Contacts of the strand formed by residues 166 - 169 (chain D) in PDB entry 4KIS
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 LYS 166 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B LEU* 4.1 8.5 - - - -
182B ASP* 3.8 9.9 - - + -
183B ILE* 4.2 6.9 - - - +
186B GLU* 2.9 27.9 + - - +
148D LEU* 3.8 19.5 - - + -
149D PRO* 4.2 7.4 - - + -
162D VAL* 3.5 7.5 - - - +
163D ILE 2.8 26.2 + - - +
164D ASP* 2.5 40.5 + - - +
165D THR* 1.3 87.7 - - - +
167D LEU* 1.3 64.1 + - - +
168D TYR* 3.3 30.3 - - + +
234D ILE* 3.7 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 167 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149D PRO* 3.6 33.8 - - + +
151D THR 4.4 2.7 - - - +
152D THR* 5.0 2.7 - - + -
157D THR* 3.9 26.0 - - + -
160D TYR* 3.8 26.0 - - + -
161D ASP 3.2 13.2 - - - +
162D VAL* 4.6 4.3 - - + -
166D LYS* 1.3 76.7 - - - +
168D TYR* 1.3 72.8 + - - +
218D LEU* 4.9 8.5 - - + -
234D ILE* 6.2 0.2 - - - +
235D HIS* 3.4 62.8 - - + +
236D GLU 4.9 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 168 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B LYS* 4.4 26.5 - - + -
178B ARG* 4.4 19.5 - - + +
179B LEU* 3.5 36.4 - - + +
182B ASP* 2.7 32.7 + - - +
160D TYR* 3.5 3.3 - - - -
161D ASP* 2.7 35.6 + - + +
163D ILE* 3.8 39.0 - - + -
166D LYS* 3.3 34.5 - - + +
167D LEU* 1.3 78.9 - - - +
169D ILE* 1.3 62.1 + - - +
234D ILE* 5.7 2.9 - - + -
235D HIS* 6.1 2.2 - - - -
236D GLU* 6.0 3.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 169 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B LYS* 4.7 10.0 + - - -
159D GLY 4.1 0.9 - - - +
160D TYR* 3.3 25.7 - - + -
161D ASP* 4.0 5.1 - - - +
168D TYR* 1.3 74.0 - - - +
170D ASN* 1.3 78.4 + - - +
171D GLU* 3.7 18.8 + - - +
174D ALA* 3.8 15.3 - - + -
178D ARG* 5.2 8.1 - - - +
236D GLU* 3.4 53.4 + - + +
237D PRO 4.0 6.5 - - - +
238D ILE* 4.0 11.9 - - + -
----------------------------------------------------------
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