Contacts of the helix formed by residues 268 - 285 (chain B) in PDB entry 4AD7
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 CYS 268 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B PRO* 1.3 73.7 - - - +
269B PRO* 1.3 67.1 - - + +
270B ASP* 3.2 1.6 - - + +
271B TYR* 3.1 8.0 + - + +
272B CYS* 2.9 27.8 + - - +
415B CYS* 2.0 47.3 - - - -
416B TRP 3.0 23.7 + - - +
417B ASN 3.9 0.9 - - - -
422B GLY 3.5 12.6 - - - -
424B TYR* 3.6 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 269 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B PRO 3.6 5.1 - - - +
268B CYS* 1.3 87.1 - - + +
270B ASP* 1.3 64.3 + - - +
272B CYS* 3.6 6.4 + - + +
273B ARG* 2.9 54.3 + - - +
401B CYS* 5.3 2.2 - - + -
402B SER* 6.2 1.3 - - - -
415B CYS* 4.6 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 270 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B CYS* 3.2 1.6 - - - +
269B PRO* 1.3 85.3 - - - +
271B TYR* 1.3 60.5 + - - +
273B ARG* 3.4 17.6 + - - +
274B ASN* 2.9 33.8 + - - +
424B TYR* 3.7 22.9 - - + +
426B PRO 4.9 3.3 - - - +
428B VAL* 3.5 25.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 271 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ALA 4.4 1.6 + - - -
252B LYS* 3.4 40.1 + - - +
253B LEU* 3.5 28.9 + - + +
267B PRO* 4.5 1.3 - - + -
268B CYS* 3.1 13.3 + - + +
270B ASP* 1.3 76.9 - - - +
272B CYS* 1.3 61.4 + - - +
274B ASN* 3.2 3.3 + - - +
275B VAL* 3.0 33.5 + - + +
416B TRP* 3.5 23.6 - + - -
417B ASN 3.6 5.6 - - - -
418B GLY* 3.6 22.1 - - - -
424B TYR* 3.5 32.3 - + + -
441B GLU* 3.1 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 272 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B LEU* 3.7 26.2 - - + +
267B PRO* 5.0 4.7 - - + +
268B CYS 2.9 15.5 + - - +
269B PRO* 3.6 6.3 - - + +
271B TYR* 1.3 77.2 - - - +
273B ARG* 1.3 55.9 + - - +
275B VAL* 3.4 0.7 + - - +
276B LEU* 2.9 28.3 + - - +
401B CYS* 2.0 52.6 - - + -
405B MET* 3.6 30.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 273 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B PRO* 2.9 46.5 + - - +
270B ASP* 3.4 23.9 + - - +
271B TYR 3.2 0.2 - - - -
272B CYS* 1.3 76.9 - - - +
274B ASN* 1.3 57.3 - - - +
276B LEU* 3.8 0.9 - - - +
277B LYS* 2.9 43.3 + - - +
397B PRO* 4.3 13.2 - - + +
398B GLY* 4.4 15.1 - - - +
401B CYS* 3.8 19.2 - - + +
402B SER* 3.8 24.7 + - - +
428B VAL* 4.4 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B ASP 2.9 13.9 + - - +
271B TYR 3.7 0.4 - - - +
273B ARG* 1.3 75.4 - - - +
275B VAL* 1.3 63.5 + - - +
277B LYS* 4.6 2.6 - - - +
278B GLY* 2.9 19.2 + - - -
424B TYR* 3.1 24.6 + - - +
426B PRO* 4.5 0.2 - - - +
427B GLU 2.7 24.6 + - - -
428B VAL* 3.3 5.6 - - - +
429B MET* 2.9 32.7 + - - +
439B ASN* 3.0 24.5 + - - +
440B PRO* 3.8 10.6 - - - +
441B GLU* 3.7 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ALA* 4.2 9.0 - - + +
250B VAL* 3.8 37.9 - - + +
253B LEU* 3.9 24.5 - - + -
271B TYR* 3.0 46.3 + - + +
272B CYS 3.7 3.6 - - - +
274B ASN* 1.3 75.9 - - - +
276B LEU* 1.3 58.7 - - + +
278B GLY* 3.2 2.8 + - - -
279B CYS* 2.9 30.6 + - - -
441B GLU* 3.7 10.8 - - + -
442B VAL* 3.6 8.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 276 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B LEU* 3.8 34.8 - - + -
250B VAL* 4.8 6.3 - - + -
253B LEU* 5.3 1.6 - - + -
272B CYS* 2.9 20.8 + - - +
275B VAL* 1.3 77.5 - - + +
277B LYS* 1.3 60.7 + - - +
279B CYS* 3.4 5.5 + - + +
280B LEU* 2.9 41.5 + - + +
397B PRO* 3.6 25.3 - - + +
400B LEU* 3.7 32.3 - - + -
401B CYS* 3.5 22.4 - - - -
405B MET* 4.2 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 277 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B ARG* 2.9 26.8 + - - +
274B ASN* 3.9 3.4 - - - +
