Contacts of the helix formed by residues 259 - 277 (chain B) in PDB entry 2D4H
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 ASP 259 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B ASP* 4.2 13.3 - - - +
240B ARG 4.4 3.0 - - - +
242B VAL* 2.8 37.1 + - + +
258B LEU* 1.3 71.2 - - - +
260B PRO* 1.3 82.3 - - - +
261B GLU* 3.9 14.1 + - - +
262B PHE* 3.2 27.7 + - + +
263B VAL* 3.0 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 260 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B ASP 5.8 0.4 - - - +
258B LEU 3.2 9.8 - - - +
259B ASP* 1.3 94.1 - - - +
261B GLU* 1.3 66.2 + - + +
263B VAL* 3.4 8.9 + - + +
264B GLN* 3.2 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 261 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B ASP* 4.1 15.0 - - - +
259B ASP* 3.3 13.7 + - - +
260B PRO* 1.3 80.9 - - + +
262B PHE* 1.3 66.9 + - - +
264B GLN* 3.2 12.1 + - - +
265B GLN* 2.9 31.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 262 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B TYR* 3.4 38.1 - + - -
65B PHE* 4.3 8.5 - + - -
183B ARG* 3.3 33.9 - - - -
238B PHE* 4.5 11.0 - - + -
239B ASP* 3.3 31.1 - - + +
241B PRO* 4.0 26.9 - - + -
258B LEU* 4.4 12.1 - - + -
259B ASP* 3.2 28.4 + - + +
261B GLU* 1.3 77.7 - - - +
263B VAL* 1.3 64.8 + - - +
265B GLN* 3.4 7.6 + - - +
266B VAL* 3.1 34.4 + - + +
593B 5GP 4.2 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 263 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B TYR* 3.9 20.5 + - - +
255B ASP* 3.5 48.0 - - + +
258B LEU* 4.0 10.5 - - + -
259B ASP 3.0 17.2 + - - +
260B PRO* 3.6 10.1 - - + +
261B GLU 3.2 0.2 - - - -
262B PHE* 1.3 76.4 - - + +
264B GLN* 1.3 59.8 + - - +
266B VAL* 3.4 3.5 + - - +
267B ALA* 2.9 29.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B PRO 3.2 10.0 + - - +
261B GLU* 3.2 17.5 + - - +
263B VAL* 1.3 77.0 - - - +
265B GLN* 1.3 56.2 + - + +
267B ALA* 3.0 12.1 + - - +
268B ASP* 2.6 66.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 265 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B PHE* 5.1 7.1 - - - -
237B VAL* 3.3 24.4 + - - +
238B PHE* 3.4 31.6 - - + -
239B ASP* 4.9 11.9 + - - +
261B GLU* 2.9 26.7 + - + +
262B PHE* 3.5 8.1 - - - +
263B VAL 3.3 0.2 - - - -
264B GLN* 1.3 76.1 - - + +
266B VAL* 1.3 57.1 + - - +
268B ASP* 3.4 8.8 + - - +
269B PHE* 2.9 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 266 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B TYR* 3.6 37.9 - - + -
54B LEU* 3.7 28.7 - - + -
57B LYS* 4.3 18.6 - - + -
183B ARG* 4.9 0.4 - - - +
238B PHE* 4.1 9.4 - - + -
262B PHE* 3.1 31.4 + - + +
263B VAL 4.0 2.7 - - - +
265B GLN* 1.3 73.7 - - - +
267B ALA* 1.3 61.3 + - - +
269B PHE* 3.4 6.3 - - + +
270B CYS* 3.0 30.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 267 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B LYS* 5.9 3.1 - - + +
263B VAL* 2.9 22.2 + - + +
264B GLN* 3.0 19.0 + - - +
266B VAL* 1.3 75.0 - - - +
268B ASP* 1.3 60.0 + - - +
270B CYS* 3.8 6.7 - - - +
271B SER* 3.2 26.7 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
236B PHE* 4.4 9.2 - - + -
264B GLN* 2.6 60.4 + - - +
265B GLN* 3.7 10.3 - - - +
267B ALA* 1.3 71.7 - - - +
269B PHE* 1.3 64.7 + - - +
271B SER* 3.7 6.9 - - - -
272B TYR* 3.4 18.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 269 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ILE* 4.6 2.7 - - + -
