Contacts of the helix formed by residues 317 - 331 (chain V) in PDB entry 5IY6
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 317 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316V LEU* 1.3 72.5 - - - +
318V PRO* 1.3 70.6 - - + +
319V TYR* 3.4 20.9 - - + +
320V GLN* 2.8 54.1 + - - +
321V GLU* 3.1 11.4 + - - +
344V ALA* 4.2 11.6 + - + +
501V TYR* 5.4 17.4 + - - -
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Residues in contact with PRO 318 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316V LEU 4.4 1.8 - - - +
317V ARG* 1.3 92.0 - - + +
319V TYR* 1.4 63.0 + - + +
321V GLU* 3.7 12.6 + - - +
322V LYS* 3.2 21.7 + - - +
325V ARG* 5.6 0.3 + - - -
499W ASN* 4.1 1.4 - - - +
500W ASP* 5.8 3.8 - - - +
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Residues in contact with TYR 319 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317V ARG* 4.0 18.3 - - + +
318V PRO* 1.4 77.8 - - + +
320V GLN* 1.4 87.6 + - + +
322V LYS* 3.5 9.4 + - - +
323V SER* 2.7 37.3 + - - -
340V LEU* 4.3 10.9 - - + +
341V PRO* 5.2 0.3 - - - +
344V ALA* 4.1 17.3 + - - +
489V TYR* 3.7 33.4 - + + +
492V ASN* 3.3 39.4 + - + +
496V LEU* 6.4 2.5 - - + -
497V GLN* 4.3 25.1 - - + -
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Residues in contact with GLN 320 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316V LEU* 3.7 21.0 - - + +
317V ARG* 2.8 39.6 + - + +
319V TYR* 1.4 96.2 + - + +
321V GLU* 1.3 57.4 + - - +
323V SER* 3.1 10.5 + - - -
324V LEU* 3.0 33.3 + - - +
340V LEU* 3.3 24.3 - - + +
344V ALA 3.0 27.0 + - - +
345V GLY* 3.9 7.7 - - - +
348V LEU* 4.9 3.3 - - - +
349V VAL* 4.1 18.6 - - + +
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Residues in contact with GLU 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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315V VAL* 3.0 4.9 - - - +
316V LEU* 3.0 39.3 + - + +
317V ARG 3.1 6.9 + - - +
318V PRO* 3.9 8.7 - - - +
320V GLN* 1.3 72.7 - - - +
322V LYS* 1.3 63.9 + - - +
323V SER 3.2 0.2 + - - -
324V LEU* 3.2 3.9 + - - +
325V ARG* 2.9 22.8 + - - +
498W GLY* 4.2 0.7 - - - -
499W ASN* 1.9 73.9 + - - +
500W ASP* 1.9 62.1 + - - +
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Residues in contact with LYS 322 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318V PRO 3.2 13.5 + - - +
319V TYR* 3.5 13.2 - - - +
321V GLU* 1.3 78.9 - - - +
323V SER* 1.3 53.9 + - - +
325V ARG* 3.4 24.0 + - - +
326V LYS* 2.9 29.8 + - + +
489V TYR* 6.2 3.4 - - + -
499W ASN* 3.7 1.2 + - - -
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Residues in contact with SER 323 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319V TYR* 2.7 23.6 + - - -
320V GLN* 3.1 14.9 + - - -
322V LYS* 1.3 76.0 - - - +
324V LEU* 1.4 59.8 + - - +
326V LYS* 3.5 6.6 + - - +
327V MET* 3.3 15.4 + - - +
338V ILE* 4.7 16.1 - - - +
349V VAL* 6.5 0.4 - - - -
488V LEU* 3.5 15.6 - - - +
489V TYR* 3.3 39.8 - - - -
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Residues in contact with LEU 324 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316V LEU* 4.0 23.6 - - + -
320V GLN 3.0 19.9 + - - +
321V GLU* 3.2 8.9 + - - +
323V SER* 1.4 69.3 - - - +
325V ARG* 1.4 66.8 + - - +
327V MET* 3.0 28.8 + - + +
328V PHE* 3.1 12.5 + - - +
338V ILE* 5.5 3.8 - - + -
349V VAL* 4.2 20.6 - - + +
352V THR* 4.0 14.1 - - - +
353V ALA* 4.4 13.2 - - + +
356V THR* 3.8 35.2 - - + +
499W ASN* 5.4 1.3 - - - +
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Residues in contact with ARG 325 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318V PRO 5.6 0.4 + - - -
321V GLU 2.9 14.7 + - - +
322V LYS* 3.6 25.2 - - - +
324V LEU* 1.4 76.4 - - - +
326V LYS* 1.3 60.9 - - - +
328V PHE* 3.4 14.9 + - - +
329V GLY* 3.5 9.2 + - - -
498W GLY* 4.4 1.8 - - - -
499W ASN* 2.0 62.5 + - - +
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Residues in contact with LYS 326 (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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322V LYS* 2.9 18.0 + - + +
323V SER* 3.7 9.4 - - - +
324V LEU 3.3 0.2 - - - -
325V ARG* 1.3 74.8 - - - +
327V MET* 1.3 54.1 - - - +
329V GLY* 3.1 4.8 + - - +
330V ASN* 2.8 54.2 + - - +
488V LEU* 3.0 39.8 + - + +
489V TYR* 6.1 3.7 - - + -
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Residues in contact with MET 327 (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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323V SER 3.3 10.3 + - - +
324V LEU* 3.0 21.7 + - + +
326V LYS* 1.3 76.0 - - - +
328V PHE* 1.3 62.6 + - - +
329V GLY 3.3 0.2 + - - -
330V ASN* 4.5 0.9 - - - +
331V GLY* 3.2 23.7 + - - -
335V SER* 4.8 11.0 - - - +
338V ILE* 4.3 13.2 - - - -
353V ALA* 4.6 9.2 - - + -
356V THR* 4.8 3.8 - - - +
357V VAL* 3.5 31.9 - - + -
464V LEU* 4.1 39.0 - - + -
488V LEU* 3.8 15.5 - - + -
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Residues in contact with PHE 328 (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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324V LEU 3.1 10.1 + - - +
325V ARG* 3.6 12.1 - - - +
326V LYS 3.3 0.2 - - - -
327V MET* 1.3 76.6 - - - +
329V GLY* 1.3 61.1 + - - +
331V GLY* 4.4 4.2 + - - -
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Residues in contact with GLY 329 (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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325V ARG 3.5 5.7 + - - -
326V LYS* 3.1 8.9 + - - -
328V PHE* 1.3 82.7 - - - +
330V ASN* 1.4 64.0 + - - +
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Residues in contact with ASN 330 (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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326V LYS* 2.8 36.5 + - - +
327V MET 3.4 0.6 + - - +
329V GLY* 1.4 77.2 - - - +
331V GLY* 1.3 62.7 + - - +
333V ALA* 5.0 2.8 + - - +
334V ARG* 2.8 46.1 + - - +
335V SER* 3.3 14.1 - - - +
488V LEU* 3.5 20.6 - - + +
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Residues in contact with GLY 331 (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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327V MET 3.2 13.7 + - - -
328V PHE 4.4 3.7 + - - -
329V GLY 3.7 1.2 - - - -
330V ASN* 1.3 75.7 - - - +
332V ARG* 1.3 56.8 + - - -
333V ALA* 3.3 2.9 - - - -
334V ARG 2.9 17.7 + - - -
335V SER* 2.6 23.3 + - - -
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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