Contacts of the helix formed by residues 294 - 314 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A PHE 5.4 7.0 - - - -
290B PRO 3.1 18.5 + - - -
291B PHE 3.6 2.7 - - - -
293B HIS* 1.3 75.5 - - - +
295B LEU* 1.3 63.0 + - - +
296B VAL 3.3 1.8 - - - -
297B VAL* 3.2 12.2 + - - +
298B ILE* 3.0 27.7 + - - +
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Residues in contact with LEU 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B LEU* 5.9 1.8 - - + -
176B VAL* 3.5 26.2 - - + -
202B ALA* 6.3 0.2 - - + -
203B THR* 4.3 9.4 - - + -
206B TYR* 4.2 23.1 - - + +
267B LEU* 6.1 0.2 - - + -
291B PHE* 3.2 47.1 + - + +
292B ILE* 3.6 17.3 - - + +
293B HIS 3.0 4.2 + - - -
294B GLY* 1.3 77.6 - - - +
296B VAL* 1.3 58.0 + - - +
298B ILE* 3.0 13.4 + - + -
299B VAL* 2.9 37.7 + - + +
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Residues in contact with VAL 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B VAL* 4.4 11.7 - - + -
89B ALA* 4.0 18.1 - - + +
176B VAL* 3.8 17.3 - - + +
177B GLY* 3.8 45.8 - - - +
178B PRO 4.2 0.2 - - - -
181B ALA* 4.2 12.8 - - + -
202B ALA* 3.7 29.8 - - + +
293B HIS 4.4 2.7 + - - +
294B GLY 3.3 0.6 - - - -
295B LEU* 1.3 76.1 - - - +
297B VAL* 1.3 61.0 + - - +
299B VAL* 3.8 2.8 + - - +
300B ALA* 3.2 21.8 + - - +
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Residues in contact with VAL 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LEU* 3.8 29.2 - - + -
74A VAL* 4.0 18.2 - - + -
85B VAL* 3.9 29.8 - - + +
88B VAL* 4.3 13.7 - - + +
89B ALA 4.8 2.5 - - - +
294B GLY* 3.2 11.3 + - - +
296B VAL* 1.3 75.2 - - - +
298B ILE* 1.3 59.0 + - + +
300B ALA* 3.1 5.9 + - + -
301B LEU* 2.7 41.6 + - + +
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Residues in contact with ILE 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A PHE* 4.3 30.3 - - + -
267B LEU* 3.8 41.5 - - + -
278B LEU* 4.5 9.2 - - + -
290B PRO 4.8 0.9 - - - +
291B PHE* 4.3 26.2 - - + +
294B GLY* 3.0 19.0 + - - +
295B LEU* 3.0 16.8 + - + +
297B VAL* 1.3 75.0 - - + +
299B VAL* 1.3 67.9 + - + +
301B LEU* 3.6 6.5 + - + +
302B ILE* 3.2 29.5 + - + +
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Residues in contact with VAL 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B LEU* 4.6 8.3 - - + -
131B LEU* 4.5 13.9 - - + -
175B LEU* 4.1 38.1 - - + -
176B VAL* 4.0 22.4 - - + +
177B GLY* 5.8 0.7 - - - -
295B LEU* 2.9 27.7 + - + +
296B VAL 4.0 4.9 - - - +
298B ILE* 1.3 77.2 - - + +
300B ALA* 1.3 62.2 + - + +
302B ILE* 3.1 13.1 + - + +
303B ALA* 2.9 27.0 + - + +
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Residues in contact with ALA 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B VAL 5.1 0.4 - - - +
89B ALA* 3.2 39.3 - - + +
92B GLY* 3.4 13.5 - - - -
93B LEU* 3.5 17.5 - - + -
178B PRO* 6.2 0.2 - - + -
296B VAL 3.2 15.7 + - - +
297B VAL* 3.1 6.1 + - + +
299B VAL* 1.3 77.0 - - - +
301B LEU* 1.3 60.3 + - - +
303B ALA* 3.4 1.2 + - - +
304B GLY 2.9 24.3 + - - -
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Residues in contact with LEU 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A PHE* 5.2 16.4 - - + -
73A LEU* 5.8 7.2 - - + -
92B GLY* 5.3 1.8 - - - -
297B VAL* 2.7 29.6 + - + +
298B ILE* 3.9 6.5 - - + +
300B ALA* 1.3 71.8 - - - +
302B ILE* 1.3 62.0 + - + +
304B GLY* 3.4 1.4 + - - -
305B ILE* 3.0 55.3 + - + +
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Residues in contact with ILE 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B LEU* 4.2 22.9 - - + -
263B LEU* 4.3 22.6 - - + +
264B LEU* 3.8 26.5 - - + -
267B LEU* 4.3 8.7 - - + -
298B ILE* 3.2 28.9 + - + +
299B VAL* 3.1 13.7 + - + +
301B LEU* 1.3 74.8 - - + +
303B ALA* 1.3 67.2 + - - +
304B GLY 3.0 0.5 + - - -
305B ILE* 3.2 3.5 + - - +
306B CYS* 2.9 30.7 + - - +
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Residues in contact with ALA 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B LEU* 3.6 31.2 - - + -
96B ALA* 3.6 24.3 - - + +
101B LEU* 4.7 2.3 - - - +
102B LEU* 5.6 6.3 - - + -
131B LEU* 6.2 2.5 - - + -
299B VAL* 2.9 15.9 + - + +
300B ALA 3.7 0.2 - - - +
302B ILE* 1.3 75.5 - - - +
304B GLY* 1.3 57.1 + - - +
306B CYS* 3.6 5.8 + - - +
307B GLY 2.9 21.5 + - - -
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Residues in contact with GLY 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B GLY* 3.5 23.3 - - - -
