Contacts of the helix formed by residues 160 - 182 (chain A) in PDB entry 6B0B
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 TYR 160 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A PRO* 1.3 83.7 - - + +
161A LYS* 1.3 70.0 + - - +
162A MET* 3.1 11.7 - - - -
163A LEU* 2.9 34.7 + - + +
164A GLU* 4.2 1.0 + - - +
43D THR* 3.9 27.4 - - + -
45D LYS* 5.1 4.2 - - - -
202D THR* 3.5 39.9 - - + -
212D GLU* 2.3 30.1 + - + -
214D TYR* 4.2 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ARG* 3.4 37.0 - - - +
20A ARG* 5.7 2.2 - - - +
157A PHE 5.4 0.9 - - - +
158A ASN* 3.5 18.0 + - - +
159A PRO* 3.9 3.8 - - + +
160A TYR* 1.3 82.3 - - - +
162A MET* 1.3 61.7 + - - +
163A LEU 3.3 0.7 + - - -
164A GLU* 3.6 11.7 + - + +
165A GLU* 3.6 23.9 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
9A PHE* 4.7 20.6 - - + -
10A ARG* 5.9 3.8 - - + -
14A ASN* 6.2 4.0 - - + -
138A PHE* 4.5 9.6 - - + -
141A PHE* 5.4 5.8 - - + -
142A ALA* 5.6 7.0 - - + +
145A TRP* 5.8 12.6 - - + -
158A ASN* 3.7 22.4 + - - +
159A PRO 4.2 6.5 - - - +
160A TYR* 3.7 19.5 - - - -
161A LYS* 1.3 77.4 - - - +
163A LEU* 1.3 83.2 + - + +
165A GLU* 2.8 9.4 + - + -
166A LEU* 2.3 65.5 + - + +
214D TYR* 6.1 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A PHE* 3.6 21.3 - - + -
160A TYR* 2.9 33.8 + - + +
162A MET* 1.3 93.3 - - - +
164A GLU* 1.3 60.0 + - + +
166A LEU* 3.2 21.7 - - - +
167A ASP* 3.3 13.9 + - + +
34D GLU* 5.2 6.5 - - + +
36D ARG* 3.4 39.5 - - - +
41D THR* 5.2 7.4 - - - +
43D THR* 4.9 11.0 - - + +
214D TYR* 5.8 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A TYR 4.2 0.6 + - - -
161A LYS* 3.6 12.8 + - + +
162A MET 3.1 0.2 - - - -
163A LEU* 1.3 81.8 - - + +
165A GLU* 1.3 67.6 + - - +
167A ASP* 3.3 5.8 + - + +
168A LYS* 2.9 54.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ARG* 5.1 0.4 - - - +
14A ASN* 3.4 31.4 + - + +
16A LYS* 3.7 23.8 + - - +
20A ARG* 2.9 32.0 + - - +
161A LYS* 3.6 24.1 + - + +
162A MET* 2.8 9.7 + - - +
164A GLU* 1.3 82.4 - - - +
166A LEU* 1.3 60.1 + - - +
168A LYS* 3.7 19.6 - - - +
169A ASN* 2.9 38.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A MET* 3.4 5.1 - - - +
137A GLY 3.8 7.9 - - - +
138A PHE* 3.5 55.9 - - + +
141A PHE* 3.5 50.7 - - + -
142A ALA 4.8 0.2 - - - +
162A MET* 2.3 45.9 + - + +
163A LEU* 3.2 25.1 - - - +
165A GLU* 1.3 66.6 - - - +
167A ASP* 1.3 66.5 + - + +
170A SER* 2.9 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A PHE* 5.8 4.3 - - + -
163A LEU* 3.3 18.7 + - + +
164A GLU* 3.6 6.7 - - + +
165A GLU 3.1 1.0 - - - -
166A LEU* 1.3 85.5 - - + +
168A LYS* 1.3 60.9 + - - +
170A SER* 2.5 25.2 + - - -
171A ARG* 2.9 20.9 + - - +
36D ARG* 5.1 8.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LYS* 3.7 38.4 - - + +
164A GLU* 2.9 41.3 + - + +
165A GLU* 3.3 21.3 + - - +
167A ASP* 1.3 76.9 - - - +
169A ASN* 1.3 67.0 + - - +
171A ARG* 3.4 25.7 + - - +
172A ALA* 3.0 26.7 + - - +
3B A 4.9 5.3 + - - -
4B A 3.8 17.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A PHE 4.3 1.4 + - - -
14A ASN* 3.8 12.0 + - - +
15A ASN* 3.2 52.6 + - - +
16A LYS* 4.2 8.1 - - - +
109A SER* 4.5 2.8 + - - +
135A VAL* 5.0 0.3 - - - +
136A MET* 3.5 18.6 - - + +
141A PHE* 4.6 5.9 - - - -
165A GLU* 2.9 19.5 + - - +
166A LEU 4.4 0.2 - - - -
168A LYS* 1.3 79.6 - - - +
170A SER* 1.3 63.7 + - - +
172A ALA* 5.1 0.2 - - - -
173A ILE* 2.9 44.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A VAL* 5.1 0.2 - - - -
136A MET* 3.4 17.8 - - - +
137A GLY* 4.1 18.8 - - - -
138A PHE 5.1 0.7 - - - -
166A LEU* 2.9 16.5 + - - +
167A ASP* 2.5 34.1 + - - -
169A ASN* 1.3 73.8 - - - +
171A ARG* 1.3 63.8 + - - -
