Contacts of the helix formed by residues 168 - 176 (chain I) in PDB entry 5L08
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 ASN 168 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111I GLU* 4.9 2.6 + - + +
164I CYS 3.1 8.4 + - - +
165I ALA 4.5 3.2 + - - -
167I ILE* 1.3 87.4 + - + +
169I LYS* 1.3 68.8 + - - +
170I SER* 2.8 43.6 + - - +
171I LEU* 2.9 36.6 + - + +
172I LEU* 3.6 2.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 169 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165I ALA 5.3 1.8 + - - -
168I ASN* 1.3 79.0 + - - +
170I SER* 1.3 60.3 + - - +
171I LEU 3.2 0.2 - - - -
172I LEU* 3.2 24.4 + - + +
173I LYS* 3.0 48.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 170 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111I GLU* 2.8 32.7 + - - +
168I ASN* 2.8 25.3 + - - +
169I LYS* 1.3 81.2 - - - +
171I LEU* 1.3 62.6 + - - +
173I LYS* 3.3 19.9 - - - +
174I ILE* 3.2 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 171 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108I ILE* 4.1 17.4 - - + +
111I GLU* 3.5 30.3 - - + -
112I VAL* 3.5 28.7 - - + -
120I PHE* 3.9 7.0 - - + -
164I CYS* 4.1 22.0 - - + +
167I ILE* 3.5 38.1 - - + -
168I ASN* 2.9 17.3 + - + +
170I SER* 1.3 78.1 + - - +
172I LEU* 1.3 61.8 + - - +
174I ILE* 3.2 7.7 + - + +
175I ILE* 2.9 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 172 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161I LYS* 3.9 26.0 - - + -
164I CYS* 4.4 0.4 - - + -
165I ALA* 3.8 45.3 - - + +
168I ASN 3.6 1.1 + - - +
169I LYS* 3.3 26.2 - - + +
171I LEU* 1.3 76.3 - - - +
173I LYS* 1.3 54.6 + - + +
175I ILE* 3.1 12.8 + - + +
176I ASN* 2.8 44.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 173 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169I LYS* 3.0 37.8 + - - +
170I SER* 3.3 22.2 - - - +
172I LEU* 1.3 76.8 - - + +
174I ILE* 1.3 64.1 + - + +
176I ASN* 3.3 26.8 + - - +
177I ASP* 4.0 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 174 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104I MET* 3.4 33.5 - - + +
107I GLN* 3.8 32.1 - - + +
108I ILE* 3.7 14.8 - - + +
111I GLU* 4.8 13.0 - - + +
170I SER 3.2 14.1 + - - +
171I LEU* 3.2 11.7 + - - +
173I LYS* 1.3 76.3 - - + +
175I ILE* 1.3 64.9 + - - +
177I ASP* 3.0 33.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 175 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104I MET* 3.3 12.2 - - + +
108I ILE* 4.6 14.8 - - + -
157I LEU* 5.5 4.9 - - + +
158I ASP* 4.4 19.7 - - - +
160I LEU* 4.3 5.8 - - + -
161I LYS* 3.7 46.4 - - + +
164I CYS* 3.7 22.9 - - + -
171I LEU 2.9 18.8 + - - +
172I LEU* 3.1 14.8 + - + +
174I ILE* 1.3 71.7 - - - +
176I ASN* 1.3 59.3 + - - +
177I ASP 2.9 5.6 - - - -
178I TYR* 2.9 27.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 176 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172I LEU* 2.8 26.9 + - - +
173I LYS* 3.4 23.3 - - - +
174I ILE 3.1 0.8 - - - -
175I ILE* 1.3 75.2 - - - +
177I ASP* 1.3 58.2 + - - +
178I TYR* 2.9 26.8 + - + -
179I GLU* 3.4 31.1 - - - +
----------------------------------------------------------
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