Contacts of the helix formed by residues 254 - 270 (chain B) in PDB entry 3HUU
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 ASN 254 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B ASN* 2.8 27.4 + - - +
253B ILE* 1.3 78.8 - - - +
255B PRO* 1.3 69.0 - - - +
256B ASP* 3.2 15.6 - - - +
257B VAL* 3.1 22.4 + - + +
258B LEU* 3.3 9.7 + - - +
282B ILE* 3.8 11.9 - - + +
283B SER* 3.0 26.1 + - - -
285B GLN* 3.0 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 255 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B PHE* 4.0 15.3 - - + -
42B ASP* 3.4 39.0 - - + +
43B VAL* 3.6 25.1 - - + -
236B ASN* 4.2 10.8 - - - +
237B THR 5.4 3.6 - - - +
252B ASN* 4.3 4.3 - - - +
253B ILE* 3.4 10.2 - - + +
254B ASN* 1.3 88.0 - - - +
256B ASP* 1.3 67.7 + - - +
258B LEU* 3.2 14.9 + - + +
259B GLY 3.0 18.4 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
42B ASP* 3.9 18.1 + - + +
45B ASN* 5.4 7.2 - - - +
46B GLY* 3.7 9.1 - - - -
49B GLN* 5.7 2.0 - - - +
254B ASN* 3.4 20.8 - - - +
255B PRO* 1.3 80.1 - - - +
257B VAL* 1.3 73.7 + - - +
259B GLY 3.4 0.2 + - - -
260B PHE* 3.0 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 257 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B ASN* 3.1 23.5 + - + +
256B ASP* 1.3 91.4 - - - +
258B LEU* 1.3 60.5 + - - +
260B PHE* 3.9 7.7 - - + +
261B THR* 2.6 41.4 + - - +
282B ILE* 3.7 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 258 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B PHE* 4.0 22.0 - - + -
43B VAL* 4.9 3.6 - - + -
110B VAL* 4.5 15.1 - - + +
122B ILE* 3.9 14.6 - - + +
123B ASP* 3.8 36.3 - - - +
124B ASN* 3.5 21.8 - - - +
253B ILE* 4.0 3.6 - - + +
254B ASN 3.3 7.3 + - - +
255B PRO* 3.2 23.2 + - + +
257B VAL* 1.3 76.4 - - - +
259B GLY* 1.3 58.2 + - - +
261B THR* 3.7 1.9 - - - -
262B ALA* 2.9 31.0 + - - +
282B ILE* 3.8 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 259 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B VAL* 3.4 30.9 - - - +
47B ILE* 3.3 21.7 + - - +
255B PRO 3.0 11.0 + - - -
256B ASP 3.8 2.5 - - - -
258B LEU* 1.3 74.9 - - - +
260B PHE* 1.3 53.6 + - - +
262B ALA* 3.1 2.3 + - - -
263B GLY* 2.7 32.9 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
46B GLY* 3.4 22.4 - - - +
49B GLN* 4.1 17.7 - - + -
50B ALA* 3.8 18.8 - - + +
53B VAL* 6.1 1.8 - - + -
256B ASP 3.0 17.2 + - - +
257B VAL* 3.9 8.7 - - + +
259B GLY* 1.3 73.3 - - - +
261B THR* 1.3 65.9 + - - +
263B GLY* 3.8 0.7 - - - +
264B ASN* 3.0 57.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 261 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ILE* 3.6 28.7 - - + -
257B VAL* 2.6 33.4 + - - +
258B LEU 3.7 3.4 - - - -
260B PHE* 1.3 78.1 - - - +
262B ALA* 1.3 59.1 + - - +
264B ASN* 3.4 4.4 + - - +
265B THR* 2.7 43.3 + - - +
280B LYS* 4.7 13.5 - - + +
282B ILE* 4.5 4.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 262 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ILE* 4.6 1.8 - - + -
86B ILE* 3.6 18.3 - - + +
108B LEU* 3.7 5.6 - - + +
110B VAL* 3.9 25.1 - - + -
122B ILE* 3.4 16.4 - - + +
