Contacts of the helix formed by residues 164 - 178 (chain A) in PDB entry 6LGV
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 VAL 164 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A MET* 3.4 33.7 - - + -
130A THR* 3.4 22.0 - - + +
134A VAL* 4.8 1.3 - - + -
160A ILE* 2.8 25.0 + - + +
163A ILE* 1.3 90.8 - - + +
165A VAL* 1.3 72.3 + - + +
166A ILE 3.6 0.7 - - - -
167A PRO* 3.5 3.4 - - - +
168A ILE* 3.1 31.1 + - + +
259A ASN* 5.5 0.9 - - - +
262A LEU* 3.8 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A LEU* 5.7 5.4 - - + -
134A VAL* 3.6 32.1 - - + -
160A ILE 3.3 1.3 + - - +
161A LEU* 3.3 37.9 + - + +
164A VAL* 1.3 76.8 - - + +
166A ILE* 1.3 69.7 + - + +
168A ILE* 3.2 6.6 + - + +
169A THR* 2.8 40.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A MET* 5.6 4.5 - - + -
161A LEU* 2.9 24.0 + - + +
162A GLN* 4.1 18.4 - - + +
165A VAL* 1.3 76.9 - - + +
167A PRO* 1.3 71.1 - - + +
169A THR* 3.6 6.3 - - - -
170A ALA* 3.0 25.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A MET* 3.4 41.5 - - + +
42A MET* 3.9 2.9 - - + -
43A PHE* 3.6 23.7 - - + +
162A GLN 3.1 20.4 - - - +
163A ILE 3.2 16.6 - - - +
164A VAL 3.5 11.2 - - - +
166A ILE* 1.3 91.9 - - + +
168A ILE* 1.3 56.4 + - - +
170A ALA* 3.4 4.6 + - + -
171A GLY 2.9 23.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A MET* 3.6 41.5 - - + +
45A MET* 4.1 10.5 - - + -
46A GLY* 4.0 19.4 - - - +
49A LEU* 4.5 8.7 - - + -
54A PHE* 6.3 0.2 - - + -
130A THR* 3.7 19.1 - - + -
164A VAL* 3.1 21.3 + - + +
165A VAL* 3.2 6.7 + - + +
167A PRO* 1.3 75.8 - - - +
169A THR* 1.3 54.2 + - - +
171A GLY* 3.1 2.9 + - - -
172A LEU* 2.8 55.0 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
165A VAL* 2.8 34.0 + - - +
166A ILE* 3.6 6.2 - - - -
168A ILE* 1.3 74.5 - - - +
170A ALA* 1.3 61.8 + - - +
172A LEU* 2.9 15.3 + - + +
173A VAL* 2.8 44.5 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
43A PHE* 3.9 13.0 - - + -
166A ILE* 3.0 19.8 + - + +
167A PRO* 3.7 6.7 - - + +
169A THR* 1.3 74.2 - - - +
171A GLY* 1.3 57.3 + - - +
173A VAL* 3.9 6.8 - - - +
174A ILE* 2.9 38.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A PHE* 3.5 19.5 - - - -
46A GLY 3.8 0.2 - - - -
47A VAL* 3.4 26.9 - - - +
167A PRO 2.9 13.6 + - - -
168A ILE 3.1 4.2 + - - -
170A ALA* 1.3 76.3 - - - +
172A LEU* 1.3 58.1 + - - +
175A HIS* 2.9 31.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
46A GLY 3.7 15.3 - - - +
49A LEU* 3.9 28.5 - - + +
54A PHE* 4.4 15.7 - - + -
168A ILE* 2.8 37.2 + - + +
169A THR* 2.9 15.2 + - + +
171A GLY* 1.3 73.1 - - - +
173A VAL* 1.3 64.0 + - + +
175A HIS* 3.6 4.8 + - + +
176A HIS* 3.1 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A THR* 2.8 35.9 + - + +
170A ALA* 3.9 6.5 - - - +
172A LEU* 1.3 75.9 - - + +
174A ILE* 1.3 60.7 + - + +
176A HIS* 3.2 6.5 + - + +
177A THR* 2.9 46.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A PHE* 4.4 15.0 - - + -
47A VAL* 4.0 9.4 - - + -
170A ALA* 2.9 25.4 + - + +
171A GLY* 3.9 2.9 - - - +
173A VAL* 1.3 77.1 - - + +
175A HIS* 1.3 60.8 + - - +
177A THR* 3.3 3.8 + - - +
178A PHE* 2.8 57.6 + - + +
181A THR* 6.6 0.2 - - + -
182A VAL* 3.9 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A VAL 2.8 29.9 + - - +
48A THR 4.2 4.3 - - - -
49A LEU 3.6 23.3 + - - +
50A ARG* 4.2 21.6 - - + +
171A GLY 2.9 15.6 + - - +
172A LEU* 3.9 6.3 - - - +
174A ILE* 1.3 78.6 - - - +
176A HIS* 1.3 58.4 + - + +
179A THR* 2.7 51.5 + - + +
182A VAL* 3.8 19.2 - - + +
183A LYS* 5.6 5.8 - - + -
186A GLU* 4.5 8.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A LEU 3.1 18.6 + - - +
173A VAL* 3.5 6.1 - - + +
175A HIS* 1.3 82.5 - - + +
177A THR* 1.3 70.6 + - + +
179A THR* 3.4 9.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A VAL* 2.9 32.7 + - + +
174A ILE* 3.3 4.9 + - - +
176A HIS* 1.3 90.0 - - + +
178A PHE* 1.3 92.4 + - + +
179A THR* 3.6 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A ILE* 2.8 43.0 + - + +
177A THR* 1.3 102.1 + - - +
179A THR* 1.3 62.7 + - - +
180A LYS 3.4 2.7 - - - -
181A THR* 3.2 21.0 + - + +
182A VAL* 3.0 22.2 + - + +
----------------------------------------------------------
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