Contacts of the helix formed by residues 294 - 314 (chain D) 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 GLY 294 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C PHE* 5.6 7.0 - - - -
290D PRO 2.9 16.5 + - - -
291D PHE 3.2 4.2 + - - -
293D HIS* 1.3 77.3 - - - +
295D LEU* 1.3 59.9 + - - +
296D VAL 3.3 2.7 - - - -
297D VAL* 3.2 12.0 + - - +
298D ILE* 2.8 36.3 + - - +
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Residues in contact with LEU 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D LEU* 6.5 0.2 - - + -
176D VAL* 3.8 23.3 - - + -
203D THR* 4.0 13.0 - - + -
206D TYR* 3.9 25.8 - - + +
267D LEU* 5.8 0.9 - - + -
291D PHE* 3.3 40.5 + - + +
292D ILE* 3.9 24.0 - - + +
293D HIS 3.4 3.4 - - - -
294D GLY* 1.3 77.2 - - - +
296D VAL* 1.3 57.2 + - - +
298D ILE* 3.3 8.1 + - + +
299D VAL* 2.9 46.0 + - + +
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Residues in contact with VAL 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85D VAL* 4.3 10.3 - - + -
89D ALA* 4.0 20.9 - - + -
176D VAL* 3.7 27.6 - - + +
177D GLY* 3.8 32.5 - - - +
181D ALA* 4.2 15.3 - - + -
202D ALA* 3.8 26.7 - - + -
203D THR* 5.8 0.4 - - + +
293D HIS 5.3 0.6 + - - +
294D GLY 3.3 0.8 - - - -
295D LEU* 1.3 77.7 - - - +
297D VAL* 1.3 58.4 + - - +
299D VAL* 3.6 3.1 + - - +
300D ALA* 3.1 26.0 + - - +
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Residues in contact with VAL 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C LEU* 4.2 16.6 - - + -
74C VAL* 4.5 9.0 - - + -
85D VAL* 3.6 33.0 - - + +
88D VAL* 4.1 29.6 - - + -
89D ALA* 4.6 4.3 - - - +
294D GLY* 3.2 10.7 + - - +
296D VAL* 1.3 74.8 - - + +
298D ILE* 1.3 56.2 + - + +
300D ALA* 3.5 4.8 - - - -
301D LEU* 2.6 39.9 + - + +
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Residues in contact with ILE 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C PHE* 4.1 32.1 - - + -
267D LEU* 3.7 33.4 - - + -
278D LEU* 4.5 1.3 - - + -
291D PHE* 3.8 41.1 - - + +
294D GLY* 2.8 24.4 + - - +
295D LEU* 3.6 11.2 - - + +
297D VAL* 1.3 73.6 - - + +
299D VAL* 1.3 67.3 + - + +
301D LEU* 3.1 7.6 + - + +
302D ILE* 2.9 33.3 + - + +
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Residues in contact with VAL 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D LEU* 5.6 2.0 - - + -
131D LEU* 4.5 13.5 - - + -
175D LEU* 3.7 39.9 - - + -
176D VAL* 4.0 21.3 - - + +
295D LEU* 2.9 40.6 + - + +
296D VAL 3.7 4.7 - - - +
298D ILE* 1.3 73.0 - - + +
300D ALA* 1.3 58.1 + - + +
302D ILE* 3.9 6.6 - - - +
303D ALA* 3.0 30.0 + - + +
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Residues in contact with ALA 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89D ALA* 3.5 37.0 - - + +
92D GLY* 3.4 15.6 - - - -
93D LEU* 4.0 21.8 - - + -
296D VAL 3.1 19.1 + - - +
297D VAL 3.8 2.9 - - - +
299D VAL* 1.3 76.0 - - + +
301D LEU* 1.3 66.1 + - - +
303D ALA* 4.0 0.8 - - - +
304D GLY 3.1 16.5 + - - -
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Residues in contact with LEU 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C PHE* 5.3 16.2 - - + -
73C LEU* 6.3 4.0 - - + -
92D GLY* 5.2 2.2 - - - -
297D VAL* 2.6 29.5 + - + +
298D ILE* 3.1 7.4 + - - +
300D ALA* 1.3 73.8 - - - +
302D ILE* 1.3 60.5 + - + +
304D GLY* 3.4 1.3 + - - -
305D ILE* 3.0 58.5 + - + +
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Residues in contact with ILE 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260D LEU* 3.9 25.6 - - + -
263D LEU* 3.8 33.7 - - + -
264D LEU* 4.2 14.4 - - + -
267D LEU* 4.0 20.2 - - + -
298D ILE* 2.9 38.0 + - + +
299D VAL* 3.9 6.1 - - - +
301D LEU* 1.3 76.8 - - + +
303D ALA* 1.3 67.4 + - - +
304D GLY 3.2 0.3 + - - -
305D ILE* 3.2 2.5 + - + +
306D CYS* 3.0 30.5 + - - -
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Residues in contact with ALA 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D LEU* 3.9 26.9 - - + -
96D ALA* 3.5 18.7 - - + +
101D LEU* 4.5 2.4 - - - +
102D LEU* 5.5 4.9 - - + -
131D LEU* 6.3 0.9 - - + -
299D VAL* 3.0 20.6 + - + +
300D ALA 4.0 2.9 - - - +
302D ILE* 1.3 78.4 - - - +
304D GLY* 1.3 57.0 + - - +
306D CYS* 3.5 6.8 + - - +
307D GLY* 2.9 22.5 + - - -
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Residues in contact with GLY 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D GLY* 3.3 27.5 + - - -
