Contacts of the helix formed by residues 308 - 325 (chain V) in PDB entry 5Z58
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 SER 308 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271V GLU* 5.4 10.3 - - - -
304V LEU* 2.7 24.1 + - - +
307V VAL* 1.3 79.3 - - - +
309V PRO* 1.3 65.2 - - - +
310V ARG 3.2 3.1 - - - -
311V GLY* 3.1 18.3 + - - +
312V ILE* 3.1 11.1 + - - +
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Residues in contact with PRO 309 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304V LEU 4.4 0.7 - - - +
305V THR* 3.5 24.9 - - - +
306V GLN 5.0 0.6 - - - +
307V VAL 4.1 0.6 - - - -
308V SER* 1.3 73.2 - - - +
310V ARG* 1.3 58.5 + - - +
312V ILE* 3.6 2.7 + - + +
313V ASN* 3.0 28.1 + - - +
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Residues in contact with ARG 310 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308V SER* 3.2 0.8 - - - -
309V PRO* 1.3 77.3 - - - +
311V GLY* 1.3 60.2 + - - +
313V ASN* 3.4 7.4 - - - +
314V ALA* 2.9 27.9 + - - +
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Residues in contact with GLY 311 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275V LEU* 6.0 7.4 - - - -
308V SER* 3.1 15.2 + - - +
310V ARG* 1.3 76.4 - - - +
312V ILE* 1.3 64.6 + - - +
314V ALA* 3.1 10.6 + - - +
315V ILE* 3.1 19.4 + - - +
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Residues in contact with ILE 312 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301V GLY* 5.3 2.2 - - - +
304V LEU* 4.4 19.7 - - + +
305V THR* 4.7 11.0 - - - +
308V SER 3.1 13.6 + - - +
309V PRO* 4.1 3.4 - - + +
311V GLY* 1.3 75.3 - - - +
313V ASN* 1.3 56.7 + - - +
315V ILE* 3.2 10.5 + - + +
316V PHE* 2.9 28.5 + - - +
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Residues in contact with ASN 313 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309V PRO 3.0 18.8 + - - +
310V ARG* 3.4 10.3 - - - +
312V ILE* 1.3 75.9 - - - +
314V ALA* 1.3 56.1 + - - +
316V PHE* 3.2 6.6 + - - +
317V GLU* 2.9 30.0 + - - +
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Residues in contact with ALA 314 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310V ARG 2.9 15.0 + - - +
311V GLY* 3.1 12.5 + - - +
313V ASN* 1.3 74.8 - - - +
315V ILE* 1.3 62.1 + - - +
317V GLU* 3.4 7.8 + - - +
318V ARG* 3.0 23.4 + - - +
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Residues in contact with ILE 315 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278V LEU* 5.3 13.5 - - + -
311V GLY 3.1 12.2 + - - +
312V ILE* 3.2 12.5 + - - +
314V ALA* 1.3 77.6 - - - +
316V PHE* 1.3 57.1 + - - +
318V ARG* 3.2 8.5 + - - +
319V LEU* 2.9 27.6 + - - +
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Residues in contact with PHE 316 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312V ILE 2.9 16.2 + - - +
313V ASN* 3.8 6.5 - - - +
315V ILE* 1.3 77.0 - - - +
317V GLU* 1.3 58.2 + - - +
319V LEU* 3.3 8.5 + - - +
320V ARG* 2.9 28.9 + - - +
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Residues in contact with GLU 317 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313V ASN 2.9 17.4 + - - +
314V ALA* 3.6 8.5 - - - +
316V PHE* 1.3 75.8 - - - +
318V ARG* 1.3 58.5 + - - +
320V ARG* 3.2 8.4 + - - +
321V ASN* 2.9 28.6 + - - +
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Residues in contact with ARG 318 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282V LEU* 5.4 12.8 - - + +
314V ALA 3.0 13.9 + - - +
315V ILE* 3.3 12.1 - - - +
317V GLU* 1.3 77.8 - - - +
319V LEU* 1.3 56.8 + - - +
321V ASN* 3.2 8.6 + - - +
322V ILE* 2.9 27.9 + - - +
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Residues in contact with LEU 319 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315V ILE 2.9 13.1 + - - +
316V PHE* 3.5 12.3 - - - +
317V GLU 3.3 0.2 - - - -
318V ARG* 1.3 76.1 - - - +
320V ARG* 1.3 56.8 + - - +
322V ILE* 3.2 9.5 + - - +
323V LEU* 2.8 30.2 + - - +
336V ILE* 5.1 15.7 - - + +
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Residues in contact with ARG 320 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316V PHE 2.9 17.2 + - - +
317V GLU* 3.2 7.4 + - - +
319V LEU* 1.3 75.7 - - - +
321V ASN* 1.3 62.8 + - - +
323V LEU* 3.1 17.0 + - - +
324V HIS* 3.1 16.8 + - - +
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Residues in contact with ASN 321 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317V GLU 2.9 12.2 + - - +
318V ARG* 3.2 11.4 + - - +
320V ARG* 1.3 76.8 - - - +
322V ILE* 1.3 54.9 + - - +
324V HIS* 5.3 0.7 - - - -
325V GLU* 2.6 49.2 + - + +
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Residues in contact with ILE 322 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282V LEU 6.2 0.2 - - - +
285V PRO* 5.3 14.4 - - + -
318V ARG 2.9 13.3 + - - +
319V LEU* 3.4 12.6 - - - +
321V ASN* 1.3 75.8 - - - +
323V LEU* 1.3 63.2 + - - +
324V HIS 3.2 0.7 + - - -
326V SER* 3.1 33.1 + - - +
328V ILE* 4.6 8.5 - - - +
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Residues in contact with LEU 323 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360A SER* 6.0 2.3 - - - -
319V LEU 2.8 17.4 + - - +
320V ARG* 3.1 10.3 + - - +
322V ILE* 1.3 76.4 - - - +
324V HIS* 1.3 58.0 + - - +
326V SER 5.1 1.8 - - - +
328V ILE* 5.9 3.9 - - - +
333V GLN* 5.7 12.0 - - + +
336V ILE* 4.9 14.8 - - + -
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Residues in contact with HIS 324 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361A HIS* 5.8 4.9 - - + -
276C TYR* 4.3 30.5 + - + +
320V ARG 3.1 11.7 + - - +
321V ASN* 5.3 0.4 - - - -
323V LEU* 1.3 79.6 - - - +
325V GLU* 1.3 57.8 + - + +
326V SER 3.1 16.3 + - - +
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Residues in contact with GLU 325 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276C TYR* 5.2 6.3 - - - +
321V ASN* 2.6 31.6 + - + +
324V HIS* 1.3 73.5 - - + +
326V SER* 1.3 56.1 + - - +
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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
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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