95B VAL* 3.8 11.5 - - - +
300B ALA 2.9 14.8 + - - -
301B LEU* 3.8 1.6 - - - -
303B ALA* 1.3 74.7 - - - +
305B ILE* 1.3 59.0 + - - +
306B CYS 3.1 1.3 - - - -
307B GLY* 3.2 0.6 + - - -
308B ALA* 2.9 29.8 + - - +
323B VAL* 5.7 0.2 - - - +
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Residues in contact with ILE 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B THR* 4.9 4.7 + - - -
263B LEU* 3.7 37.7 - - + -
301B LEU* 3.0 43.4 + - + +
304B GLY* 1.3 74.5 - - - +
306B CYS* 1.3 59.5 + - - +
308B ALA* 3.8 7.3 - - + +
309B VAL* 3.2 29.4 + - + +
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Residues in contact with CYS 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B LEU* 3.9 15.7 - - + -
256B THR* 4.0 8.2 + - + -
259B THR* 3.8 11.9 - - - -
260B LEU* 3.8 41.3 - - - -
263B LEU* 4.7 5.2 - - - -
302B ILE* 2.9 23.2 + - - +
303B ALA* 3.8 6.5 - - - +
305B ILE* 1.3 77.8 - - - +
307B GLY* 1.3 60.1 + - - +
308B ALA 3.2 0.7 - - - -
309B VAL* 3.3 9.0 + - - +
310B TYR* 2.9 30.1 + - - +
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Residues in contact with GLY 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B VAL* 4.1 5.2 - - - -
96B ALA* 4.2 9.4 - - - -
99B SER* 3.2 28.9 - - - -
101B LEU* 4.1 6.0 - - - +
303B ALA 2.9 18.9 + - - -
304B GLY 3.2 2.6 + - - -
306B CYS* 1.3 75.9 - - - +
308B ALA* 1.3 63.1 + - - +
310B TYR* 4.4 0.2 - - - -
311B GLY 3.0 19.9 + - - -
317B PHE* 3.7 2.1 - - - -
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Residues in contact with ALA 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B VAL* 4.0 2.3 - - - +
304B GLY 2.9 17.2 + - - +
305B ILE* 3.8 10.5 - - + +
307B GLY* 1.3 78.3 - - - +
309B VAL* 1.3 61.2 + - + +
311B GLY* 4.1 0.2 - - - -
312B ARG* 2.9 38.8 + - + +
317B PHE* 4.2 10.2 - - - -
323B VAL* 4.6 17.9 - - + -
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Residues in contact with VAL 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B TRP* 4.3 4.5 - - + +
256B THR* 3.5 31.2 - - - +
259B THR* 3.6 28.7 - - + +
305B ILE* 3.2 19.3 - - + +
306B CYS 3.3 10.2 + - - +
308B ALA* 1.3 75.2 - - + +
310B TYR* 1.3 72.6 + - - +
312B ARG* 4.4 4.7 - - - -
313B VAL* 3.1 29.4 + - + +
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Residues in contact with TYR 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B SER* 3.3 30.3 - - - +
100B GLY* 4.2 3.1 - - - -
101B LEU* 3.8 27.8 - - + -
104B VAL* 3.5 30.6 - - + +
249B HIS* 4.4 7.4 - - + +
252B ALA* 3.8 17.3 - - + -
253B MET* 3.8 35.0 - - + +
256B THR* 3.3 21.5 - - - +
306B CYS 2.9 15.3 + - - +
307B GLY 3.8 3.1 - - - +
309B VAL* 1.3 81.2 - - - +
311B GLY* 1.3 50.7 + - - +
313B VAL* 3.5 1.4 - - - +
314B SER* 2.5 52.6 + - - -
316B GLN* 5.9 0.2 - - + -
53C GLU* 4.1 12.6 + - - +
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Residues in contact with GLY 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B SER* 4.1 5.8 - - - -
307B GLY 3.0 13.8 + - - -
310B TYR* 1.3 81.4 - - - +
312B ARG* 1.3 55.3 + - - +
314B SER* 3.9 7.2 - - - -
315B GLY 2.9 6.4 + - - -
316B GLN* 2.8 26.1 + - - -
317B PHE* 2.8 33.3 + - - -
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Residues in contact with ARG 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B ALA* 2.9 29.7 + - + +
309B VAL* 4.0 5.4 - - - +
311B GLY* 1.3 76.6 - - - +
313B VAL* 1.3 66.7 + - + +
315B GLY* 3.5 6.9 + - - -
317B PHE* 2.7 44.4 + - + +
318B ARG* 3.9 4.6 + - - +
319B ASN* 3.8 34.3 - - - +
320B SER* 4.1 10.7 + - - +
323B VAL* 4.4 9.9 - - + -
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Residues in contact with VAL 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B HIS* 5.2 1.2 + - - -
251B ARG* 4.5 24.4 + - + +
252B ALA* 3.0 39.0 - - + +
255B TRP* 3.8 29.8 - - + +
309B VAL* 3.1 19.3 + - + +
312B ARG* 1.3 77.8 - - + +
314B SER* 1.3 57.6 + - - +
315B GLY* 2.9 10.9 + - - -
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Residues in contact with SER 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B HIS* 3.5 42.6 + - - -
252B ALA* 4.0 11.2 - - - -
310B TYR* 2.5 46.8 + - - -
311B GLY* 3.9 2.2 - - - -
313B VAL* 1.3 72.3 - - - +
315B GLY* 1.3 56.2 + - - +
316B GLN* 3.2 20.8 + - - +
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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