Contacts of the strand formed by residues 160 - 165 (chain K) in PDB entry 6LTJ
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 THR 160 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153K MET* 3.7 13.9 - - + -
154K ASP* 3.1 13.7 - - - +
155K SER* 3.7 17.3 - - - -
156K GLY 4.1 0.2 - - - +
159K VAL* 1.3 79.9 - - - +
161K HIS* 1.3 70.2 + - - +
177K ARG* 3.5 1.2 - - - -
178K LEU* 2.8 57.8 + - - +
180K LEU* 2.8 19.7 + - + +
181K ALA* 3.8 10.8 - - + -
261K LEU* 6.0 2.7 - - + -
274K ILE* 4.7 4.4 - - + +
303K THR* 5.4 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 161 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108K ALA* 5.2 4.0 - - + -
109K PRO* 3.6 40.3 - - + +
110K LEU* 4.5 14.2 - - + +
138K ALA* 6.2 0.4 - - + -
152K VAL 3.4 1.3 - - - +
153K MET* 3.3 7.2 - - - +
154K ASP* 2.8 45.9 + - + +
159K VAL* 3.5 34.3 - - + +
160K THR* 1.3 78.9 + - - +
162K THR* 1.3 64.3 - - - +
163K VAL* 4.1 3.4 - - + -
175K ILE* 4.3 9.2 - - + -
176K LEU 3.4 17.7 - - - -
177K ARG* 3.4 27.0 + - + +
178K LEU 4.7 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 162 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151K ILE* 6.2 2.2 - - - -
152K VAL 3.3 6.5 - - - -
153K MET* 3.6 19.7 - - - -
161K HIS* 1.3 75.9 - - - +
163K VAL* 1.3 63.6 + - - +
175K ILE* 3.7 0.3 - - - -
176K LEU* 2.9 35.8 + - - +
178K LEU* 5.5 1.5 - - + +
274K ILE* 4.9 0.9 - - + +
277K THR* 3.7 23.4 + - + -
278K THR* 3.8 21.5 - - + +
281K SER* 2.4 36.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 163 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109K PRO* 4.2 20.9 - - + -
136K ILE* 5.9 0.9 - - + -
138K ALA* 3.6 28.0 - - + -
139K VAL* 5.9 0.2 - - + -
150K GLY 3.9 0.2 - - - +
151K ILE* 3.0 8.1 - - - +
152K VAL* 2.9 45.0 + - + +
161K HIS* 4.7 4.9 - - + -
162K THR* 1.3 81.2 - - - +
164K PRO* 1.3 66.6 - - + +
165K ILE* 4.0 20.6 - - + -
175K ILE* 3.7 30.5 - - + -
281K SER* 5.5 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 164 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151K ILE* 3.7 9.2 - - + -
162K THR 4.3 1.1 - - - +
163K VAL* 1.3 87.7 - - + +
165K ILE* 1.3 61.9 + - - +
170K ALA 2.9 23.7 - - - +
171K LEU* 3.3 19.1 - - + +
174K ALA* 3.3 35.0 - - + +
175K ILE* 4.2 3.4 - - + +
281K SER* 3.5 29.4 - - - +
293K LEU* 3.7 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 165 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139K VAL* 4.0 26.9 - - + -
142K LEU* 3.7 18.2 - - + -
143K TYR* 6.0 1.1 - - + -
148K THR 4.1 6.5 - - - +
149K THR* 3.4 3.7 - - - -
150K GLY 2.8 40.3 + - - +
152K VAL* 4.3 4.9 - - + -
163K VAL* 4.0 21.8 - - + -
164K PRO* 1.3 85.0 - - - +
166K TYR* 1.3 64.4 + - - +
168K GLY* 3.5 26.5 - - - +
169K TYR 3.3 9.4 - - - +
170K ALA* 3.7 20.4 - - + +
293K LEU* 4.2 6.8 - - - +
----------------------------------------------------------
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