54B LEU* 3.8 31.4 - - + -
58B LEU* 4.0 24.5 - - + -
127B VAL* 4.0 20.0 - - + -
179B VAL* 3.7 22.7 - - + -
181B THR* 4.0 9.0 - - + -
236B PHE* 3.8 31.1 - + + -
238B PHE* 3.8 13.7 - + + -
265B GLN 2.9 14.8 + - - +
266B VAL 3.4 10.3 - - - +
268B ASP* 1.3 73.6 - - - +
270B CYS* 1.3 80.0 + - - +
272B TYR* 2.9 20.6 + - - +
273B ILE* 3.2 26.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 270 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B LEU 4.7 1.3 - - - -
57B LYS* 3.9 35.0 - - - +
58B LEU* 3.4 31.4 - - + -
266B VAL* 3.0 26.3 + - - +
267B ALA* 3.8 7.0 - - - +
269B PHE* 1.3 81.9 - - - +
271B SER* 1.3 63.7 + - - +
273B ILE* 2.9 6.4 + - - +
274B PHE* 2.9 38.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 271 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B LYS* 6.1 0.6 - - - +
267B ALA 3.2 16.0 + - - -
268B ASP* 3.7 9.9 - - - -
270B CYS* 1.3 77.5 - - - +
272B TYR* 1.3 59.1 + - - +
274B PHE* 3.5 10.3 + - - +
275B SER* 2.7 35.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 272 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B THR* 6.0 0.7 - - + -
177B ASP* 5.3 6.1 + - + +
178B PHE 5.0 1.2 + - - -
179B VAL* 3.7 25.9 - - + +
232B LYS* 4.7 16.3 - - - +
233B LYS 5.4 0.2 - - - -
234B LYS* 3.4 47.5 - - + +
236B PHE* 3.8 24.5 - + + -
268B ASP 3.4 6.2 + - - +
269B PHE 2.9 11.2 + - - +
271B SER* 1.3 75.8 - - - +
273B ILE* 1.3 70.1 + - + +
275B SER* 3.0 2.3 + - - -
276B ASN* 2.8 74.1 + - + +
277B SER* 5.7 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 273 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B VAL* 3.8 26.0 - - + -
58B LEU* 4.3 16.6 - - + -
85B HIS* 4.5 2.3 + - - -
93B LEU* 4.8 4.3 - - + -
125B THR* 3.9 16.2 - - + -
127B VAL* 4.0 11.4 - - + -
179B VAL* 4.3 9.4 - - + -
269B PHE* 3.8 41.5 - - + +
270B CYS 2.9 6.6 + - - +
272B TYR* 1.3 79.6 - - + +
274B PHE* 1.3 63.9 + - + +
275B SER 3.0 5.4 + - - -
277B SER* 3.0 48.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B LYS 4.5 3.6 - - - -
58B LEU* 3.5 46.4 - - + -
60B GLY* 5.6 1.6 - - - -
85B HIS* 3.2 28.4 - + + -
86B PRO* 3.9 33.7 - - + -
87B LYS* 3.4 28.9 + - + +
88B LYS* 5.0 5.0 - - - +
93B LEU* 3.7 23.1 - - + -
270B CYS* 2.9 30.7 + - + +
271B SER* 3.8 9.2 - - - +
273B ILE* 1.3 78.5 - - + +
275B SER* 1.3 57.3 + - - +
277B SER 5.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B LYS* 3.4 30.5 + - - +
88B LYS* 5.9 4.5 - - - +
271B SER* 2.7 25.9 + - - -
272B TYR* 3.0 3.6 + - - -
274B PHE* 1.3 80.9 - - - +
276B ASN* 1.3 71.6 + - - +
277B SER 3.9 0.9 - - - -
278B LYS* 6.0 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 276 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B ASP* 3.9 14.0 - - - +
232B LYS* 5.0 13.6 + - - +
272B TYR* 2.8 66.8 + - + +
275B SER* 1.3 88.8 - - - +
277B SER* 1.3 64.3 - - - +
278B LYS* 3.4 20.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 277 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B VAL* 3.4 21.7 - - - +
41B VAL* 4.6 0.4 - - - -
85B HIS* 4.8 0.9 + - - -
88B LYS* 3.8 17.1 - - - -
125B THR* 2.6 38.3 + - - +
177B ASP* 4.9 1.8 - - - -
272B TYR* 5.7 1.4 - - - -
273B ILE* 3.0 36.7 + - - +
276B ASN* 1.3 76.6 - - - +
278B LYS* 1.3 65.7 + - - +
----------------------------------------------------------
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