Contacts of the helix formed by residues 249 - 272 (chain A) in PDB entry 4R0C
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 HIS 249 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A GLN 3.5 1.2 + - - +
248A ILE* 1.3 71.6 - - - +
250A SER* 1.3 64.9 + - - +
251A ARG* 3.4 43.1 + - + -
252A ALA* 3.1 23.4 + - + +
253A MET* 3.0 21.5 + - - +
310A TYR* 3.1 18.7 + - - +
313A VAL 4.0 4.9 - - - -
314A SER* 3.3 31.3 - - - -
805A LMT 3.5 19.4 + - - -
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Residues in contact with SER 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A ILE* 3.4 14.9 + - - +
249A HIS* 1.3 73.2 + - - +
251A ARG* 1.3 63.8 + - - +
253A MET* 3.3 3.5 + - - +
254A LYS* 3.0 36.0 + - - +
802A LMT 4.4 16.2 - - - +
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Residues in contact with ARG 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A HIS* 3.4 20.4 + - + -
250A SER* 1.3 76.6 - - - +
252A ALA* 1.3 65.2 + - - +
254A LYS* 3.1 31.5 + - + +
255A TRP* 3.3 28.3 + - + +
313A VAL* 4.2 8.3 - - + +
805A LMT 3.2 82.8 + - - -
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Residues in contact with ALA 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A HIS* 3.1 25.7 + - + +
251A ARG* 1.3 80.3 - - - +
253A MET* 1.3 57.4 + - - +
255A TRP* 3.3 3.8 + - - +
256A THR* 3.0 28.6 + - - -
309A VAL* 4.8 0.3 - - - +
310A TYR* 3.5 36.5 - - + +
313A VAL* 3.4 24.1 - - + +
314A SER* 3.9 1.8 - - - +
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Residues in contact with MET 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LEU* 3.6 22.9 - - + -
104A VAL* 3.9 15.0 - - + -
105A SER* 3.3 26.9 - - - +
248A ILE* 3.5 26.9 - - + -
249A HIS 3.0 8.2 + - - +
250A SER* 3.7 7.2 - - - +
251A ARG 3.3 0.2 - - - -
252A ALA* 1.3 73.6 - - - +
254A LYS* 1.3 67.3 + - - +
256A THR* 3.8 4.6 - - - -
257A GLY* 2.9 21.7 + - - -
310A TYR* 3.8 8.7 - - + -
802A LMT 3.6 37.5 - - + +
803A BOG 4.1 25.7 - - + +
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Residues in contact with LYS 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A SER* 3.0 21.9 + - - -
251A ARG* 3.1 30.1 + - - +
253A MET* 1.3 76.8 - - - +
255A TRP* 1.3 66.5 + - + +
257A GLY* 3.6 1.6 + - - -
258A LEU* 3.2 18.5 + - - +
803A BOG 5.6 4.0 - - - +
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Residues in contact with TRP 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A ARG* 3.3 35.5 + - + +
252A ALA 3.7 5.8 - - - +
253A MET 3.2 0.2 - - - -
254A LYS* 1.3 78.8 - - + +
256A THR* 1.3 54.9 + - - +
258A LEU* 2.9 40.1 + - + +
259A THR* 2.6 35.7 + - - -
309A VAL* 4.2 11.2 - - + -
313A VAL* 4.6 9.0 - - + -
805A LMT 3.4 65.9 + - + +
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Residues in contact with THR 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LEU* 3.8 33.7 - - + -
252A ALA 3.0 17.5 + - - -
253A MET* 3.3 9.4 + - - -
255A TRP* 1.3 75.5 - - - +
257A GLY* 1.3 52.3 + - - +
259A THR* 3.0 3.9 + - - -
260A LEU* 2.6 33.4 + - - +
306A CYS* 3.8 17.0 - - + +
309A VAL* 3.3 15.9 - - - +
310A TYR* 3.3 23.1 - - - +
803A BOG 4.3 10.5 - - + -
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Residues in contact with GLY 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A MET 2.9 15.5 + - - -
254A LYS 4.0 1.3 - - - -
256A THR* 1.3 76.1 - - - +
258A LEU* 1.3 61.8 + - - +
260A LEU* 3.2 8.6 + - - +
261A ALA* 3.1 24.1 + - - +
803A BOG 4.0 26.4 + - - -
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Residues in contact with LEU 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A LYS 3.2 13.2 + - - +
255A TRP* 2.9 43.4 + - + +
257A GLY* 1.3 74.6 - - - +
259A THR* 1.3 63.0 + - - +
261A ALA* 3.3 8.2 + - + +
262A ILE* 3.1 49.9 + - + +
805A LMT 6.3 2.2 - - + -
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Residues in contact with THR 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A TRP 2.6 17.0 + - - -
256A THR* 3.3 11.7 - - - -
258A LEU* 1.3 74.9 - - - +
260A LEU* 1.3 63.2 + - - +
261A ALA 3.2 0.2 + - - -
262A ILE* 3.4 7.6 + - - +
263A LEU* 3.1 36.8 + - + +
305A ILE* 4.1 14.4 - - + -
306A CYS* 3.7 19.7 - - - -
309A VAL* 3.5 24.5 - - + +
805A LMT 3.5 25.6 - - + +
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Residues in contact with LEU 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A THR 2.6 18.7 + - - +
257A GLY* 3.2 9.2 + - - +
259A THR* 1.3 72.2 - - - +
261A ALA* 1.3 57.6 + - - +
263A LEU* 3.7 2.6 + - - +
264A LEU* 3.0 45.9 + - + +
302A ILE* 4.0 25.1 - - + -
306A CYS* 3.9 14.4 - - - -
