Contacts of the helix formed by residues 360 - 365 (chain C) in PDB entry 6XWQ
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 360 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278C ARG* 2.9 22.7 - - - +
359C PRO* 1.3 72.0 - - - +
361C ALA* 1.3 55.4 - - - -
362C GLY 3.5 2.7 - - - -
363C ALA* 4.1 3.9 + - - +
364C ILE* 3.3 27.2 + - - +
394C ASP* 3.8 16.0 - - - +
398C ASP* 2.9 4.1 + - - -
501C ASP* 2.7 8.1 + - - -
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Residues in contact with ALA 361 (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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355C THR* 3.2 30.6 - - + +
356C ALA* 3.7 9.6 - - + +
358C VAL* 3.4 30.1 - - + +
359C PRO 3.1 0.6 + - - -
360C GLY* 1.3 68.2 - - - +
362C GLY* 1.3 59.7 + - - +
363C ALA 3.3 2.2 - - - -
364C ILE* 3.9 13.2 - - + +
365C MET* 3.4 17.9 + - + +
501C ASP* 2.3 20.6 + - - +
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Residues in contact with GLY 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317C THR* 3.9 19.7 - - - -
320C TYR* 3.2 19.7 - - - -
321C GLN* 3.7 9.8 + - - +
355C THR* 4.7 0.2 - - - -
361C ALA* 1.3 78.7 - - - +
363C ALA* 1.3 58.8 + - - +
365C MET 4.3 0.7 - - - -
366C LEU* 3.7 13.5 + - - +
401C ARG* 3.4 5.7 - - - +
501C ASP* 2.9 22.9 + - - -
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Residues in contact with ALA 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320C TYR* 3.8 13.0 - - - +
360C GLY 4.1 3.9 + - - +
361C ALA 3.3 0.2 - - - -
362C GLY* 1.3 78.3 - - - +
364C ILE* 1.3 59.2 + - + +
365C MET 3.4 0.2 - - - -
366C LEU* 3.2 14.2 - - + +
387C TYR* 2.3 31.0 + - + +
390C ILE* 5.6 0.7 - - + -
391C LEU* 4.6 21.1 - - + -
394C ASP* 3.7 30.7 - - + +
401C ARG* 3.9 3.4 - - - +
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Residues in contact with ILE 364 (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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358C VAL* 6.2 1.1 - - + -
359C PRO 5.5 1.1 - - - +
360C GLY 3.3 20.9 - - - +
361C ALA* 3.8 16.2 + - + +
362C GLY 3.6 0.2 - - - -
363C ALA* 1.3 77.9 - - + +
365C MET* 1.3 70.9 + - + +
366C LEU 3.1 1.2 + - - -
367C ALA* 3.2 20.4 + - - +
368C MET* 5.9 0.9 - - - +
387C TYR* 3.6 4.2 + - - -
391C LEU* 6.5 1.3 - - + -
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Residues in contact with MET 365 (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* 3.4 15.5 + - - +
350C LEU 5.0 1.8 - - - +
351C ALA* 3.2 33.1 - - - +
354C GLY* 4.5 14.8 - - - +
355C THR* 3.5 23.1 - - + +
361C ALA* 3.4 14.9 + - + +
364C ILE* 1.3 81.7 - - + +
366C LEU* 1.3 59.1 + - - +
367C ALA 3.0 6.3 + - - -
368C MET* 3.2 55.3 + - + +
369C VAL* 3.8 4.3 + - - +
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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