258B LEU 2.9 20.4 + - - +
259B GLY* 3.6 6.3 - - - +
261B THR* 1.3 76.7 - - - +
263B GLY* 1.3 63.5 + - - +
266B ILE* 3.2 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 263 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ILE* 4.5 10.5 - - - -
50B ALA* 3.9 15.9 - - - -
51B CYS* 4.7 2.9 - - - -
86B ILE* 4.1 11.6 - - - +
259B GLY 2.7 19.2 + - - -
260B PHE 3.8 1.1 - - - -
262B ALA* 1.3 75.1 - - - +
264B ASN* 1.3 59.0 + - - +
266B ILE* 3.3 10.1 - - - +
267B ILE* 2.9 25.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ALA* 3.7 12.2 - - - +
54B ARG* 3.7 28.7 + - - +
260B PHE* 3.0 60.7 + - - +
261B THR* 4.0 3.8 - - - +
263B GLY* 1.3 75.8 - - - +
265B THR* 1.3 63.8 + - - +
267B ILE* 3.2 7.0 + - - +
268B ASP* 3.0 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 265 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B LEU* 3.8 19.5 - - + -
120B ILE* 3.9 20.9 - - + -
122B ILE* 3.8 7.5 - - + +
261B THR* 2.7 30.8 + - - +
264B ASN* 1.3 77.8 - - - +
266B ILE* 1.3 58.0 + - - +
268B ASP* 3.4 11.5 + - + +
269B VAL* 3.1 30.1 + - + +
280B LYS* 4.1 18.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 266 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ILE* 3.9 23.1 - - + -
51B CYS* 5.8 0.2 - - - -
84B GLY* 3.8 7.6 - - - -
85B PHE 2.9 48.7 - - - +
86B ILE* 3.9 13.0 - - + -
106B PRO 5.3 0.9 - - - +
107B TYR* 4.6 7.0 - - - +
108B LEU* 3.5 22.4 - - + +
262B ALA 3.2 10.6 + - - +
263B GLY* 3.3 13.9 - - - +
265B THR* 1.3 76.6 - - - +
267B ILE* 1.3 69.8 + - + +
269B VAL* 3.3 10.1 + - + +
270B LEU* 3.1 28.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 267 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ILE* 4.2 18.4 - - + -
50B ALA 5.5 0.9 - - - +
51B CYS* 4.5 8.5 - - - -
54B ARG* 3.2 36.8 - - + +
56B TYR* 3.3 57.8 + - + +
263B GLY 2.9 24.0 - - - +
264B ASN* 3.2 7.8 + - - +
266B ILE* 1.3 74.6 - - + +
268B ASP* 1.3 66.9 + - - +
270B LEU* 3.2 24.2 + - - +
271B ARG 4.6 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 268 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ARG* 2.8 32.9 + - - +
264B ASN* 3.0 16.5 + - - +
265B THR* 3.4 13.6 - - + +
267B ILE* 1.3 77.1 - - - +
269B VAL* 1.3 57.2 + - + +
271B ARG 2.9 24.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 269 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B PRO* 4.2 25.6 - - + -
107B TYR 5.5 4.9 - - - +
108B LEU* 5.6 2.7 - - + -
120B ILE* 5.0 13.2 - - + -
265B THR* 3.1 23.6 + - + +
266B ILE* 3.5 15.7 - - + +
267B ILE 3.2 0.2 - - - -
268B ASP* 1.3 77.9 - - + +
270B LEU* 1.3 52.8 + - + +
271B ARG* 2.7 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 270 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ILE* 3.5 33.0 - - + -
56B TYR* 4.2 23.2 + - + +
83B ASP* 3.2 43.1 - - + +
84B GLY* 4.2 1.6 - - - +
106B PRO* 3.9 26.2 - - + -
266B ILE* 3.1 16.6 + - + +
267B ILE* 3.2 13.3 + - - +
269B VAL* 1.3 74.8 - - - +
271B ARG* 1.3 69.8 + - - +
----------------------------------------------------------
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