Contacts of the strand formed by residues 316 - 322 (chain F) in PDB entry 3KQG
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 LEU 316 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210F SER* 3.5 10.8 - - - +
211F LEU 3.6 32.3 - - - +
212F ILE 3.7 11.7 - - - -
213F PRO* 3.8 12.0 - - + +
249F LEU* 3.8 33.0 - - + -
250F ILE 3.6 8.0 + - - +
251F TYR* 3.0 33.2 - - + +
252F TRP* 2.8 20.6 + - - +
315F PHE* 1.3 80.9 - - - +
317F PHE* 1.3 58.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 317 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208F TYR* 3.3 2.2 - + - +
210F SER* 2.9 49.7 + - - -
212F ILE* 3.3 22.4 - - + -
214F LYS* 3.7 21.1 - - + -
219F ALA* 3.5 28.9 - - + -
222F PHE* 3.2 56.3 - + + -
223F CYS* 4.0 4.0 - - - -
230F LEU* 3.9 3.1 - - + -
251F TYR* 3.7 2.6 - - - -
252F TRP* 3.7 16.4 - - + +
315F PHE 4.0 5.8 - - - +
316F LEU* 1.3 77.8 - - - +
318F ILE* 1.3 64.8 + - - +
319F CYS* 3.8 17.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 318 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207F TYR* 4.3 6.7 - - + -
208F TYR 3.2 6.1 - - - +
209F PHE* 3.3 44.4 - - + -
230F LEU* 3.4 10.2 - - - +
231F THR* 2.8 50.8 + - + +
242F LEU* 4.4 11.0 - - + +
246F ALA* 5.2 0.9 - - + -
251F TYR* 3.6 30.7 - - + -
252F TRP 3.2 8.8 + - - +
253F ILE* 4.5 10.8 - - + -
298F ILE* 4.8 8.7 - - + -
317F PHE* 1.3 77.9 - - - +
319F CYS* 1.3 63.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 319 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199F TRP* 4.0 6.3 - - + -
207F TYR* 3.2 5.4 - - - -
208F TYR* 2.8 46.7 + - + -
222F PHE* 4.0 8.5 - - - -
223F CYS* 2.0 52.0 - - - -
226F ARG* 5.6 0.7 - - - -
228F SER* 3.4 12.3 - - - +
229F HIS 3.4 4.9 - - - -
317F PHE* 3.8 16.6 - - - -
318F ILE* 1.3 77.5 - - - +
320F LYS* 1.3 61.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 320 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199F TRP* 4.8 0.2 - - - -
205F ASN* 3.9 27.8 - - + +
206F PHE 3.4 6.5 - - - +
207F TYR* 3.6 17.5 - - + -
228F SER* 3.1 4.1 - - - -
229F HIS* 2.6 35.6 + - + +
231F THR* 3.2 31.9 - - - +
232F SER* 3.1 30.4 + - - +
234F THR* 4.3 7.9 + - - +
238F GLU* 2.9 24.4 + - - -
268F ASP* 4.6 6.3 - - - +
319F CYS* 1.3 77.2 - - - +
321F ARG* 1.3 65.0 + - - +
322F PRO* 4.8 2.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 321 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194F VAL* 3.9 36.6 - - - +
199F TRP* 3.8 39.1 - - + +
205F ASN* 3.5 5.7 - - - -
206F PHE* 2.8 52.1 + - + -
226F ARG 4.2 7.5 + - - -
227F ASN* 3.6 34.7 - - - +
228F SER* 3.7 2.7 - - - +
320F LYS* 1.3 76.6 - - - +
322F PRO* 1.3 77.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 322 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204F GLY 4.5 1.1 - - - +
205F ASN* 3.1 17.7 - - - +
206F PHE* 4.2 6.3 - - - -
227F ASN 5.5 0.7 - - - +
320F LYS* 4.8 2.7 - - + +
321F ARG* 1.3 97.7 + - + +
323F TYR* 1.3 62.1 + - - +
324F VAL* 3.6 19.1 + - + +
----------------------------------------------------------
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