Contacts of the helix formed by residues 319 - 327 (chain C) in PDB entry 6GYS
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 LEU 319 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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317C SER 3.7 1.6 + - - -
318C SER* 1.3 71.0 - - - +
320C LEU* 1.3 59.8 + - - +
322C HIS* 3.5 4.6 + - - +
323C ALA* 2.9 33.3 + - + +
347C LYS* 5.0 20.2 - - + +
350C SER* 4.3 17.5 - - - +
351C LEU* 4.7 13.9 - - + +
353C ARG* 4.3 1.8 - - - +
354C ASP* 3.0 12.4 + - - +
376C GLU* 5.2 3.4 - - - +
380C PHE* 5.8 5.2 - - + -
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Residues in contact with LEU 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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318C SER* 3.2 4.6 - - - -
319C LEU* 1.3 78.4 - - - +
321C GLN* 1.3 58.5 + - - +
322C HIS 3.1 0.4 - - - -
324C ALA* 3.0 36.3 + - + +
351C LEU* 5.4 2.8 - - + +
354C ASP* 3.8 10.5 + - + +
369C THR* 4.8 18.2 - - + -
372C ALA* 5.7 4.3 - - + -
373C ILE* 5.7 6.1 - - + -
376C GLU* 4.4 13.9 - - - +
36G A 6.4 0.9 - - + -
37G T 5.1 8.3 - - - +
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Residues in contact with GLN 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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317C SER* 6.1 2.2 - - - -
318C SER* 3.7 18.5 + - - +
319C LEU 3.4 0.4 - - - -
320C LEU* 1.3 78.1 - - - +
322C HIS* 1.3 57.4 + - - +
325C TYR* 5.0 0.5 - - - +
17F T 4.6 3.3 - - - +
18F G 3.9 15.0 - - - +
19F T 5.0 8.5 - - - +
37G T 4.0 21.5 - - + -
38G A 3.4 20.2 + - - -
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Residues in contact with HIS 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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318C SER 3.9 8.7 + - - +
319C LEU* 3.5 7.1 + - - +
320C LEU 3.1 0.2 - - - -
321C GLN* 1.3 80.5 - - - +
323C ALA* 1.3 64.7 + - - +
324C ALA 3.3 0.9 - - - -
325C TYR* 3.4 17.5 + - - +
326C LEU* 3.8 6.1 + - - +
347C LYS* 6.3 0.9 - - - +
17F T 3.7 30.8 - - + +
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Residues in contact with ALA 323 (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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319C LEU* 2.9 18.7 + - + +
322C HIS* 1.3 73.7 - - + +
324C ALA* 1.3 60.1 + - - +
325C TYR 3.1 2.5 - - - -
326C LEU* 3.5 4.5 + - - +
327C GLN* 3.0 32.6 + - + +
376C GLU* 3.2 27.8 - - + +
380C PHE* 6.0 3.8 - - + -
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Residues in contact with ALA 324 (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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320C LEU* 3.0 19.3 + - - +
323C ALA* 1.3 76.8 - - - +
325C TYR* 1.3 61.1 + - - +
327C GLN* 4.5 4.7 - - - +
328C ASP* 3.2 23.1 + - - +
372C ALA* 6.2 0.7 - - + -
376C GLU* 4.0 6.0 + - - +
37G T 3.7 47.2 - - + +
38G A 3.9 9.0 + - - +
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Residues in contact with TYR 325 (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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321C GLN 5.0 0.9 - - - +
322C HIS 3.4 12.2 + - - +
323C ALA 3.1 0.6 - - - -
324C ALA* 1.3 77.9 - - - +
326C LEU* 1.3 61.0 + - - +
328C ASP* 2.9 27.9 + - - +
17F T 5.2 2.0 - - - +
38G A 3.5 15.9 + - - +
39G C 3.4 31.4 - - + +
40G A 4.6 7.2 - - - +
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Residues in contact with LEU 326 (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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322C HIS 3.8 6.1 + - - +
323C ALA* 3.5 6.3 + - - +
325C TYR* 1.3 75.7 - - - +
327C GLN* 1.3 61.7 + - - +
328C ASP 3.0 11.7 - - - +
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Residues in contact with GLN 327 (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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323C ALA* 3.0 20.8 + - + +
324C ALA* 4.5 5.2 - - - +
326C LEU* 1.3 76.7 - - - +
328C ASP* 1.3 57.4 + - - +
376C GLU* 5.5 8.3 - - + +
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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