276B LEU* 1.3 75.3 - - - +
278B GLY* 1.3 60.1 + - - +
280B LEU* 5.1 1.1 - - - -
281B ALA* 3.0 33.7 + - - +
394B ILE 5.7 1.3 - - - -
397B PRO* 3.9 21.5 - - + -
428B VAL* 3.6 19.4 - - + +
429B MET* 2.5 33.5 + - + +
430B GLY* 4.0 8.4 - - - +
431B ASP* 3.3 28.7 + - - +
436B GLN* 3.5 16.1 + - - +
439B ASN* 5.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 278 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B ASN 2.9 14.3 + - - -
275B VAL 3.2 4.5 + - - -
277B LYS* 1.3 79.6 - - - +
279B CYS* 1.3 60.9 + - - +
281B ALA* 4.1 6.9 + - - +
436B GLN* 3.3 17.6 + - - -
439B ASN* 4.2 0.9 - - - -
442B VAL* 3.9 20.0 - - - +
444B VAL* 3.7 19.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 279 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B LEU* 4.9 1.8 - - + -
242B LEU* 4.7 5.0 - - + +
246B CYS* 2.0 60.9 - - - +
250B VAL* 3.8 14.1 - - - -
275B VAL* 2.9 23.7 + - - +
276B LEU* 3.4 9.6 + - + +
278B GLY* 1.3 79.1 - - - +
280B LEU* 1.3 70.3 + - + +
281B ALA 3.5 1.1 + - - -
282B ASN* 5.0 2.1 + - - +
283B GLN* 3.9 7.4 + - - +
442B VAL* 4.8 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 280 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B LEU* 5.9 1.1 - - + -
89B LEU* 3.8 39.0 - - + -
242B LEU* 4.3 7.9 - - + -
276B LEU* 2.9 32.8 + - + +
277B LYS* 3.8 2.2 - - - -
279B CYS* 1.3 82.0 - - + +
281B ALA* 1.3 64.4 + - - +
283B GLN* 2.8 39.6 + - + +
284B ALA* 2.9 19.2 + - + +
393B TRP 5.7 1.3 - - - +
396B LEU* 3.7 34.3 - - + -
397B PRO* 4.7 10.1 - - + -
400B LEU* 5.3 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 281 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B LYS 3.0 17.7 + - - +
278B GLY 4.2 5.2 - - - +
279B CYS 3.5 2.2 - - - -
280B LEU* 1.3 75.8 - - - +
282B ASN* 1.3 58.7 + - - +
284B ALA* 2.9 25.5 + - - +
285B ASP* 3.0 16.6 + - - +
432B GLY* 3.4 26.0 - - - +
433B LEU* 3.6 16.1 + - + -
436B GLN* 3.6 11.2 - - + -
444B VAL* 5.5 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 282 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B VAL* 5.9 2.1 - - + +
279B CYS 5.0 2.0 + - - +
280B LEU 3.3 0.6 - - - -
281B ALA* 1.3 77.1 - - - +
283B GLN* 1.3 69.0 + - - +
285B ASP* 3.1 22.5 + - - +
433B LEU* 3.3 33.1 - - - +
448B LYS 4.5 5.3 + - - -
449B PRO* 3.8 1.0 - - - +
450B ASP* 3.6 33.9 + - + +
453B ILE* 3.3 31.6 - - + +
454B ARG* 3.9 5.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 283 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B LEU* 5.8 1.0 - - - +
237B VAL* 4.1 14.8 + - + +
240B VAL* 3.9 29.3 + - - +
241B PRO 5.1 1.8 + - - -
242B LEU* 5.2 4.4 - - - +
279B CYS 3.9 5.4 + - - +
280B LEU* 2.8 47.6 - - + +
282B ASN* 1.3 79.7 + - - +
284B ALA* 1.3 60.7 + - - +
286B LEU* 3.3 15.6 + - - +
393B TRP* 3.4 34.4 - - + +
396B LEU* 4.9 8.3 - - + -
453B ILE* 3.7 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 284 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B LEU* 2.9 12.0 + - + +
281B ALA* 2.9 14.5 + - - +
283B GLN* 1.3 75.2 - - - +
285B ASP* 1.3 64.3 + - - +
286B LEU 3.2 0.7 + - - -
287B ASP* 3.4 20.4 + - - +
393B TRP 3.6 20.8 + - - +
394B ILE* 4.1 12.5 - - + +
431B ASP* 4.6 4.1 - - + +
432B GLY* 3.9 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 285 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B ALA 3.0 12.7 + - - +
282B ASN* 3.1 13.7 + - - +
284B ALA* 1.3 74.4 - - - +
286B LEU* 1.3 57.9 + - - +
287B ASP* 3.1 7.0 + - - -
288B ALA* 4.2 7.4 + - - +
289B GLU* 5.3 0.7 + - - +
432B GLY* 3.4 6.6 - - - -
433B LEU* 3.3 33.0 + - - +
454B ARG* 2.4 41.7 + - - +
457B ILE* 3.8 13.9 - - + +
----------------------------------------------------------
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