Contacts of the helix formed by residues 306 - 318 (chain P) in PDB entry 3HX0
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 306 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300P CYS* 4.9 4.3 - - - -
305P ILE* 1.3 74.3 - - - +
307P LYS* 1.3 67.7 + - - -
308P ARG 3.3 2.2 - - - -
309P MET 3.2 1.2 + - - -
310P ALA* 2.8 26.5 + - - +
2S C 2.8 22.3 + - - -
3S C 4.4 9.4 - - - -
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Residues in contact with LYS 307 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296P TYR* 3.6 26.1 + - + +
300P CYS* 4.9 6.7 - - - -
306P GLY* 1.3 68.4 - - - +
308P ARG* 1.3 59.6 + - + +
310P ALA* 3.8 1.5 - - - +
311P GLU* 2.8 38.2 + - - +
2S C 5.1 0.4 + - - -
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Residues in contact with ARG 308 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306P GLY 3.3 1.0 + - - -
307P LYS* 1.3 78.8 - - + +
309P MET* 1.3 63.3 + - - +
311P GLU* 3.1 37.2 + - - +
312P LYS* 3.4 26.6 + - - +
1S G 2.6 54.3 + - - -
2S C 3.7 17.6 + - - +
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Residues in contact with MET 309 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260P LEU* 4.5 20.2 - - + -
278P GLY 4.4 1.3 - - - +
279P TYR* 3.7 59.2 - - + +
282P ALA* 3.9 24.2 - - + -
286P LEU* 6.3 0.4 - - + -
305P ILE* 3.8 12.8 - - + -
306P GLY 3.8 2.0 - - - +
308P ARG* 1.3 71.8 - - - +
310P ALA* 1.3 68.4 + - - +
311P GLU 3.0 0.9 + - - -
312P LYS* 3.0 20.7 + - - +
313P ILE* 3.1 20.8 + - + +
1S G 3.8 20.4 + - + +
2S C 3.0 24.5 + - - +
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Residues in contact with ALA 310 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296P TYR* 4.0 8.5 - - + +
299P ALA* 3.4 21.9 - - + +
300P CYS* 3.9 21.3 - - - -
305P ILE* 3.6 5.7 - - + +
306P GLY 2.8 20.1 + - - +
307P LYS 3.8 2.2 - - - +
309P MET* 1.3 72.7 - - - +
311P GLU* 1.3 64.2 + - - +
313P ILE* 3.2 28.8 + - - +
314P ILE* 3.3 13.2 + - - +
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Residues in contact with GLU 311 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296P TYR* 3.5 23.3 + - + -
307P LYS* 2.8 24.7 + - - +
308P ARG* 3.1 30.6 + - - +
310P ALA* 1.3 77.0 - - - +
312P LYS* 1.3 63.7 + - + +
314P ILE* 3.2 14.0 + - - +
315P GLU* 3.2 11.9 + - - +
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Residues in contact with LYS 312 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260P LEU* 4.9 12.3 - - + -
263P LEU* 4.4 13.2 - - + -
279P TYR* 3.6 20.0 - - + +
308P ARG* 3.6 34.2 + - - +
309P MET* 3.0 11.6 + - - +
311P GLU* 1.3 75.2 - - + +
313P ILE* 1.3 66.2 + - - +
315P GLU* 3.0 19.7 + - - +
316P ILE* 3.2 19.9 - - - +
322P LEU* 3.9 23.3 - - + +
324P LYS* 5.1 8.1 - - - -
1S G 2.5 34.4 + - - -
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Residues in contact with ILE 313 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256P ILE* 4.1 27.0 - - + +
260P LEU* 5.0 6.9 - - + +
286P LEU* 4.5 14.1 - - + -
293P VAL* 4.0 24.7 - - + -
299P ALA* 3.8 17.9 - - + -
305P ILE* 4.0 21.1 - - + -
309P MET* 3.1 18.7 + - + +
310P ALA* 3.2 23.8 - - - +
311P GLU 3.2 0.4 - - - -
312P LYS* 1.3 78.5 - - + +
314P ILE* 1.3 61.6 + - + +
316P ILE* 3.6 6.1 + - - +
317P LEU* 3.0 32.7 + - + +
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Residues in contact with ILE 314 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294P THR 4.0 5.2 - - - +
295P SER* 3.6 5.8 - - - -
296P TYR* 3.1 53.4 - - + +
299P ALA* 5.8 0.9 - - + -
310P ALA 3.6 9.0 - - - +
311P GLU 3.2 7.5 + - - +
312P LYS 3.1 0.4 - - - -
313P ILE* 1.3 77.6 - - + +
315P GLU* 1.3 52.9 + - - +
316P ILE 2.7 16.5 + - - -
317P LEU* 3.0 33.6 + - + +
318P GLU* 3.4 35.7 + - - +
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Residues in contact with GLU 315 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311P GLU 3.2 9.3 + - - +
312P LYS* 3.0 11.8 + - - +
314P ILE* 1.3 76.3 - - - +
316P ILE* 1.3 56.4 + - - +
318P GLU* 4.8 4.9 - - - -
319P SER* 2.4 34.5 + - - +
321P HIS* 2.9 9.4 - - - +
322P LEU* 3.0 33.3 - - - +
323P ARG* 3.6 28.0 + - - +
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Residues in contact with ILE 316 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255P HIS* 4.0 26.3 - - + +
256P ILE* 4.5 22.9 - - + +
259P LYS* 4.2 14.4 - - + -
260P LEU* 4.8 4.5 - - + -
312P LYS 3.2 19.3 - - - +
313P ILE 3.7 5.8 - - - +
314P ILE 2.8 0.6 - - - -
315P GLU* 1.3 78.8 - - - +
317P LEU* 1.3 59.9 + - + +
318P GLU 3.0 5.6 + - - -
320P GLY* 2.9 36.8 + - - +
321P HIS 3.0 20.2 - - - +
322P LEU* 3.9 28.3 - - + -
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Residues in contact with LEU 317 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255P HIS* 3.5 22.0 - - + +
256P ILE* 3.5 28.7 - - + -
293P VAL 3.2 30.7 - - - +
294P THR* 3.8 9.6 - - - +
313P ILE* 3.0 23.8 - - + +
314P ILE* 3.0 30.1 + - + +
316P ILE* 1.3 77.5 - - - +
318P GLU* 1.3 58.0 + - + +
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Residues in contact with GLU 318 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314P ILE* 3.4 35.6 - - - +
315P GLU* 4.8 2.9 - - - -
316P ILE 3.0 0.2 - - - -
317P LEU* 1.3 81.4 - - + +
319P SER* 1.3 65.1 + - - +
320P GLY 3.7 0.7 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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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