Contacts of the helix formed by residues 303 - 317 (chain B) in PDB entry 5Y7G
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 ARG 303 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317A ALA* 5.3 1.6 - - - -
276B ASP* 2.9 36.9 + - - +
279B GLN* 4.2 15.6 + - - +
298B LEU* 3.0 39.0 + - + +
301B GLY* 3.4 13.9 - - - +
302B GLU* 1.3 74.3 - - - +
304B PHE* 1.3 64.3 + - - +
305B ALA 3.6 1.3 - - - -
306B GLU* 2.9 42.8 + - - +
307B ALA* 3.2 22.2 + - - +
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Residues in contact with PHE 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A CYS* 4.7 13.5 - - + -
317A ALA* 4.4 14.1 - - + +
299B GLU* 3.4 30.3 - - + -
302B GLU* 3.2 44.4 + - + -
303B ARG* 1.3 71.7 - - - +
305B ALA* 1.3 59.6 + - - +
307B ALA* 2.9 4.1 + - - +
308B HIS* 2.7 35.7 + - - +
334B LEU* 3.7 22.1 - - + +
337B LYS* 4.7 25.8 - - + -
338B LEU* 3.8 20.4 - - + -
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Residues in contact with ALA 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A ARG* 5.4 5.2 - - - +
313A GLU* 3.2 42.0 - - + +
303B ARG 3.6 0.2 - - - -
304B PHE* 1.3 76.0 - - - +
306B GLU* 1.3 62.5 + - + +
308B HIS* 3.7 4.9 + - - +
309B ALA* 2.8 28.0 + - - +
338B LEU* 3.9 16.3 - - + +
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Residues in contact with GLU 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B ARG* 6.3 0.4 - - - +
298B LEU* 4.1 14.5 - - + +
303B ARG* 2.9 52.2 + - - +
304B PHE 3.2 0.4 - - - -
305B ALA* 1.3 78.7 - - + +
307B ALA* 1.3 56.0 + - - +
309B ALA* 2.9 9.0 + - + +
310B LEU* 2.7 36.0 + - - +
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Residues in contact with ALA 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B ILE* 3.5 29.5 - - - +
298B LEU* 3.8 12.4 - - + +
299B GLU 3.7 9.4 - - - +
303B ARG 3.2 20.7 + - - +
304B PHE* 2.9 4.6 + - - +
306B GLU* 1.3 76.2 - - - +
308B HIS* 1.3 59.6 + - - +
310B LEU* 3.4 1.1 + - - +
311B ALA* 2.9 27.7 + - - +
334B LEU* 3.4 19.7 - - + -
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Residues in contact with HIS 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B PHE 2.7 19.5 + - - +
305B ALA 3.7 3.6 + - - +
307B ALA* 1.3 70.4 - - - +
309B ALA* 1.3 69.6 + - - +
311B ALA* 3.2 1.4 + - - +
312B ARG* 3.0 49.9 + - + +
331B LEU* 4.1 12.1 - - + -
334B LEU* 3.3 20.9 - - + +
335B GLN* 3.9 32.8 + - + +
338B LEU* 3.8 23.0 - - + +
340B LEU* 4.2 19.8 - - + +
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Residues in contact with ALA 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B ALA 2.8 22.4 + - - +
306B GLU* 2.9 10.7 + - + +
308B HIS* 1.3 78.2 - - - +
310B LEU* 1.3 61.4 + - - +
312B ARG* 3.6 7.0 + - - +
313B GLU* 3.3 19.2 + - - +
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Residues in contact with LEU 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B ARG* 3.8 39.0 - - - +
291B ARG* 4.1 13.9 - - + +
294B ALA* 3.7 28.7 - - + -
295B ILE* 3.5 28.5 - - + +
298B LEU* 4.2 5.4 - - + -
306B GLU 2.7 18.7 + - - +
307B ALA* 3.8 1.6 - - - +
309B ALA* 1.3 70.1 - - - +
311B ALA* 1.3 61.2 + - - +
313B GLU* 3.0 33.1 + - - +
314B ALA* 2.8 27.9 + - - +
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Residues in contact with ALA 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B ILE* 3.5 20.8 - - + +
307B ALA 2.9 18.5 + - - +
308B HIS* 3.2 7.2 + - - +
310B LEU* 1.3 76.5 - - - +
312B ARG* 1.3 60.9 + - - +
314B ALA* 3.4 3.1 + - - +
315B SER 3.0 17.3 + - - -
327B LEU* 3.6 16.5 - - + +
330B LEU* 5.1 0.4 - - + -
331B LEU* 3.4 32.1 - - + +
334B LEU* 4.2 4.7 - - + -
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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
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308B HIS* 3.0 38.4 + - + +
309B ALA* 3.7 11.2 - - - +
310B LEU 3.2 0.2 - - - -
311B ALA* 1.3 73.5 - - - +
313B GLU* 1.3 65.9 + - - +
315B SER* 3.0 30.2 + - - +
316B CYS* 3.2 14.0 + - - -
331B LEU* 4.3 8.1 - - - +
335B GLN* 5.1 11.4 - - - +
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Residues in contact with GLU 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283B ARG* 4.9 6.2 + - - -
291B ARG* 3.7 23.6 + - - +
309B ALA 3.3 10.2 + - - +
310B LEU* 3.0 31.7 + - + +
312B ARG* 1.3 77.9 - - - +
314B ALA* 1.3 61.0 + - - +
316B CYS* 3.2 21.4 + - - +
317B ALA* 3.7 4.3 + - - +
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Residues in contact with ALA 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B ARG* 3.5 34.5 - - - +
295B ILE* 4.1 5.4 - - + -
310B LEU 2.8 12.0 + - - +
311B ALA 3.6 5.4 - - - +
312B ARG 3.2 0.2 - - - -
313B GLU* 1.3 77.6 - - - +
315B SER* 1.3 62.0 + - - +
316B CYS 3.3 0.5 + - - -
317B ALA 3.5 0.3 + - - -
318B PRO* 3.3 28.9 - - - +
323B GLU* 3.9 2.9 - - - +
327B LEU* 3.4 26.9 - - + -
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Residues in contact with SER 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B ALA 3.0 11.8 + - - -
312B ARG* 3.0 27.1 + - - +
314B ALA* 1.3 76.5 - - - +
316B CYS* 1.4 61.3 + - - +
318B PRO* 4.1 11.2 - - - +
327B LEU* 3.8 7.4 - - - +
331B LEU* 4.2 16.8 - - - +
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Residues in contact with CYS 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B ARG* 3.2 18.8 + - - -
313B GLU* 3.6 11.4 - - - +
314B ALA 3.2 1.0 - - - -
315B SER* 1.4 79.3 + - - +
317B ALA* 1.3 61.8 + - + +
318B PRO* 3.9 4.1 - - - +
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Residues in contact with ALA 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B ARG* 3.0 24.7 + - - +
313B GLU 3.7 4.8 + - - +
314B ALA 3.5 3.0 + - - -
316B CYS* 1.3 82.5 - - + +
318B PRO* 1.3 66.8 - - - +
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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
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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