Contacts of the strand formed by residues 343 - 347 (chain C) in PDB entry 6NYY
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 343 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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323C PHE* 3.7 13.1 - - - -
341C PRO* 3.5 1.2 - - - +
342C LYS* 1.3 81.8 + - - +
344C ALA* 1.3 64.1 + - - +
448C VAL* 4.6 4.3 - - - -
449C ILE* 3.3 17.0 - - - -
468C ARG 4.0 3.1 + - - -
469C PHE* 4.0 11.7 - - - -
470C ASP* 3.6 18.3 + - - +
471C ARG* 3.7 6.1 + - - +
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Residues in contact with ALA 344 (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 ILE* 4.6 0.4 - - + -
323C PHE* 3.6 25.1 - - + -
343C GLY* 1.3 76.1 - - - +
345C ILE* 1.3 65.7 + - - +
346C LEU* 5.4 0.4 - - + -
449C ILE 3.1 8.4 + - - +
450C LEU* 3.8 11.2 - - + -
451C ALA* 2.9 29.5 + - - +
469C PHE* 3.6 4.3 - - - -
471C ARG* 3.4 13.5 - - + +
473C ILE* 4.3 17.9 - - + -
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Residues in contact with ILE 345 (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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344C ALA* 1.3 72.5 - - - +
346C LEU* 1.3 63.6 + - - +
347C THR* 3.7 21.8 - - + -
409C ILE* 5.2 2.0 - - + -
451C ALA* 3.4 10.8 - - + +
453C THR* 4.2 17.0 - - + -
456C PRO* 5.6 0.4 - - + -
459C LEU* 4.9 7.2 - - + -
464C LEU* 3.7 29.2 - - + -
469C PHE* 3.5 43.5 - - + -
471C ARG 3.1 8.0 + - - +
472C GLN* 3.7 21.5 - - + +
473C ILE* 2.8 32.4 + - - +
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Residues in contact with LEU 346 (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 ILE* 4.1 18.2 - - + -
344C ALA* 5.4 0.4 - - + -
345C ILE* 1.3 74.1 - - - +
347C THR* 1.3 61.6 + - - +
354C LYS* 3.3 44.3 - - + +
357C LEU* 4.5 11.9 - - + -
358C ALA* 5.0 4.5 - - + +
405C PHE* 4.6 10.1 - - + -
450C LEU* 4.9 10.3 - - + -
451C ALA 2.6 19.1 + - - +
452C GLY* 4.2 1.8 - - - -
453C THR 3.0 24.7 + - - +
473C ILE* 3.5 33.0 - - + -
475C ILE* 3.7 18.8 - - + -
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Residues in contact with THR 347 (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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601B LYS* 4.7 2.4 + - - -
345C ILE* 3.7 22.9 - - + -
346C LEU* 1.3 78.4 - - - +
348C GLY* 1.3 60.0 + - - +
354C LYS* 3.6 6.7 + - - -
453C THR* 3.3 11.2 - - + -
456C PRO* 3.8 34.8 - - + -
472C GLN* 5.4 5.5 - - + +
473C ILE 2.8 20.0 + - - +
474C PHE* 3.3 21.0 - - - +
475C ILE* 2.8 29.4 + - - +
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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