Contacts of the helix formed by residues 317 - 322 (chain A) in PDB entry 6CCY
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 ALA 317 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315A TYR 3.4 2.8 + - - -
316A LEU* 1.3 76.1 - - - +
318A PRO* 1.4 73.5 - - + +
319A GLU* 3.6 24.5 - - - +
320A VAL* 3.2 27.1 + - + +
321A LEU* 3.3 10.2 + - - +
330A VAL* 4.0 9.4 - - + +
333A TRP* 3.5 24.9 - - + -
361A ILE* 4.4 0.4 - - - -
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Residues in contact with PRO 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316A LEU 4.0 0.2 - - - -
317A ALA* 1.4 79.1 - - - +
319A GLU* 1.4 59.5 + - - +
321A LEU* 2.8 26.2 + - + +
322A GLU* 2.9 24.5 + - - +
333A TRP* 3.6 34.5 - - + -
361A ILE* 4.0 14.1 - - + +
362A LEU* 4.1 19.7 - - + -
386A LYS* 3.3 41.1 - - + +
391A ARG* 3.8 0.9 - - - +
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Residues in contact with GLU 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A ALA* 3.6 8.3 - - - -
318A PRO* 1.4 77.1 - - - +
320A VAL* 1.3 62.2 + - - +
322A GLU* 3.7 11.3 + - - -
323A ASP 3.5 2.4 + - - -
324A ASN* 3.3 41.4 + - + +
326A TYR* 3.8 27.1 - - + +
327A GLY 5.7 0.2 - - - +
330A VAL* 3.6 16.7 + - + +
386A LYS 4.6 0.6 + - - -
388A PRO* 3.4 32.1 - - + +
391A ARG* 2.6 48.6 + - - -
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Residues in contact with VAL 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A TPO 4.8 0.2 - - - +
309A PHE* 3.7 22.9 - - + -
310A CYS 4.2 10.8 - - - +
316A LEU* 4.1 22.7 - - + -
317A ALA* 3.4 20.2 - - + +
318A PRO 3.2 0.6 - - - -
319A GLU* 1.3 73.7 - - - +
321A LEU* 1.3 63.8 + - - +
323A ASP* 3.2 21.1 + - - +
326A TYR* 4.2 27.8 - - + -
330A VAL* 3.6 31.0 - - + -
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Residues in contact with LEU 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A PHE* 4.2 8.7 - - + -
316A LEU* 4.0 24.5 - - + +
317A ALA 3.3 7.1 + - - +
318A PRO* 2.8 7.9 + - + +
320A VAL* 1.3 73.6 - - - +
322A GLU* 1.4 55.9 + - - +
323A ASP* 3.0 22.6 + - - +
358A PHE* 3.6 67.1 - - + +
361A ILE* 4.1 28.5 - - + -
362A LEU* 4.6 14.4 - - + -
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Residues in contact with GLU 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A PRO* 2.9 21.8 + - - +
319A GLU* 4.1 3.9 + - - +
320A VAL 3.4 0.2 - - - -
321A LEU* 1.4 73.4 - - - +
323A ASP* 1.4 65.3 + - - +
324A ASN* 3.3 29.7 + - - +
362A LEU* 3.4 31.3 - - + +
386A LYS 5.0 2.9 - - - +
388A PRO* 6.2 0.2 - - - +
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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