172A ALA 3.0 0.2 + - - -
174A LYS* 2.9 38.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ASP* 2.9 17.3 + - - +
168A LYS* 3.6 39.3 + - - +
170A SER* 1.3 79.0 + - - +
172A ALA* 1.3 57.6 + - - +
175A ARG* 2.3 55.5 + - - +
4B A 3.2 31.8 + - - -
5B A 3.9 23.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ARG* 4.9 17.0 - - - +
168A LYS 3.0 18.0 + - - +
169A ASN* 5.1 0.2 - - - -
170A SER 3.0 0.4 + - - -
171A ARG* 1.3 86.1 - - - +
173A ILE* 1.3 67.8 + - + +
175A ARG* 3.3 16.0 + - - +
176A ARG* 3.0 25.1 + - - +
5B A 4.9 5.6 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
15A ASN 4.3 3.8 - - - +
109A SER 3.6 16.2 - - - +
110A ARG* 3.5 48.9 - - - +
111A LEU* 3.7 28.5 - - + +
135A VAL* 3.9 10.2 - - + +
169A ASN* 2.9 39.2 + - + +
172A ALA* 1.3 77.2 - - + +
174A LYS* 1.3 60.0 + - - +
176A ARG* 3.6 5.6 - - + -
177A LEU* 2.8 27.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
107A PHE* 5.8 1.4 - - - -
134A GLU* 3.8 23.2 + - + +
135A VAL* 3.4 37.8 + - + +
136A MET 4.2 6.1 - - - +
137A GLY* 4.3 16.1 - - - +
140A GLU* 4.4 8.7 + - - -
170A SER* 2.9 24.0 + - - +
173A ILE* 1.3 75.0 - - - +
175A ARG* 1.3 60.3 + - + +
177A LEU* 3.3 1.9 + - + +
178A ASP* 2.9 45.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ARG* 2.3 59.5 + - - +
172A ALA* 3.3 10.7 + - - +
174A LYS* 1.3 74.4 - - + +
176A ARG* 1.3 66.1 + - - +
178A ASP* 3.7 8.2 - - - +
179A ARG* 2.9 45.7 + - - +
5B A 3.0 35.4 + - - -
6B A 5.1 6.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ARG* 4.9 7.0 - - - +
111A LEU* 3.6 16.8 - - + +
113A TYR* 2.5 30.7 + - - -
115A TRP* 5.1 4.0 - - - -
120A GLN* 4.4 7.5 + - - +
172A ALA 3.0 13.6 + - - +
173A ILE* 3.4 15.3 - - + +
175A ARG* 1.3 77.7 - - - +
177A LEU* 1.3 57.4 + - - +
179A ARG* 3.3 10.2 + - - +
180A ILE* 2.9 57.1 + - - +
6B A 6.2 0.4 - - - -
7B A 3.5 56.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LEU* 4.0 30.5 - - + -
123A LEU* 4.6 13.5 - - + -
133A VAL* 3.5 31.0 - - + +
134A GLU* 3.6 14.8 - - + -
135A VAL* 4.0 13.9 - - + +
173A ILE 2.8 19.1 + - - +
174A LYS* 3.9 3.6 - - + +
176A ARG* 1.3 72.9 - - - +
178A ASP* 1.3 64.0 + - - +
180A ILE* 3.2 12.7 + - + -
181A LYS* 2.9 45.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A GLU* 4.8 6.8 - - - +
174A LYS* 2.9 33.3 + - - +
175A ARG* 3.7 7.9 - - - +
176A ARG 3.3 0.4 - - - -
177A LEU* 1.3 80.2 - - - +
179A ARG* 1.3 60.0 + - + +
181A LYS* 3.3 21.1 + - - +
182A GLN* 2.9 49.6 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
124A ARG* 4.4 2.3 + - - -
175A ARG* 2.9 36.9 + - + +
176A ARG* 3.7 10.5 - - - +
178A ASP* 1.3 76.1 - - + +
180A ILE* 1.3 64.0 + - + +
182A GLN* 3.7 25.8 + - - +
6B A 2.4 38.7 + - - -
7B A 5.0 19.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
111A LEU* 3.6 23.8 - - + -
113A TYR* 4.4 5.4 - - + +
120A GLN* 3.5 30.1 - - - +
123A LEU* 4.4 22.2 - - + -
124A ARG* 2.6 49.7 + - + +
176A ARG* 2.9 55.1 + - - +
177A LEU* 3.5 13.0 - - + +
178A ASP 3.1 0.2 - - - -
179A ARG* 1.3 74.1 - - - +
181A LYS* 1.3 59.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A LEU* 6.4 0.7 - - + -
124A ARG* 4.5 6.6 + - + +
127A CYS* 3.7 35.7 - - + +
132A PRO* 6.1 0.6 - - - +
133A VAL 3.4 19.4 + - - +
134A GLU* 3.3 32.8 + - - +
177A LEU* 2.9 36.7 + - + +
178A ASP* 3.3 15.2 + - - +
180A ILE* 1.3 77.8 - - + +
182A GLN* 1.3 65.9 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
124A ARG* 3.6 21.1 + - - -
178A ASP* 2.9 36.9 + - - +
179A ARG* 3.9 21.2 - - - +
180A ILE 3.2 0.8 - - - -
181A LYS* 1.3 83.5 - - + +
----------------------------------------------------------
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