Contacts of the helix formed by residues 474 - 484 (chain G) in PDB entry 1YYL
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 ASP 474 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105G HIS* 4.7 5.0 + - - -
453G LEU* 5.3 0.3 - - - +
472G GLY 3.7 2.2 - - - -
473G GLY* 1.3 73.2 + - - +
475G MET* 1.3 56.7 + - - +
476G ARG* 2.6 66.4 + - + +
477G ASP* 3.0 27.0 + - - +
478G ASN* 3.8 5.4 + - - -
20M ALA* 3.9 1.6 + - - +
21M GLY* 3.6 28.1 + - - +
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Residues in contact with MET 475 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105G HIS* 4.1 5.1 - - + -
255G VAL* 3.6 17.5 - - + -
256G SER 3.3 43.3 - - - +
257G THR* 4.2 6.3 - - + -
427G TRP* 3.6 33.2 - - + +
473G GLY* 3.0 41.0 + - - +
474G ASP* 1.3 71.2 + - - +
476G ARG* 1.3 57.5 + - - +
477G ASP 3.4 0.4 - - - -
478G ASN* 3.0 31.1 - - - +
479G TRP* 3.1 34.1 - - + +
23M BIF 4.2 8.1 - - + -
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Residues in contact with ARG 476 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101G VAL* 3.7 9.9 - - + +
102G GLU* 3.1 44.2 + - - -
105G HIS* 3.6 35.6 + - + -
474G ASP* 2.6 44.6 + - - +
475G MET* 1.3 71.2 - - - +
477G ASP* 1.3 60.1 + - - +
478G ASN 3.0 1.3 - - - -
479G TRP* 2.9 12.5 + - - +
480G ARG* 2.8 44.3 + - - +
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Residues in contact with ASP 477 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96G TRP* 4.2 9.9 - - - -
283G THR* 3.8 25.5 + - - +
285G ILE* 3.7 16.5 - - + +
453G LEU* 4.3 19.8 - - + +
472G GLY* 5.6 2.4 - - - -
474G ASP* 3.0 23.4 + - - +
476G ARG* 1.3 77.8 - - - +
478G ASN* 1.3 62.2 + - - +
480G ARG* 2.5 36.5 + - - +
481G SER* 3.0 22.0 + - - -
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Residues in contact with ASN 478 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254G VAL 4.1 7.2 - - - +
256G SER* 3.5 30.8 + - - +
260G LEU* 2.8 30.1 - - + +
453G LEU* 3.9 12.7 - - - +
474G ASP 3.8 4.2 + - - -
475G MET* 3.0 37.6 + - - +
477G ASP* 1.3 79.1 - - - +
479G TRP* 1.3 75.9 + - + +
481G SER* 2.7 23.3 + - - -
482G GLU* 3.9 8.0 + - - +
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Residues in contact with TRP 479 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G VAL* 4.0 11.2 - - + +
104G MET* 4.0 26.9 - - + -
105G HIS* 3.0 54.7 + - + +
108G ILE* 4.0 31.4 - - + -
251G ILE* 6.4 0.9 - - + -
253G PRO* 4.5 9.4 - - + -
254G VAL 3.7 39.0 - - - -
255G VAL* 4.3 6.7 - - + -
427G TRP* 4.7 1.8 - + - -
475G MET* 3.1 33.7 + - + -
476G ARG* 2.9 11.3 + - - +
478G ASN* 1.3 87.5 - - + +
480G ARG* 1.3 62.2 + - - +
482G GLU* 3.4 6.8 + - + +
483G LEU* 3.1 31.0 + - + +
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Residues in contact with ARG 480 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95G MET* 2.9 32.5 + - + +
96G TRP* 3.6 41.3 + - - +
98G ASN 5.5 0.4 - - - +
101G VAL* 3.9 24.8 - - + +
102G GLU* 4.6 13.3 + - - -
285G ILE* 4.1 8.3 - - + -
476G ARG* 2.8 24.0 + - - +
477G ASP* 2.5 47.8 + - - +
479G TRP* 1.3 73.5 - - - +
481G SER* 1.3 53.8 + - - +
482G GLU 2.7 16.6 + - - -
483G LEU 2.9 0.4 + - - +
484G TYR* 2.8 30.5 + - - +
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Residues in contact with SER 481 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95G MET* 5.3 1.8 - - - -
260G LEU* 3.1 33.3 - - - +
264G SER* 5.4 2.3 - - - +
285G ILE* 3.6 22.3 - - - +
287G GLN* 4.6 7.6 + - - +
477G ASP 3.0 3.9 + - - -
478G ASN 2.7 22.0 + - - -
480G ARG* 1.3 77.4 - - - +
482G GLU* 1.3 66.6 + - - +
484G TYR* 3.2 26.4 - - - -
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Residues in contact with GLU 482 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104G MET* 6.0 0.7 - - - -
249G HIS* 2.8 40.9 + - - -
250G GLY 5.1 0.2 - - - +
251G ILE* 4.2 33.7 - - + +
263G GLY* 3.1 12.7 - - - -
264G SER* 2.6 51.5 + - - +
478G ASN 4.3 9.4 - - - +
479G TRP* 3.4 11.1 + - + +
480G ARG 2.7 1.6 + - - -
481G SER* 1.3 88.5 + - - +
483G LEU* 1.3 59.5 + - + +
484G TYR* 3.5 5.9 + - - -
485G LYS* 5.0 2.4 + - - +
486G TYR* 3.9 4.3 - - - -
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Residues in contact with LEU 483 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95G MET* 5.8 0.2 - - - -
98G ASN* 3.7 14.3 + - - +
100G MET* 3.8 34.8 - - + +
101G VAL* 4.0 21.5 - - + -
104G MET* 3.9 20.6 - - + -
217G TYR* 4.6 14.1 - - + -
248G THR* 4.6 5.6 - - + -
251G ILE* 3.8 23.8 - - + -
479G TRP 3.1 17.0 + - - +
480G ARG* 2.9 4.2 + - - +
482G GLU* 1.3 77.1 - - + +
484G TYR* 1.3 64.0 + - - +
485G LYS 3.2 4.4 + - - -
486G TYR* 3.2 33.3 + - + +
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Residues in contact with TYR 484 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93G PHE* 4.9 3.6 - - - +
95G MET* 3.7 47.2 + - + +
98G ASN* 5.3 0.2 + - - -
233G PHE* 3.9 29.2 - + + -
235G GLY* 4.6 1.0 - - - +
264G SER* 6.3 0.9 - - - -
266G ALA* 5.8 0.2 - - - -
273G ARG* 2.9 45.3 + - - -
287G GLN* 3.3 21.5 + - - -
480G ARG* 2.8 11.3 + - - +
481G SER* 3.2 29.4 - - - -
482G GLU 3.5 4.2 - - - -
483G LEU* 1.3 77.8 - - - +
485G LYS* 1.3 87.9 + - + +
486G TYR 3.4 3.1 + - - +
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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