASP 3.0 12.8 + - - -
156A ASN 3.4 0.2 + - - -
157A TYR 3.2 0.2 - - - -
158A ASN* 1.3 76.7 - - - +
160A GLY* 1.3 56.1 + - - +
162A MET* 3.3 6.1 + - - +
163A ALA* 3.0 27.9 + - - +
266A PHE* 3.7 22.7 - - - -
282A ILE* 3.8 9.5 - - - +
315A VAL* 3.7 18.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ASN 3.0 13.9 + - - -
157A TYR 3.1 2.9 + - - -
159A GLY* 1.3 73.1 - - - +
161A ARG* 1.3 65.0 + - - +
163A ALA* 3.3 1.2 + - - +
164A PHE 3.1 17.2 + - - -
190A ARG* 3.5 24.0 - - - -
194A PHE* 3.5 19.4 - - - -
236A PHE* 4.2 13.2 - - - -
266A PHE* 4.1 0.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A TYR* 3.1 20.5 + - + +
158A ASN* 3.2 15.7 + - - +
160A GLY* 1.3 76.4 - - - +
162A MET* 1.3 57.0 + - + +
164A PHE* 3.1 1.8 + - - -
165A ASP* 2.9 55.4 + - - +
193A GLY* 3.5 14.3 - - - +
194A PHE* 4.6 0.4 - - - +
196A ASP* 4.3 9.1 + - - +
197A GLY* 3.4 34.4 - - - +
200A ALA* 4.0 20.6 - - - +
201A LYS* 4.4 11.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ASP* 5.8 0.4 - - - +
158A ASN* 2.9 25.8 + - + +
159A GLY* 3.6 7.2 - - - +
160A GLY 3.3 0.2 - - - -
161A ARG* 1.3 79.3 - - + +
163A ALA* 1.3 57.6 + - - +
165A ASP* 3.3 8.7 + - - +
166A HIS* 2.9 31.2 + - - +
282A ILE* 4.0 11.2 - - + +
314A GLU* 5.9 0.9 - - + -
315A VAL* 3.4 47.1 - - + +
316A LYS* 4.1 13.7 - - - -
317A LEU* 4.1 14.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A GLY 3.0 13.6 + - - +
160A GLY 3.6 7.6 - - - +
161A ARG 3.2 0.2 - - - -
162A MET* 1.3 79.1 - - - +
164A PHE* 1.3 63.2 + - - +
166A HIS* 3.4 1.7 + - - +
167A LEU* 3.1 26.3 + - - +
194A PHE* 3.9 1.8 - - - -
236A PHE* 3.7 38.6 - - + -
264A ILE* 3.8 22.9 - - + +
282A ILE* 4.2 3.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A GLY 3.1 9.1 + - - +
161A ARG 3.1 7.2 + - - +
163A ALA* 1.3 77.5 - - - +
165A ASP* 1.3 75.4 + - - +
167A LEU* 3.2 3.8 + - - +
168A TYR* 2.9 54.4 + + + -
175A ILE* 3.9 20.6 - - + -
194A PHE* 3.4 52.6 - + + +
197A GLY* 3.4 23.6 - - - -
198A ALA* 3.5 28.3 - - + -
201A LYS* 3.9 14.4 - - + -
203A LEU* 4.1 5.4 - - + -
205A ILE* 4.0 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ARG* 2.9 56.4 + - - +
162A MET* 3.8 7.6 - - - +
164A PHE* 1.3 86.8 - - - +
166A HIS* 1.3 57.4 + - - +
168A TYR* 3.5 3.7 + - - +
169A GLU* 2.9 32.2 + - - +
201A LYS* 4.8 6.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A MET 2.9 18.1 + - - +
163A ALA 3.8 3.4 - - - +
165A ASP* 1.3 74.3 - - - +
167A LEU* 1.3 68.2 + - + +
169A GLU* 3.3 18.2 + - - +
170A LYS* 3.0 46.1 + - + +
264A ILE* 4.1 7.0 - - + -
280A THR* 3.7 21.8 - - + +
317A LEU* 3.5 24.8 - - + +
319A GLU* 3.4 34.7 - - + -
323A THR* 2.9 35.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ALA 3.1 10.9 + - - +
164A PHE 3.8 5.4 - - - +
166A HIS* 1.3 76.8 - - + +
168A TYR* 1.3 63.6 + - - +
170A LYS* 3.1 10.8 + - - -
171A GLY 3.3 0.3 + - - -
172A CYS* 3.0 43.7 + - + +
175A ILE* 4.4 10.5 - - + -
194A PHE* 4.1 24.5 - - + -
234A GLY* 4.2 7.9 - - - -
235A ILE 4.1 19.5 - - - +
262A GLN* 4.4 11.9 - - + +
264A ILE* 4.0 27.6 - - + -
323A THR* 4.3 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A PHE* 2.9 45.4 + + + +
165A ASP* 3.8 4.5 - - - +
167A LEU* 1.3 77.8 - - - +
169A GLU* 1.3 59.7 + - - +
171A GLY* 2.9 17.0 + - - -
172A CYS 3.9 9.4 - - - -
173A ARG* 2.9 62.9 + - - +
175A ILE* 4.9 0.6 - - - +
201A LYS* 3.8 50.9 + - + +
203A LEU* 4.3 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A ASP 2.9 18.4 + - - +
166A HIS* 3.7 25.1 + - - +
168A TYR* 1.3 79.4 - - - +
170A LYS* 1.3 84.7 + - - +
171A GLY* 3.3 3.3 + - - -
317A LEU* 5.7 0.3 - - - +
319A GLU* 5.6 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A HIS* 3.0 47.9 + - + +
167A LEU* 3.7 5.4 - - - +
168A TYR 3.1 0.6 - - - -
169A GLU* 1.3 104.1 + - - +
171A GLY* 1.3 57.6 + - - +
172A CYS 3.4 2.7 - - - -
262A GLN* 3.3 29.2 + - - +
319A GLU* 4.0 10.5 + - - -
323A THR* 4.7 0.4 - - - -
324A ILE* 3.3 53.4 + - + +
325A SER* 4.5 6.2 + - - +
----------------------------------------------------------
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