Contacts of the strand formed by residues 239 - 249 (chain B) in PDB entry 4WGK
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 239 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B HIS* 3.3 5.7 - - - -
104B ILE* 2.6 39.5 + - - +
237B ASN* 3.8 16.6 - - - +
238B MET* 1.3 80.6 - - - +
240B PRO* 1.3 76.9 - - + +
241B GLY 3.4 0.7 + - - -
288B ASP* 4.6 17.6 + - + +
294B LEU* 3.9 31.6 - - + +
340B PRO* 6.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A ASN* 3.9 26.2 - - + +
292A ASP* 5.6 4.3 - - - +
99B PHE* 3.8 13.5 - - + -
102B TYR 3.7 3.1 - - - +
103B HIS* 3.6 26.2 - - + +
238B MET 4.7 1.1 - - - +
239B LYS* 1.3 85.8 - - + +
241B GLY* 1.3 57.9 + - - +
288B ASP* 3.5 8.3 - - - +
289B LEU* 3.3 40.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B PHE* 3.3 17.0 - - - -
101B GLY* 4.6 0.3 - - - -
102B TYR* 3.1 27.0 + - - +
104B ILE* 4.0 10.5 - - - +
239B LYS 3.4 2.0 + - - -
240B PRO* 1.3 75.6 - - - +
242B LYS* 1.3 64.9 + - - +
287B VAL 3.2 13.5 - - - -
288B ASP* 3.9 3.1 - - - -
289B LEU* 3.9 6.1 - - - -
294B LEU* 5.3 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B PHE* 4.7 12.8 - - + -
102B TYR* 5.4 2.9 - - - -
104B ILE* 3.4 6.7 - - - +
241B GLY* 1.3 78.9 - - - +
243B ILE* 1.3 65.7 + - - +
244B PHE* 3.7 30.3 - - + -
285B LYS 3.9 0.3 - - - +
286B MET* 3.7 0.5 - - - -
287B VAL* 2.9 35.7 + - + +
288B ASP 5.6 1.1 - - - +
289B LEU* 4.3 19.5 - - + +
418B GLU* 3.4 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B TYR* 3.6 27.7 - - + -
104B ILE* 3.6 14.8 - - + -
144B MET* 3.7 30.5 - - + -
242B LYS* 1.3 79.5 - - - +
244B PHE* 1.3 59.5 + - - +
284B LEU* 3.6 37.5 - - + -
285B LYS 3.3 5.6 - - - +
286B MET* 4.2 6.7 - - + -
418B GLU* 3.4 7.2 - - - +
419B VAL* 2.6 51.8 + - + +
529B LEU* 4.6 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B LYS* 3.7 38.8 - - + -
243B ILE* 1.3 75.9 - - - +
245B ILE* 1.3 60.0 - - - +
284B LEU* 3.6 6.4 - - - +
285B LYS* 2.7 52.6 + - + -
287B VAL* 3.9 21.3 - - + -
415B ALA* 4.1 21.8 - - + -
416B SER* 3.2 32.3 - - - -
417B GLN 3.3 5.2 - - - +
418B GLU* 3.5 23.6 - - + -
419B VAL* 4.3 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 245 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B PHE* 1.3 76.6 - - - +
246B ASN* 1.3 68.6 + - - +
247B LYS* 4.6 9.9 - - - -
282B ILE* 4.0 23.1 - - + -
283B VAL 3.5 11.9 - - - +
284B LEU* 4.1 9.9 - - + -
415B ALA* 4.4 4.5 - - - +
416B SER 4.5 0.5 + - - -
417B GLN* 3.0 51.8 + - - +
419B VAL* 3.7 23.3 - - + -
531B SER* 6.0 0.2 - - - +
532B LEU* 4.2 16.2 - - + -
566B THR* 4.2 24.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 246 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B ILE* 1.3 76.6 - - - +
247B LYS* 1.3 84.0 + - - +
281B MET 3.9 0.3 - - - +
282B ILE* 3.6 1.9 - - - +
283B VAL* 3.0 34.7 + - + +
411B LEU* 2.9 46.9 + - + +
414B SER* 3.1 24.2 + - - -
415B ALA* 3.5 16.2 - - + +
416B SER 5.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 247 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B ILE* 4.6 11.4 - - + -
246B ASN* 1.3 90.5 + - - +
248B GLY* 1.3 59.3 + - - +
280B GLU* 3.6 31.4 + - - +
281B MET 3.3 8.3 - - - +
282B ILE* 4.0 11.7 - - + -
411B LEU* 3.4 12.7 - - - +
417B GLN* 6.3 0.7 - - - +
566B THR* 2.8 43.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 248 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B LYS* 1.3 75.5 - - - +
249B ASN* 1.3 63.3 + - - -
280B GLU* 3.4 3.2 - - - +
281B MET* 2.7 42.7 + - - +
407B ARG* 3.4 19.3 - - - -
411B LEU* 3.7 5.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 249 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B GLY* 1.3 73.9 - - - -
250B VAL* 1.3 61.0 + - - +
251B ASP* 4.1 13.3 + - - +
279B LYS* 3.4 19.1 - - + +
280B GLU* 3.6 24.1 + - - +
407B ARG* 2.8 26.5 + - - +
----------------------------------------------------------
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