Contacts of the strand formed by residues 209 - 215 (chain B) in PDB entry 4LKC
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 TYR 209 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B LEU* 3.9 28.5 - - + -
169B TRP* 4.4 4.5 - + + -
170B ASN* 3.5 4.7 - - - -
174B LEU* 3.7 27.6 - - + -
199B VAL* 3.4 39.0 - - + +
200B PRO* 4.9 0.7 - - - +
203B SER* 2.6 33.6 + - - -
204B LEU* 4.5 11.2 - - + -
207B GLN* 3.4 38.8 - - + +
208B THR* 1.3 74.0 - - - +
210B ILE* 1.3 58.8 + - - +
211B CYS 4.4 0.2 - - - -
225B ARG* 3.4 5.5 - - - +
226B VAL* 2.7 49.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B TRP* 3.4 7.3 - - - -
170B ASN* 2.8 45.9 + - - +
208B THR* 4.1 20.9 - - + -
209B TYR* 1.3 77.9 - - - +
211B CYS* 1.3 67.4 + - - +
212B ASN* 3.7 19.6 + - - +
223B ASP* 3.8 18.4 - - + -
224B LYS 3.3 11.9 - - - +
225B ARG* 4.1 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B VAL* 3.9 8.3 - - - -
155B CYS* 2.0 50.7 - - + -
167B VAL* 4.1 7.6 - - + -
168B SER 3.4 6.5 - - - +
169B TRP* 3.6 23.8 - - + -
210B ILE* 1.3 70.6 - - - +
212B ASN* 1.3 59.4 + - - +
213B VAL* 4.1 4.0 - - - -
222B VAL 3.6 2.3 - - - +
223B ASP* 3.4 4.3 - - - -
224B LYS* 2.9 45.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B THR* 3.6 2.1 + - - +
167B VAL* 3.3 3.6 - - - -
168B SER* 2.6 62.4 + - - +
170B ASN 3.5 1.9 + - - -
171B SER* 2.9 37.4 + - - +
210B ILE* 3.7 18.6 + - - +
211B CYS* 1.3 69.8 - - - +
213B VAL* 1.3 63.4 + - - +
214B ASN* 4.0 0.7 + - - +
223B ASP* 3.0 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B PRO* 4.5 9.4 - - + -
136B VAL* 3.9 36.6 - - + -
157B VAL* 3.8 37.9 - - + -
165B VAL* 5.0 2.9 - - + -
166B THR 3.4 6.5 - - - +
167B VAL* 4.1 11.2 - - + -
211B CYS* 4.1 13.9 - - - -
212B ASN* 1.3 74.0 - - - +
214B ASN* 1.3 67.2 + - - +
215B HIS 4.9 0.7 - - - +
220B THR 3.9 1.3 - - - +
221B LYS* 3.5 4.9 - - - +
222B VAL* 2.8 40.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B PRO 4.3 0.3 - - - +
165B VAL* 3.3 4.4 - - - -
166B THR* 2.8 51.7 + - - +
212B ASN 5.3 1.1 - - - +
213B VAL* 1.3 75.1 - - - +
215B HIS* 1.3 62.5 + - - +
216B LYS* 3.7 40.6 + - + +
219B ASN* 5.6 0.3 - - - -
220B THR 3.5 9.2 + - - +
221B LYS* 3.6 37.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B LYS 3.2 25.1 + - - -
134B PRO* 3.5 22.8 - - + +
160B TYR* 3.7 6.0 - + + -
161B PHE 3.6 11.2 - - - -
162B PRO 2.6 25.8 + - - -
164B PRO 3.3 20.4 - - - -
165B VAL* 3.4 22.9 - - + -
213B VAL* 4.3 0.8 - - - +
214B ASN* 1.3 70.6 - - - +
216B LYS* 1.4 64.3 + - - +
217B PRO* 3.6 10.7 - - + +
218B SER* 2.7 31.5 + - - +
219B ASN 3.2 3.1 + - - -
220B THR 2.8 31.2 + - - +
----------------------------------------------------------
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