Contacts of the helix formed by residues 318 - 327 (chain Z) in PDB entry 5V09
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 318 (chain Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317Z VAL* 1.3 76.4 - - - +
319Z ASP* 1.3 67.3 + - - +
320Z SER* 2.6 35.6 + - - +
321Z ILE* 3.0 29.6 + - + +
322Z ALA* 3.0 10.1 + - - -
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Residues in contact with ASP 319 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288Z PHE* 4.4 3.5 - - - -
293Z ARG 3.9 14.1 - - - +
294Z LYS* 3.4 30.3 + - - +
295Z LEU* 3.2 27.2 + - - +
317Z VAL 3.5 3.0 + - - +
318Z ASP* 1.3 77.6 + - - +
320Z SER* 1.3 57.6 + - - +
322Z ALA* 3.8 6.2 - - - +
323Z LEU* 2.9 28.6 + - - +
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Residues in contact with SER 320 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318Z ASP* 2.6 24.2 + - - -
319Z ASP* 1.3 76.0 - - - +
321Z ILE* 1.3 66.7 + - - +
323Z LEU* 3.3 10.6 + - - +
324Z GLN* 2.9 36.8 + - - +
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Residues in contact with ILE 321 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317Z VAL* 4.4 12.6 - - + -
318Z ASP* 3.0 26.4 + - + +
320Z SER* 1.3 82.6 - - - +
322Z ALA* 1.3 58.8 + - - +
324Z GLN* 3.1 7.8 + - - +
325Z ILE* 2.9 32.0 + - + +
330Z LYS* 3.9 18.6 - - + +
335Z PHE* 3.8 33.0 - - + -
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Residues in contact with ALA 322 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148Z PRO* 5.8 2.5 - - + +
288Z PHE* 4.1 12.5 - - + -
295Z LEU* 3.7 36.6 - - + -
317Z VAL* 4.1 9.6 - - + +
318Z ASP 3.0 10.7 + - - +
319Z ASP* 3.8 8.7 - - - +
321Z ILE* 1.3 75.8 - - - +
323Z LEU* 1.3 57.3 + - - +
325Z ILE* 3.4 9.1 + - - +
326Z ALA* 2.9 29.3 + - - +
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Residues in contact with LEU 323 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288Z PHE* 3.7 29.1 - - + -
293Z ARG* 4.2 39.0 - - + +
319Z ASP 2.9 19.0 + - - +
320Z SER* 3.4 9.9 - - - +
322Z ALA* 1.3 77.0 - - - +
324Z GLN* 1.3 66.7 + - - +
326Z ALA* 3.2 1.4 + - - +
327Z LEU* 2.9 61.2 + - + +
356Z TYR* 4.9 3.1 - - + -
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Residues in contact with GLN 324 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320Z SER* 2.9 23.3 + - - +
321Z ILE* 3.1 8.2 + - - +
323Z LEU* 1.3 89.5 - - - +
325Z ILE* 1.3 58.8 + - - +
327Z LEU* 3.7 6.8 + - - +
328Z GLY 3.4 1.6 + - - -
329Z ASN* 3.0 62.2 + - - +
330Z LYS* 3.0 12.9 + - + -
337Z GLN* 3.9 25.9 + - - +
341Z TYR 5.6 0.4 + - - -
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Residues in contact with ILE 325 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80Z CYS* 4.3 6.5 - - - -
127Z HIS* 5.2 0.2 + - - -
146Z VAL* 3.1 27.7 - - + +
147Z ALA 4.3 7.0 - - - +
148Z PRO* 5.1 6.5 - - + +
317Z VAL* 5.5 2.2 - - + -
321Z ILE* 2.9 23.5 + - + +
322Z ALA* 3.7 8.7 - - - +
323Z LEU 3.2 0.2 - - - -
324Z GLN* 1.3 75.0 - - - +
326Z ALA* 1.3 60.3 + - - +
328Z GLY* 2.9 19.1 + - - -
330Z LYS* 4.0 27.2 - - + +
331Z ASP 5.5 0.9 - - - +
332Z ILE* 3.9 23.1 - - + -
335Z PHE* 4.2 19.7 - - + -
402Z MN 4.0 24.2 - - - +
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Residues in contact with ALA 326 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144Z CYS 4.1 2.4 - - - +
145Z LEU* 3.5 22.3 + - + +
146Z VAL* 2.8 36.4 + - - +
288Z PHE* 3.6 31.4 - - + -
322Z ALA 2.9 18.6 + - - +
323Z LEU* 3.2 5.1 + - + +
325Z ILE* 1.3 76.8 - - - +
327Z LEU* 1.3 62.7 + - + +
328Z GLY 3.1 0.7 + - - -
356Z TYR* 5.0 1.1 - - - +
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Residues in contact with LEU 327 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131Z HIS* 5.6 0.3 + - - -
134Z ILE* 4.5 4.1 - - - +
138Z ARG* 3.1 34.6 + - - +
146Z VAL* 5.0 0.4 - - - -
323Z LEU* 2.9 41.2 + - + +
324Z GLN* 4.1 9.9 - - - +
325Z ILE 3.2 0.2 - - - -
326Z ALA* 1.3 76.9 - - + +
328Z GLY* 1.3 59.3 + - - +
329Z ASN* 3.2 32.8 + - - +
341Z TYR* 4.0 15.0 - - + +
343Z PRO* 4.2 22.7 - - + -
356Z TYR* 3.4 39.0 - - + +
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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