Contacts of the helix formed by residues 159 - 170 (chain I) in PDB entry 3A68
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 159 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40I LYS 3.3 11.6 - - - +
41I TYR* 3.4 13.7 - - - -
42I VAL* 4.9 0.6 + - + -
45I SER* 4.1 16.2 + - - +
105I ARG* 2.9 44.5 + - - -
154I ALA* 2.8 19.4 + - + +
155I THR* 5.8 0.4 - - - -
157I ASN* 3.3 3.7 - - + +
158I GLY* 1.3 69.5 - - - +
160I VAL* 1.3 65.6 + - - +
161I GLN* 3.4 2.4 + - - +
162I LEU* 3.0 19.2 + - + -
163I ALA* 3.2 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 160 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158I GLY* 3.2 12.0 + - - +
159I ASP* 1.3 73.4 + - - +
161I GLN* 1.3 59.1 + - - +
163I ALA* 3.5 5.9 + - - +
164I ASP* 3.0 25.3 + - - +
148W LEU* 4.0 19.0 - - + +
151W HIS* 3.5 39.5 - - + +
152W SER* 6.0 1.1 - - - +
167W GLU* 4.1 7.5 - - + +
171W LEU* 3.5 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 161 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101I TYR* 2.5 40.6 + - - -
105I ARG* 3.6 9.0 + - - +
159I ASP* 3.4 2.6 + - - +
160I VAL* 1.3 78.8 - - - +
162I LEU* 1.3 60.8 + - - +
164I ASP* 3.6 10.2 + - + +
165I PHE* 2.8 33.8 + - - +
148W LEU* 5.3 4.0 - - + +
171W LEU* 3.7 37.2 - - + +
172W GLY* 3.6 18.3 - - - +
175W VAL* 3.6 24.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 162 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41I TYR* 4.5 2.9 - - + -
45I SER* 3.8 32.1 - - - +
49I VAL* 3.9 23.6 - - + -
101I TYR* 3.2 35.1 + - + +
105I ARG* 4.0 2.0 - - - +
150I LEU* 4.5 10.3 - - + -
153I VAL* 6.0 0.2 - - + -
154I ALA* 3.6 22.4 - - + +
159I ASP* 3.0 23.0 + - - +
161I GLN* 1.3 72.5 - - - +
163I ALA* 1.3 67.3 + - - +
165I PHE* 3.2 4.0 + - + +
166I VAL* 3.0 35.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 163 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151I HIS* 3.3 34.4 + - + +
154I ALA* 3.7 14.5 - - + +
155I THR* 4.2 12.1 - - - +
159I ASP 3.2 15.7 + - - +
160I VAL* 3.7 5.6 - - - +
162I LEU* 1.3 80.9 - - - +
164I ASP* 1.3 60.6 + - - +
166I VAL* 3.3 2.8 + - - -
167I GLU* 3.1 20.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 164 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331D CA 4.0 4.0 - - - -
160I VAL 3.0 17.2 + - - +
161I GLN* 3.6 14.4 + - + +
162I LEU 3.2 0.2 - - - -
163I ALA* 1.3 74.9 - - - +
165I PHE* 1.3 58.4 + - - +
167I GLU* 3.4 16.8 - - - +
168I THR* 2.7 49.3 + - - -
167W GLU* 3.6 51.4 - - + +
168W THR* 4.4 5.2 + - - -
171W LEU* 5.6 1.1 - - + +
172W GLY* 5.5 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 165 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97I LYS* 4.1 17.5 - - + -
98I LEU* 3.7 16.6 - - + -
101I TYR* 3.6 60.3 - + + -
104I LYS* 6.2 2.2 - - - -
161I GLN* 2.8 25.2 + - - +
162I LEU* 3.2 5.4 + - + +
164I ASP* 1.3 75.6 + - - +
166I VAL* 1.3 69.1 - - + +
168I THR* 4.6 3.6 - - - -
169I GLU* 2.9 54.9 + - + +
170I TYR* 3.6 28.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 166 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98I LEU* 5.7 0.2 - - + -
147I LEU* 3.8 34.1 - - + +
150I LEU* 3.7 30.1 - - + -
151I HIS* 4.3 13.5 - - + +
162I LEU* 3.0 24.1 + - + +
163I ALA* 3.7 7.0 - - - +
165I PHE* 1.3 85.3 - - + +
167I GLU* 1.3 58.4 + - - +
170I TYR* 2.9 30.9 + - + +
171I LEU* 3.2 21.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 167 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160D VAL* 4.0 5.7 - - + +
164D ASP* 2.9 33.2 - - + +
167D GLU* 3.7 2.1 - - - +
331D CA 2.5 28.2 - - - -
151I HIS* 3.1 20.0 + - + -
163I ALA 3.1 7.1 + - - +
164I ASP* 3.4 19.6 - - - +
166I VAL* 1.3 80.1 - - - +
168I THR* 1.3 65.9 + - - +
171I LEU* 3.6 38.8 + - + +
172I GLY 4.0 4.5 + - - -
332I CA 2.6 27.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 168 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164D ASP* 4.7 6.5 + - - -
164I ASP* 2.7 39.1 + - - -
165I PHE* 4.0 3.4 - - - -
167I GLU* 1.3 80.1 - - - +
169I GLU* 1.3 75.6 + - - +
173I GLU* 3.9 0.9 - - - +
215I CA 2.5 28.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 169 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94I HIS* 6.1 0.7 - - - -
97I LYS* 2.7 45.7 + - + +
165I PHE* 2.9 43.1 + - + +
168I THR* 1.3 92.5 - - - +
170I TYR* 1.3 77.2 + - + +
173I GLU* 3.2 24.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 170 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56I GLU* 4.4 5.6 - - - -
94I HIS* 2.7 56.2 + + + -
97I LYS* 3.3 23.3 - - - +
98I LEU* 3.2 23.0 + - + +
147I LEU* 3.8 33.9 - - + +
165I PHE* 3.6 32.5 - + - -
166I VAL* 2.9 18.2 + - + +
168I THR 3.5 0.2 - - - -
169I GLU* 1.3 92.1 - - + +
171I LEU* 1.3 61.3 + - - +
172I GLY 3.5 2.2 - - - -
173I GLU* 3.5 6.2 + - + +
174I GLN* 2.9 31.3 + - - +
----------------------------------------------------------
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