Contacts of the helix formed by residues 164 - 172 (chain A) in PDB entry 4TMU
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 ALA 164 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A MET* 3.3 10.2 - - + +
160A PRO 3.3 4.0 + - - +
161A GLU* 3.0 37.4 + - - +
163A ALA* 1.3 75.5 - - - +
165A LEU* 1.3 57.0 + - - +
166A GLY 3.2 3.6 - - - -
167A GLN* 3.0 53.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A VAL* 4.3 16.4 - - + -
123A PRO* 4.0 13.2 - - + -
126A LEU* 4.0 17.3 - - + -
127A MET* 3.7 30.5 - - + -
145A VAL* 4.4 16.4 - - + -
151A ILE* 4.5 1.3 - - + -
161A GLU 3.6 6.7 - - - +
162A TYR* 3.6 34.5 - - + +
163A ALA 3.3 2.2 - - - -
164A ALA* 1.3 74.7 - - - +
166A GLY* 1.3 64.1 + - - +
167A GLN 3.1 0.4 - - - -
168A LEU* 3.1 18.6 + - + +
169A ARG* 3.1 10.6 + - - +
177A PHE* 4.3 5.4 - - + -
195A LEU 4.8 0.6 + - - +
196A LEU* 3.6 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ALA 4.2 0.9 + - - -
164A ALA 3.2 1.6 - - - -
165A LEU* 1.3 75.0 - - - +
167A GLN* 1.3 63.0 + - - +
169A ARG* 3.0 12.5 + - - +
170A ALA* 3.0 15.2 + - - +
195A LEU 3.3 25.1 + - - -
196A LEU* 3.8 16.9 - - - +
197A GLY* 4.6 1.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A MET* 3.9 14.7 - - + +
132A ILE* 5.9 0.2 - - - -
164A ALA* 3.0 35.4 + - - +
166A GLY* 1.3 76.2 - - - +
168A LEU* 1.3 63.5 + - - +
170A ALA* 3.4 6.9 + - - +
171A ARG* 3.1 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ILE* 5.7 1.1 - - + -
126A LEU* 3.7 35.0 - - + -
127A MET* 3.9 13.4 - - - +
132A ILE* 4.1 19.7 - - + -
135A LEU* 4.3 10.3 - - + -
140A LEU* 5.2 2.5 - - + -
143A VAL* 4.6 12.6 - - + -
165A LEU* 3.1 14.6 + - + +
167A GLN* 1.3 79.2 - - - +
169A ARG* 1.3 63.9 + - - +
171A ARG* 3.2 4.2 + - - -
172A PHE* 3.1 58.9 + - + +
177A PHE* 4.2 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ASP* 2.8 41.8 + - - -
165A LEU 3.1 2.5 + - - +
166A GLY 3.0 11.5 + - - +
168A LEU* 1.3 80.5 - - - +
170A ALA* 1.3 61.4 + - - +
172A PHE 3.0 38.4 + - - -
173A PRO* 3.6 18.7 + - - +
175A VAL 2.9 22.6 + - - -
176A PRO* 3.9 0.8 - - - +
177A PHE* 3.6 33.1 - - + +
196A LEU 3.2 24.0 - - - +
197A GLY* 3.2 19.8 + - - +
199A ASP* 5.1 4.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A GLY 3.0 11.0 + - - +
167A GLN* 3.8 9.9 - - - +
169A ARG* 1.3 75.3 - - - +
171A ARG* 1.3 64.9 + - - +
172A PHE 3.4 0.5 + - - -
173A PRO* 3.8 14.3 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
129A ASP* 5.0 10.5 + - - +
132A ILE* 3.4 35.7 + - + +
133A ASP* 3.2 27.9 + - - +
167A GLN 3.1 13.1 + - - +
168A LEU* 3.2 11.0 + - - +
170A ALA* 1.3 76.7 - - - +
172A PHE* 1.3 85.9 + - + +
173A PRO* 3.5 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ILE* 4.4 7.2 - - + -
135A LEU* 4.0 16.4 - - + -
136A GLY* 3.9 35.7 - - - -
140A LEU* 3.9 20.4 - - + -
168A LEU* 3.1 43.9 + - + +
169A ARG* 3.0 14.7 + - - -
170A ALA 3.2 0.2 - - - -
171A ARG* 1.3 98.5 - - + +
173A PRO* 1.3 66.9 - - - +
174A ALA 3.1 2.2 - - - -
175A VAL* 3.0 34.5 + - + +
177A PHE* 4.9 2.5 - - + -
----------------------------------------------------------
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