803A BOG 4.2 42.8 - - + +
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Residues in contact with ALA 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A GLY 3.1 15.7 + - - +
258A LEU* 3.7 10.5 - - + +
259A THR 3.1 0.2 - - - -
260A LEU* 1.3 76.6 - - - +
262A ILE* 1.3 62.2 + - + +
264A LEU* 3.5 4.6 + - - +
265A ALA* 2.9 29.6 + - - +
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Residues in contact with ILE 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A LEU* 3.1 40.4 + - + +
259A THR* 3.9 6.7 - - - +
261A ALA* 1.3 74.3 - - + +
263A LEU* 1.3 61.1 + - + +
265A ALA* 3.1 6.6 + - + +
266A GLY* 2.8 28.6 + - - -
805A LMT 4.6 26.2 - - + -
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Residues in contact with LEU 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A THR* 3.1 27.6 + - + +
260A LEU 3.9 3.6 - - - +
262A ILE* 1.3 79.9 - - + +
264A LEU* 1.3 58.2 + - - +
266A GLY* 3.5 1.8 + - - +
267A LEU* 2.9 27.5 + - - +
302A ILE* 4.1 38.1 - - + +
305A ILE* 3.7 48.0 - - + -
306A CYS* 4.1 4.9 - - - -
805A LMT 4.7 12.8 - - + -
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Residues in contact with LEU 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A LEU* 3.0 42.0 + - + +
261A ALA* 3.5 5.1 + - - +
263A LEU* 1.3 74.1 - - + +
265A ALA* 1.3 66.4 + - - +
266A GLY 3.1 0.2 - - - -
267A LEU* 3.2 9.7 + - + +
268A ALA* 3.1 23.7 + - - +
302A ILE* 4.2 22.2 - - + -
804A LMT 4.4 17.9 - - + -
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Residues in contact with ALA 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A ALA 2.9 19.1 + - - +
262A ILE* 3.1 6.9 + - + +
264A LEU* 1.3 75.9 - - - +
266A GLY* 1.3 61.5 + - - +
268A ALA* 3.5 7.1 + - - +
269A LEU* 3.4 26.9 + - + +
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Residues in contact with GLY 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A ILE 2.8 14.6 + - - -
263A LEU* 3.8 2.0 - - - -
265A ALA* 1.3 74.2 - - - +
267A LEU* 1.3 65.6 + - - +
268A ALA 3.1 1.3 - - - -
269A LEU* 3.0 22.6 + - - +
270A LEU* 3.2 18.2 + - - +
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Residues in contact with LEU 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A LEU 2.9 17.9 + - - +
264A LEU* 3.2 12.3 + - + +
266A GLY* 1.3 74.8 - - - +
268A ALA* 1.3 60.6 - - - +
270A LEU* 3.2 30.2 + - + +
271A VAL* 3.1 21.9 + - + +
278A LEU* 4.8 1.1 - - + -
291A PHE* 4.1 20.6 - - + -
298A ILE* 3.7 38.1 - - + -
302A ILE* 4.0 13.0 - - + -
804A LMT 4.0 26.0 - - + -
70B PHE* 5.4 2.5 - - + -
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Residues in contact with ALA 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A LEU 3.1 11.2 + - - +
265A ALA* 3.6 11.9 - - - +
266A GLY 3.1 0.4 - - - -
267A LEU* 1.3 78.2 - - - +
269A LEU* 1.3 57.9 + - + +
271A VAL* 4.0 7.4 - - - -
272A LEU* 2.8 48.7 + - + +
273A PRO* 3.1 7.4 - - - +
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Residues in contact with LEU 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A ALA* 3.4 15.0 + - + +
266A GLY* 3.0 14.5 + - - +
268A ALA* 1.3 78.1 - - + +
270A LEU* 1.3 62.0 + - + +
271A VAL 3.3 0.2 - - - -
273A PRO* 3.6 26.7 - - + +
276A ALA* 3.9 3.3 - - - +
277A PRO* 4.2 6.4 - - - +
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Residues in contact with LEU 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A GLY 3.2 14.2 + - - +
267A LEU* 3.3 21.8 - - + +
268A ALA 3.1 0.6 - - - -
269A LEU* 1.3 80.5 - - + +
271A VAL* 1.3 56.1 + - - +
276A ALA* 3.2 6.8 - - - +
277A PRO* 3.6 23.5 - - + -
278A LEU* 2.8 50.9 + - + +
66B LEU* 3.6 24.5 - - + -
70B PHE* 3.6 31.0 - - + -
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Residues in contact with VAL 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A LEU* 3.1 21.8 - - + +
268A ALA* 3.2 5.8 + - - +
269A LEU 3.3 0.6 - - - -
270A LEU* 1.3 80.0 - - + +
272A LEU* 1.3 83.1 + - + +
276A ALA* 3.6 4.0 - - - -
278A LEU* 4.8 5.6 - - + -
279A ARG* 3.1 28.1 + - - +
286A VAL* 4.0 20.9 - - + -
291A PHE* 3.8 54.1 - - + -
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Residues in contact with LEU 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A ALA* 2.8 36.0 + - + +
271A VAL* 1.3 83.3 - - + +
273A PRO* 1.4 56.4 - - + +
274A ASN* 3.7 1.4 + - - +
279A ARG* 2.3 27.2 + - - +
286A VAL* 5.8 4.3 - - + -
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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) + - + + + + + -
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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