Contacts of the helix formed by residues 317 - 322 (chain C) in PDB entry 4JUO
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 GLY 317 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295C THR* 3.2 33.7 - - - +
316C GLU* 1.3 80.6 - - - +
318C SER* 1.3 60.6 + - - -
319C ASP 3.1 4.8 + - - -
320C TYR* 3.5 17.5 + - - +
321C ARG* 4.1 3.4 + - - -
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Residues in contact with SER 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316C GLU 4.3 1.0 + - - -
317C GLY* 1.3 67.3 - - - -
319C ASP* 1.3 67.9 + - - +
320C TYR 3.1 2.5 - - - -
321C ARG* 2.9 50.6 + - - +
322C GLU* 3.4 9.0 + - - +
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Residues in contact with ASP 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316C GLU* 3.1 38.2 - - + +
317C GLY 3.1 0.2 - - - -
318C SER* 1.3 87.5 + - - +
320C TYR* 1.3 59.3 + - - +
321C ARG 3.4 0.5 + - - -
322C GLU* 3.6 10.9 + - - +
381C LYS* 5.3 3.6 - - - -
382C ALA* 3.5 29.4 - - + +
385C ALA* 3.8 28.8 - - + +
386C ARG* 4.0 15.5 - - - +
389C ARG* 4.2 10.7 - - - +
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Residues in contact with TYR 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263C TYR* 2.4 38.3 + - - +
294C ILE* 4.4 16.3 - - + +
295C THR* 4.0 17.3 - - - -
298C MET* 3.4 45.3 + - + -
299C ASN* 2.6 38.4 + - - -
302C ALA* 4.6 6.2 - - - +
316C GLU* 3.9 20.3 + - + +
317C GLY 3.6 20.9 - - - +
318C SER 3.1 0.8 - - - -
319C ASP* 1.3 78.1 - - - +
321C ARG* 1.3 58.7 + - - +
322C GLU 3.4 0.4 - - - -
324C LEU* 4.2 1.7 - - - +
378C LEU* 5.5 3.4 - - + -
379C ILE* 4.8 11.1 - - + +
382C ALA* 3.9 24.0 - - + +
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Residues in contact with ARG 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269C ASP* 3.0 40.1 + - + +
271C ILE* 4.0 12.1 - - - -
291C LYS* 3.6 30.2 - - - +
294C ILE* 4.2 10.5 - - + +
295C THR* 3.8 22.2 - - - +
317C GLY 4.4 0.8 - - - -
318C SER* 2.9 43.0 + - - +
320C TYR* 1.3 80.7 - - - +
322C GLU* 1.3 59.6 + - - +
324C LEU* 2.9 37.7 + - + +
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Residues in contact with GLU 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263C TYR* 3.5 3.8 - - - -
266C GLY 4.3 5.4 - - - +
267C PHE* 3.6 22.2 - - + +
269C ASP* 5.2 0.2 - - - -
318C SER 3.4 7.0 + - - +
319C ASP* 3.8 13.9 - - - +
320C TYR 3.4 1.2 - - - -
321C ARG* 1.3 73.1 - - - +
323C GLY* 1.3 59.2 + - - +
324C LEU 3.0 4.9 + - - -
381C LYS* 3.4 28.9 - - - +
385C ALA* 4.7 12.6 - - + -
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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