Contacts of the helix formed by residues 167 - 174 (chain A) in PDB entry 7CAL
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 LEU 167 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A PHE* 4.4 40.0 - - + -
163A GLY* 3.6 22.9 - - - +
164A PHE* 3.8 14.5 + - + +
165A ARG 3.2 0.8 - - - -
166A ILE* 1.3 82.6 - - + +
168A SER* 1.3 58.2 + - - +
169A MET 3.2 0.9 - - - -
170A LEU* 3.4 46.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A CYS* 3.3 18.7 + - - -
80A GLN* 4.4 5.5 + - - -
148A PHE* 5.3 2.0 - - - +
149A GLN* 4.8 18.9 - - - +
164A PHE 4.1 2.1 + - - -
165A ARG* 3.2 22.4 + - - -
166A ILE 3.1 1.6 - - - -
167A LEU* 1.3 74.2 - - - +
169A MET* 1.3 56.9 + - - +
170A LEU 3.2 5.1 + - - -
171A ARG* 3.2 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A CYS* 3.3 36.6 - - - +
78A PRO* 3.7 6.1 - - + -
81A PHE* 3.6 29.8 - - + -
165A ARG 3.8 2.4 + - - +
166A ILE* 2.9 28.0 + - + +
168A SER* 1.3 75.0 - - - +
170A LEU* 1.3 58.7 + - + +
171A ARG 3.1 5.8 - - - -
172A LEU* 3.1 41.5 + - + +
173A TRP* 4.4 1.9 + - - -
215A PHE* 3.6 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A CYS* 3.5 32.3 - - + +
144A SER* 3.1 24.1 + - - -
148A PHE* 5.0 7.9 - - + -
166A ILE 5.3 2.0 - - - +
167A LEU* 3.4 42.2 - - + +
168A SER 3.2 1.0 - - - -
169A MET* 1.3 78.0 - - + +
171A ARG* 1.3 56.5 + - + +
172A LEU 3.1 4.9 - - - -
173A TRP* 3.1 47.9 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
72A TYR* 5.7 0.4 - - - -
73A SER* 3.5 31.9 + - - +
74A ALA* 5.2 0.7 - - - +
76A ILE* 3.6 32.7 - - - +
77A CYS* 3.6 30.9 - - - +
80A GLN* 3.4 19.8 - - - +
95A ASP* 4.4 17.9 + - - +
98A VAL* 6.1 2.0 - - - +
99A ASN* 5.4 11.2 - - - +
144A SER 4.3 4.7 - - - +
168A SER* 3.2 32.2 + - - +
169A MET 3.1 1.2 - - - -
170A LEU* 1.3 76.4 - - + +
172A LEU* 1.3 56.1 + - - +
173A TRP 3.3 1.1 - - - -
174A ARG* 3.3 49.2 - - - +
175A LEU* 5.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ALA* 3.8 28.0 - - + +
77A CYS* 4.0 18.6 - - + -
78A PRO* 4.9 3.4 - - + -
169A MET* 3.1 30.7 + - + +
170A LEU 3.1 1.0 - - - -
171A ARG* 1.3 75.1 - - - +
173A TRP* 1.3 65.8 + - + +
174A ARG 3.2 2.9 - - - -
175A LEU* 3.4 30.0 - - + +
207A PHE* 3.7 35.4 - - + -
211A CYS* 4.7 12.1 - - - -
215A PHE* 5.7 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ALA 5.5 0.9 - - - -
140A PHE* 3.2 71.1 - + + -
143A CYS* 4.4 19.1 - - + -
144A SER* 3.3 12.6 - - - +
169A MET 5.4 1.6 - - - -
170A LEU* 3.1 46.5 + - + +
172A LEU* 1.3 80.0 - - + +
174A ARG* 1.3 55.6 + - - +
175A LEU 3.1 8.1 + - - -
176A ARG* 3.8 7.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A VAL* 3.3 28.6 - - + +
73A SER* 3.3 31.2 + - - +
98A VAL* 3.9 18.6 - - - +
99A ASN* 3.4 20.4 + - - +
102A PHE* 3.7 46.0 - - + +
144A SER* 2.4 37.6 + - - -
145A THR* 4.4 0.8 + - - +
170A LEU 4.4 1.0 + - - -
171A ARG* 3.3 39.2 + - - +
173A TRP* 1.3 75.5 - - - +
175A LEU* 1.3 57.9 + - + +
176A ARG* 3.2 9.8 + - - +
177A ARG* 3.7 12.9 + - - +
----------------------------------------------------------
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