Contacts of the strand formed by residues 181 - 186 (chain B) in PDB entry 5LS6
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 GLN 181 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A LYS* 4.3 19.3 - - - +
101A LEU* 5.4 1.1 - - - -
138B TYR* 4.5 2.1 - - - -
175B ILE* 4.5 4.5 - - - -
176B ASN 3.1 25.0 + - - +
179B THR* 3.2 21.5 + - - +
180B MET* 1.3 85.8 - - + +
182B CYS* 1.3 62.7 + - - +
183B ILE* 3.0 19.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LEU* 3.9 27.3 - - + +
102A ASN* 5.7 4.3 - - - +
173B ARG* 3.3 39.7 - - - +
174B ILE 3.2 10.3 - - - +
175B ILE* 4.1 4.7 - - + -
181B GLN* 1.3 70.0 - - - +
183B ILE* 1.3 59.3 + - - +
184B LYS 3.3 26.5 - - - -
185B HIS* 4.7 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 183 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B ASP* 5.5 5.6 - - - +
162B LEU* 3.9 25.6 - - + -
174B ILE* 3.1 18.9 + - + +
176B ASN* 4.1 13.7 - - + +
179B THR* 4.2 16.8 - - + +
181B GLN* 3.0 22.9 + - + +
182B CYS* 1.3 72.7 - - - +
184B LYS* 1.3 81.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 184 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B ARG* 3.8 0.3 - - - -
174B ILE* 3.0 43.5 + - + -
182B CYS* 3.3 12.1 - - - -
183B ILE* 1.3 99.1 - - + +
185B HIS* 1.3 63.7 + - - +
186B TYR* 3.4 27.1 - - + +
220B ILE* 2.6 25.9 + - + +
221B GLN* 3.6 13.1 + - - +
223B ASP* 3.3 21.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 185 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A VAL* 3.9 31.2 - - + +
171B ILE* 4.8 6.5 - - + -
172B ILE 3.4 11.0 - - - +
173B ARG* 4.9 2.7 - - + -
182B CYS* 4.7 8.4 - - - -
184B LYS* 1.3 79.0 - - - +
186B TYR* 1.3 74.0 + - - +
187B VAL* 4.4 22.6 - - + +
223B ASP* 5.0 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B GLY 4.4 1.4 - - - +
171B ILE* 4.0 2.4 - - - -
172B ILE* 3.2 46.7 + - + +
174B ILE* 4.8 7.6 - - + +
184B LYS* 3.4 19.8 - - + +
185B HIS* 1.3 85.1 - - - +
187B VAL* 1.3 62.4 + - - +
188B GLY 3.7 2.0 + - - -
189B HIS 5.4 0.3 + - - -
206B LEU* 4.8 4.0 - - + -
218B TRP* 3.7 49.2 - + + -
219B ASN 5.2 0.2 - - - -
220B ILE* 3.2 54.6 + - + +
223B ASP* 3.6 35.2 + - + -
224B THR 5.7 0.4 - - - -
572C LEU* 5.8 1.6 - - + -
----------------------------------------------------------
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