Contacts of the helix formed by residues 164 - 171 (chain A) in PDB entry 1LCI
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 MET 164 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A MET* 3.6 13.9 - - + -
63A LEU* 3.8 14.9 - - + +
87A GLN* 3.9 14.4 - - + +
90A MET* 3.7 30.3 - - - -
91A PRO* 3.7 24.9 - - - -
127A PHE* 3.9 14.1 - - + -
150A ILE* 3.7 20.9 - - + -
151A ILE 3.2 8.7 + - - +
152A MET* 3.5 28.0 - - - +
154A SER 4.6 0.4 + - - -
163A SER* 1.3 74.3 - - - +
165A TYR* 1.3 61.9 + - + +
167A PHE* 3.9 2.7 - - - +
168A VAL* 3.1 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A MET* 4.0 33.1 - - + +
62A ARG* 5.2 2.5 + - - -
87A GLN* 5.6 4.6 + - + +
90A MET* 4.1 19.8 - - - +
152A MET 5.2 1.8 - - - -
154A SER 3.8 13.0 - - - -
155A LYS* 3.7 50.8 + - + +
163A SER* 3.1 5.8 - - - +
164A MET* 1.3 91.3 - - + +
166A THR* 1.3 63.6 + - + +
168A VAL* 3.6 5.1 + - + +
169A THR* 3.1 27.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A LYS 3.9 9.4 - - - +
156A THR* 4.4 1.8 - - - -
157A ASP* 2.8 35.4 + - - +
162A GLN* 3.2 11.6 + - - +
163A SER* 2.9 28.2 + - - +
165A TYR* 1.3 75.5 - - + +
167A PHE* 1.3 64.2 + - - +
169A THR* 3.4 8.8 + - - +
170A SER* 3.0 25.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LEU* 4.2 14.6 - - + -
66A ALA* 3.7 22.4 - - + -
67A MET* 4.0 22.0 - - + -
70A TYR* 3.8 34.8 - + + -
125A VAL* 5.7 2.0 - - + -
148A LYS* 3.6 25.1 - - + -
150A ILE* 3.6 26.5 - - + -
162A GLN* 3.5 15.5 - - + +
163A SER 3.0 18.7 + - - +
164A MET* 3.9 2.2 - - - +
166A THR* 1.3 78.6 + - - +
168A VAL* 1.3 63.3 + - - +
170A SER 3.1 3.8 + - - -
171A HIS* 3.0 52.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A MET* 4.0 8.3 - - + -
62A ARG* 3.2 60.8 - - + +
63A LEU* 3.8 21.3 - - + +
66A ALA* 3.8 7.7 - - + +
164A MET 3.1 19.2 + - - +
165A TYR* 3.8 6.3 - - + +
166A THR 3.3 0.2 - - - -
167A PHE* 1.3 79.2 - - - +
169A THR* 1.3 57.5 + - - +
171A HIS* 3.0 4.3 + - - -
172A LEU* 2.9 45.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ARG* 4.4 10.9 + - - +
165A TYR 3.1 16.8 + - - -
166A THR* 3.6 9.0 - - - +
168A VAL* 1.3 78.2 - - - +
170A SER* 1.3 60.6 + - - +
171A HIS 3.3 0.4 + - - -
172A LEU* 4.4 9.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
162A GLN* 2.9 28.7 + - - -
166A THR 3.0 5.4 + - - -
167A PHE* 3.1 13.2 + - - -
169A THR* 1.3 78.9 - - - +
171A HIS* 1.3 77.2 + - - +
172A LEU 5.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ALA* 3.5 28.3 - - + +
69A ARG* 3.2 29.1 + - + +
70A TYR* 3.5 31.9 + + + -
148A LYS* 5.4 1.0 - - - -
162A GLN* 4.8 1.8 + - - -
167A PHE* 3.0 49.8 - + - -
168A VAL 3.0 2.4 + - - -
170A SER* 1.3 95.5 + - - +
172A LEU* 1.3 66.3 + - - +
173A PRO* 3.6 0.5 - - - +
----------------------------------------------------------
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