95D VAL* 3.6 7.7 - - - +
96D ALA 4.4 2.5 - - - -
300D ALA 3.1 15.2 + - - -
301D LEU 3.8 0.9 - - - -
303D ALA* 1.3 75.5 - - - +
305D ILE* 1.3 59.4 - - - +
307D GLY* 3.1 1.8 + - - -
308D ALA* 2.8 28.9 + - - +
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Residues in contact with ILE 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259D THR* 5.5 4.3 - - - -
263D LEU* 3.9 37.9 - - + -
301D LEU* 3.0 45.4 + - + +
302D ILE* 3.8 3.6 - - + +
304D GLY* 1.3 75.1 - - - +
306D CYS* 1.3 62.8 + - - +
308D ALA* 3.4 7.9 + - + +
309D VAL* 3.2 29.4 + - + +
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Residues in contact with CYS 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D LEU* 3.8 9.4 - - + -
256D THR* 3.7 18.7 + - + -
259D THR* 4.3 8.1 - - - -
260D LEU* 4.0 40.4 - - - -
263D LEU* 4.1 5.4 - - - -
302D ILE* 3.0 32.5 + - - +
303D ALA* 3.7 6.1 - - - +
305D ILE* 1.3 75.9 - - - +
307D GLY* 1.3 58.2 + - - +
309D VAL* 3.3 2.9 + - - +
310D TYR* 2.9 30.7 + - - +
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Residues in contact with GLY 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D VAL* 4.0 5.8 - - - -
96D ALA* 4.2 8.7 - - - -
99D SER* 3.3 25.8 - - - -
101D LEU* 3.8 8.3 - - - +
303D ALA 2.9 16.1 + - - -
304D GLY 3.1 4.0 + - - -
306D CYS* 1.3 75.1 - - - +
308D ALA* 1.3 59.6 + - - +
310D TYR* 4.5 0.9 - - - -
311D GLY* 2.9 25.1 + - - -
317D PHE* 3.6 1.2 - - - -
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Residues in contact with ALA 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D VAL* 3.9 7.1 - - + +
304D GLY 2.8 12.5 + - - +
305D ILE* 3.4 14.6 - - + +
307D GLY* 1.3 77.0 - - - +
309D VAL* 1.3 63.4 + - + +
311D GLY* 3.9 0.3 - - - -
312D ARG* 3.0 33.5 + - + +
317D PHE* 4.2 6.0 - - - -
323D VAL* 4.7 17.0 - - + -
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Residues in contact with VAL 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252D ALA 4.7 0.2 - - - +
255D TRP* 3.7 32.1 - - + -
256D THR* 3.8 12.3 - - - +
259D THR* 3.7 28.3 - - + +
305D ILE* 3.3 17.9 - - + +
306D CYS 3.5 6.7 - - - +
308D ALA* 1.3 78.2 - - + +
310D TYR* 1.3 65.4 + - - +
312D ARG* 4.8 2.5 - - - -
313D VAL* 3.0 35.0 + - + +
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Residues in contact with TYR 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D SER* 3.6 25.6 - - - -
100D GLY* 4.3 2.0 - - - -
101D LEU* 3.9 34.5 - - + -
104D VAL* 3.4 29.4 - - + +
247D GLN 4.2 1.4 + - - -
249D HIS* 3.4 33.2 + - + +
252D ALA* 3.5 25.8 - - + +
253D MET* 3.9 17.7 - - + -
256D THR* 3.2 19.5 + - - +
306D CYS 2.9 16.8 + - - +
307D GLY 4.1 2.0 - - - +
309D VAL* 1.3 73.5 - - - +
311D GLY* 1.3 58.3 + - - +
314D SER* 2.8 43.4 + - - -
316D GLN* 5.5 0.7 - - + -
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Residues in contact with GLY 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D SER* 3.7 16.8 - - - -
307D GLY 2.9 17.7 + - - -
310D TYR* 1.3 76.4 - - - +
312D ARG* 1.3 58.5 + - - +
314D SER* 3.8 4.9 - - - -
315D GLY 3.2 2.3 + - - -
316D GLN* 2.8 17.7 + - - -
317D PHE* 2.7 36.5 + - - -
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Residues in contact with ARG 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308D ALA* 3.0 27.6 + - + +
309D VAL* 3.7 3.4 - - - +
311D GLY* 1.3 74.7 - - - +
313D VAL* 1.3 69.5 - - + +
315D GLY* 2.9 15.1 + - - -
317D PHE* 2.7 34.0 + - - -
318D ARG* 3.2 14.6 + - - +
319D ASN* 3.2 37.2 - - - +
320D SER* 3.8 10.0 + - - +
323D VAL* 4.2 10.8 - - + -
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Residues in contact with VAL 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D HIS* 3.9 4.0 + - - -
251D ARG* 3.8 29.3 + - + +
252D ALA* 3.6 32.1 - - - +
255D TRP* 3.8 28.3 - - + +
309D VAL* 3.0 28.0 + - + +
312D ARG* 1.3 81.9 - - + +
314D SER* 1.3 60.3 + - - +
315D GLY* 3.5 0.7 + - - -
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Residues in contact with SER 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D HIS* 3.5 44.9 + - - -
252D ALA* 3.5 7.0 - - - -
310D TYR* 2.8 35.1 + - - -
311D GLY* 3.8 3.1 + - - -
313D VAL* 1.3 78.0 - - - +
315D GLY* 1.3 59.3 + - - +
316D GLN* 3.6 15.1 + - - +
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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