Contacts of the helix formed by residues 473 - 482 (chain A) in PDB entry 6IY6
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 473 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199A GLN* 3.6 32.5 - - + +
202A ILE* 3.6 28.9 - - + -
203A CYS* 3.5 29.8 - - - -
287A VAL* 3.0 40.6 + - + +
289A LEU* 4.1 13.5 - - + -
471A ILE 3.6 4.0 + - - -
472A GLY* 1.3 69.5 - - - +
474A GLU* 1.3 59.0 + - - +
476A VAL* 3.4 6.8 + - - +
477A THR* 2.7 32.8 + - - +
219B GLN* 3.9 16.2 - - + -
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Residues in contact with GLU 474 (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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199A GLN* 3.7 10.3 - - - +
285A GLU 4.9 0.5 - - - +
286A PHE* 3.5 21.0 - - + +
287A VAL* 3.1 49.4 + - - +
472A GLY 4.2 0.3 - - - -
473A LEU* 1.3 72.1 + - + +
475A ARG* 1.3 53.0 + - - +
477A THR 3.3 1.4 + - - -
478A MET* 2.9 24.6 + - - +
486A VAL* 3.7 15.7 - - + -
489A THR* 2.8 40.7 + - - +
490A SER* 3.6 22.1 + - - +
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Residues in contact with ARG 475 (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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273A ARG* 4.6 25.3 - - - +
370A THR* 6.3 0.8 - - - +
423A GLU* 3.5 36.1 + - - +
424A GLU* 2.7 31.5 + - - +
425A ILE* 4.6 11.2 - - + +
472A GLY* 2.8 17.5 + - - +
474A GLU* 1.3 74.8 - - - +
476A VAL* 1.3 59.5 + - - +
478A MET* 3.4 28.2 + - + +
479A LEU* 3.1 43.4 + - + +
486A VAL* 4.4 8.6 - - + +
606A PO4 4.9 1.7 + - - -
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Residues in contact with VAL 476 (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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202A ILE* 4.0 24.7 - - + -
310A MET* 4.2 11.4 - - + -
313A ILE* 5.4 2.0 - - + -
314A PHE* 4.9 4.3 - - + -
317A LEU* 6.4 0.2 - - + -
420A MET* 3.7 23.3 - - + +
425A ILE* 4.3 21.1 - - + -
471A ILE* 3.9 33.0 - - + -
472A GLY 2.8 21.2 + - - +
473A LEU* 3.7 8.5 - - - +
475A ARG* 1.3 69.9 - - - +
477A THR* 1.3 58.6 + - - +
479A LEU 3.4 0.7 + - - -
480A PHE* 2.9 30.5 + - + +
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Residues in contact with THR 477 (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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195A VAL* 4.0 24.7 - - + +
198A LEU* 4.1 15.3 - - + -
199A GLN* 3.3 21.5 + - + +
202A ILE* 3.4 18.7 - - - +
473A LEU 2.7 19.5 + - - -
474A GLU 3.3 7.8 + - - -
476A VAL* 1.3 75.0 - - - +
478A MET* 1.3 62.6 + - - +
480A PHE* 3.8 3.1 - - - +
481A LEU* 3.3 33.4 + - + +
489A THR* 3.6 17.7 - - + -
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Residues in contact with MET 478 (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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423A GLU* 4.6 5.2 - - - +
474A GLU 2.9 16.7 + - - +
475A ARG* 3.5 37.9 - - + +
477A THR* 1.3 76.2 - - - +
479A LEU* 1.3 75.3 + - + +
481A LEU 3.5 0.5 + - - -
482A GLY 2.9 8.3 + - - -
483A LEU* 2.9 54.0 + - + +
484A HIS 3.5 16.6 - - - +
485A ASN 3.6 2.7 - - - +
486A VAL* 3.5 35.0 - - + -
489A THR* 3.4 18.3 - - + +
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Residues in contact with LEU 479 (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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337A PHE* 3.9 2.1 - - - -
420A MET* 3.4 37.2 - - + +
421A ARG* 2.7 44.6 + - + +
423A GLU* 3.3 39.0 - - + +
425A ILE* 3.6 25.6 - - + -
475A ARG* 3.1 25.3 + - + +
476A VAL 4.1 1.8 - - - +
478A MET* 1.3 89.2 - - + +
480A PHE* 1.3 55.7 + - - +
482A GLY* 3.7 4.3 - - - +
483A LEU 4.9 4.3 - - - +
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Residues in contact with PHE 480 (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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198A LEU* 4.5 2.0 - - + -
202A ILE* 5.5 0.2 - - + -
314A PHE* 3.6 39.3 - + + -
317A LEU* 3.7 43.5 - - + -
318A GLN* 4.1 19.1 - - + -
325A ILE* 4.0 22.4 - - + -
334A CYS* 4.9 0.2 - - - -
337A PHE* 3.7 31.6 + + + +
420A MET* 3.7 8.0 - - + +
421A ARG* 3.1 21.0 + - - -
476A VAL* 2.9 20.5 + - + +
477A THR* 3.8 6.7 - - - +
478A MET 3.3 0.4 - - - -
479A LEU* 1.3 78.1 - - - +
481A LEU* 1.3 69.8 - - + +
482A GLY 3.3 0.7 - - - -
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Residues in contact with LEU 481 (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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195A VAL* 3.9 31.6 - - + -
198A LEU* 4.1 20.4 - - + -
325A ILE* 4.4 20.9 - - + +
328A VAL* 4.1 18.9 - - + +
332A PHE* 4.8 2.8 - - - +
334A CYS* 3.4 21.4 - - - +
477A THR* 3.3 30.5 + - + +
480A PHE* 1.3 93.9 - - + +
482A GLY* 1.3 61.5 + - - +
483A LEU* 3.4 23.3 + - + +
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Residues in contact with GLY 482 (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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332A PHE* 5.8 1.4 - - - +
333A PRO 5.4 0.9 - - - +
334A CYS* 3.7 13.7 - - - +
421A ARG* 3.7 23.1 - - - -
478A MET 2.9 7.1 + - - -
479A LEU* 3.6 3.3 + - - -
480A PHE 3.3 4.0 + - - -
481A LEU* 1.3 79.3 - - - +
483A LEU* 1.3 64.4 + - - +
484A HIS* 4.8 10.0 + - - -
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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