Contacts of the helix formed by residues 255 - 267 (chain B) in PDB entry 3HAD
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 255 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B LEU* 3.5 27.4 - - + +
251B ASP* 3.6 9.9 - - - +
254B GLY* 1.3 70.1 - - - -
256B ASP* 1.3 60.5 + - - +
258B THR* 3.4 3.6 + - - -
259B LYS* 2.8 30.7 + - - +
281B LEU* 4.0 15.6 - - + +
284B LEU* 3.8 24.7 - - + -
285B VAL* 4.0 7.7 - - + +
289B LYS 3.2 23.3 - - - +
290B PHE* 2.8 18.3 + - - +
297B GLY* 3.5 20.9 - - - -
298B PHE* 3.5 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 256 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B LEU* 1.3 72.1 + - - +
257B THR* 1.3 74.0 + - - +
259B LYS* 3.3 1.9 + - - +
260B PHE* 2.9 27.3 + - - +
285B VAL* 4.1 17.3 - - + +
290B PHE* 3.4 40.5 + - + +
293B LYS* 2.8 39.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 257 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B VAL* 3.4 24.0 + - + +
254B GLY* 3.7 1.2 - - - -
255B LEU 3.3 0.4 - - - -
256B ASP* 1.3 82.6 + - - +
258B THR* 1.3 61.6 + - - +
260B PHE* 3.5 6.4 + - - +
261B ILE* 3.3 35.8 + - + +
293B LYS* 3.2 23.6 + - - -
750B NAD 4.2 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 258 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B VAL* 4.1 23.6 - - + +
215B LEU* 5.3 3.7 - - + +
216B MET* 4.5 10.1 - - + -
250B LEU* 4.0 23.6 - - + +
253B VAL* 3.7 17.3 - - - +
254B GLY 2.9 17.8 + - - -
255B LEU* 3.6 4.7 - - - -
256B ASP 3.2 0.2 - - - -
257B THR* 1.3 76.5 - - - +
259B LYS* 1.3 66.9 + - - +
261B ILE* 3.0 12.2 + - - +
262B VAL* 2.9 26.7 + - + +
281B LEU* 4.6 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 259 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B LEU 2.8 21.5 + - - +
256B ASP 3.7 3.4 - - - +
258B THR* 1.3 73.3 - - - +
260B PHE* 1.3 57.8 + - - +
262B VAL* 3.1 5.0 + - + +
263B ASP* 2.6 68.2 + - - +
281B LEU* 4.1 19.7 - - + +
282B ASN* 2.8 39.6 + - - +
285B VAL* 3.5 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 260 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B GLU* 3.4 45.3 - - + -
138B SER* 3.9 14.4 + - - -
139B LEU* 5.8 3.6 - - + -
256B ASP 2.9 18.3 + - - +
257B THR* 3.6 7.0 - - - +
259B LYS* 1.3 78.1 - - - +
261B ILE* 1.3 66.1 + - + +
263B ASP* 3.5 9.1 + - + +
264B GLY* 3.2 19.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 261 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B SER* 4.3 22.0 - - - -
138B SER* 3.9 26.8 - - - +
208B ASN* 5.2 9.9 - - + +
212B VAL* 4.8 14.1 - - + -
257B THR* 3.4 25.4 - - + +
258B THR* 3.0 10.2 + - - +
260B PHE* 1.3 80.3 - - + +
262B VAL* 1.3 62.9 + - - +
264B GLY* 3.5 1.8 + - - -
265B TRP* 3.2 61.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 262 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B VAL* 3.6 25.4 - - + -
216B MET* 3.7 38.8 - - + -
258B THR* 2.9 15.5 + - + +
259B LYS* 3.7 8.5 - - - +
261B ILE* 1.3 74.6 - - - +
263B ASP* 1.3 63.6 + - - +
265B TRP* 3.3 11.5 + - + +
266B HIS* 2.8 25.8 + - - +
274B LEU 4.9 0.4 - - - +
275B HIS* 3.6 31.9 - - + +
276B GLN 4.7 1.3 - - - +
277B PRO* 5.4 2.5 - - + -
281B LEU* 5.5 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 263 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B LYS* 2.6 64.0 + - - +
260B PHE* 3.9 9.9 - - + +
262B VAL* 1.3 71.4 - - - +
264B GLY* 1.3 56.9 + - - +
266B HIS* 2.8 13.1 + - + +
267B GLU* 2.7 36.7 + - - +
277B PRO* 5.1 10.7 - - - +
282B ASN* 4.7 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B SER* 6.1 2.7 - - - -
260B PHE 3.2 12.6 + - - -
261B ILE* 3.5 3.3 + - - -
262B VAL 3.2 0.2 - - - -
263B ASP* 1.3 80.5 - - - +
265B TRP* 1.3 64.4 + - - +
267B GLU* 3.1 7.8 + - - +
268B MET* 2.9 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 265 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B SER 6.1 0.2 - - - -
138B SER* 4.8 10.9 - - - +
203B PRO* 3.8 19.5 - - + +
204B GLY* 4.0 24.4 - - - +
208B ASN* 3.6 24.2 - - + -
209B ARG* 4.5 8.5 - - - -
212B VAL* 3.6 30.5 - - + -
213B PRO* 3.9 12.6 - - + -
261B ILE* 3.2 35.1 + - + +
262B VAL* 3.8 9.0 - - + +
264B GLY* 1.3 76.2 - - - +
266B HIS* 1.3 60.7 + - - +
268B MET* 3.7 25.4 - - + +
269B ASP* 3.1 21.5 + - - +
275B HIS* 3.2 55.9 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 266 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B VAL 2.8 13.4 + - - +
263B ASP* 2.8 17.8 + - - +
265B TRP* 1.3 75.8 - - - +
267B GLU* 1.3 59.8 + - - +
269B ASP 4.3 0.9 - - - -
270B ALA* 2.7 64.7 + - + +
275B HIS* 3.4 27.6 + - - +
276B GLN* 3.6 25.2 + - - -
277B PRO* 3.7 21.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 267 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B ASP 2.7 17.9 + - - +
264B GLY* 3.7 6.6 - - - +
266B HIS* 1.3 71.7 - - - +
268B MET* 1.3 58.3 + - - +
269B ASP* 3.0 9.3 + - - -
270B ALA* 4.3 5.1 + - - +
----------------------------------------------------------
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