Contacts of the helix formed by residues 315 - 324 (chain G) in PDB entry 4HY0
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 ASP 315 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258B ARG* 4.0 24.7 - - - +
283G GLN* 3.8 12.4 - - - +
310G TRP* 4.7 0.2 - - - -
313G SER 4.0 0.8 + - - -
314G GLU* 1.3 72.3 - - - +
316G PRO* 1.3 75.0 - - - +
317G TRP* 3.5 27.4 + - - +
318G GLU* 3.8 21.4 + - + +
319G GLN* 3.2 25.0 + - - +
338G TYR* 4.3 5.0 + - - -
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Residues in contact with PRO 316 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279G VAL* 5.5 3.4 - - + -
280G ASN 4.8 0.7 - - - +
283G GLN* 3.7 34.5 - - + +
284G LEU* 3.7 33.4 - - + +
287G ALA* 3.8 19.1 - - + -
289G PHE* 3.6 8.9 - - + -
310G TRP* 3.9 13.0 - - + -
314G GLU 3.4 9.4 - - - +
315G ASP* 1.3 91.2 - - - +
317G TRP* 1.3 56.4 + - + +
319G GLN* 3.4 1.2 + - - +
320G HIS* 3.0 29.5 + - - +
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Residues in contact with TRP 317 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283G GLN* 5.2 4.9 + - + -
286G ARG* 3.4 31.1 - - + +
287G ALA* 3.7 28.8 - - + +
315G ASP* 3.2 16.2 + - - +
316G PRO* 1.3 77.3 - - + +
318G GLU* 1.3 66.2 + - - +
320G HIS* 3.2 6.4 + - - +
321G ALA* 3.0 23.4 + - - +
329G TYR* 3.9 3.6 - + - -
330G LEU* 3.5 38.6 - - + +
333G GLN* 3.5 38.6 - - + -
334G LYS* 3.6 34.7 - - + +
338G TYR* 3.4 18.2 + - + +
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Residues in contact with GLU 318 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258B ARG* 4.6 8.7 + - - +
299B LYS* 3.3 28.5 + - - -
315G ASP* 3.4 24.5 + - + +
317G TRP* 1.3 77.6 - - - +
319G GLN* 1.3 73.5 + - - +
321G ALA* 3.3 2.1 + - - +
322G LYS* 2.8 36.5 + - + +
338G TYR* 3.2 13.5 + - - +
342G ILE* 3.7 26.6 - - + +
345G THR* 4.8 11.1 - - - +
349G GLU* 5.6 1.4 - - - +
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Residues in contact with GLN 319 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307G LEU* 3.9 16.2 - - + +
310G TRP* 3.9 16.6 - - + -
314G GLU* 3.2 30.7 + - + +
315G ASP 3.2 16.1 + - - +
316G PRO 3.9 3.8 - - - +
317G TRP 3.2 0.6 - - - -
318G GLU* 1.3 91.4 - - - +
320G HIS* 1.3 66.4 + - - +
322G LYS* 4.1 17.4 - - - +
323G TRP* 3.4 37.1 + - - +
403G 1AQ 3.4 29.7 + - + +
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Residues in contact with HIS 320 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287G ALA* 3.2 24.8 + - + -
289G PHE* 3.8 17.4 - + + -
300G CYS* 3.3 17.9 - - + +
303G CYS* 3.5 2.2 - - - -
307G LEU* 4.3 2.2 - - - +
316G PRO 3.0 14.7 + - - +
317G TRP* 3.4 11.6 - - - +
319G GLN* 1.3 76.3 - - - +
321G ALA* 1.3 57.1 + - - +
324G TYR* 2.8 50.6 + + + +
327G CYS* 3.5 8.3 - - + -
329G TYR* 4.8 2.7 - + - -
330G LEU* 4.1 17.9 - - + +
401G ZN 2.1 38.6 - - - -
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Residues in contact with ALA 321 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317G TRP 3.0 12.6 + - - +
318G GLU 3.7 3.4 - - - +
320G HIS* 1.3 79.6 - - - +
322G LYS* 1.3 63.9 + - - +
323G TRP 3.5 0.2 + - - -
325G PRO* 3.5 23.4 - - - +
330G LEU* 3.6 20.8 - - + +
338G TYR* 3.8 24.2 - - + -
339G ILE* 4.7 9.5 - - - +
342G ILE* 3.9 16.3 - - + +
343G HIS* 5.4 3.1 + - - +
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Residues in contact with LYS 322 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343F HIS* 2.9 19.6 + - - -
318G GLU* 2.8 28.5 + - + +
319G GLN* 4.0 22.8 - - - +
320G HIS 3.4 0.4 - - - -
321G ALA* 1.3 74.5 - - - +
323G TRP* 1.3 89.7 + - + +
342G ILE* 3.7 14.1 - - + +
345G THR* 6.2 0.2 - - - +
346G HIS* 3.7 37.1 - - + +
349G GLU* 3.3 28.3 + - - +
402G ZN 3.1 13.0 - - - -
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Residues in contact with TRP 323 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343F HIS* 3.3 16.8 - + - -
344F LEU* 3.7 10.4 - - + +
347F SER* 4.1 16.6 - - - -
307G LEU* 3.6 18.4 - - + -
319G GLN* 3.4 34.9 + - - +
322G LYS* 1.3 101.3 - - + +
324G TYR* 1.3 86.5 + - + +
325G PRO* 3.4 5.8 - - - -
346G HIS* 4.0 23.1 - + - -
350G GLU* 4.5 7.6 - - - -
403G 1AQ 3.4 69.5 + - + -
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Residues in contact with TYR 324 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340F ASN* 3.3 19.3 - - + +
344F LEU* 4.5 14.6 - - + -
289G PHE* 5.8 1.1 - + - -
303G CYS* 4.0 9.4 - - - -
305G GLY* 3.4 26.9 - - - -
306G GLY 3.0 40.0 + - - -
307G LEU* 4.0 17.3 - - + -
319G GLN 5.0 1.1 - - - -
320G HIS* 2.8 38.9 + + + +
323G TRP* 1.3 94.5 - - + +
325G PRO* 1.3 57.4 - - - +
326G GLY 3.1 10.5 + - - -
327G CYS* 3.4 9.5 + - - +
330G LEU* 3.9 1.2 - - - +
403G 1AQ 3.3 24.2 + - - +
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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