Contacts of the strand formed by residues 486 - 490 (chain G) in PDB entry 1G9N
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 TYR 486 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93G PHE* 3.7 7.3 - - - -
94G ASN 5.8 0.7 + - - -
95G MET 5.8 0.2 + - - -
98G ASN* 2.6 22.7 + - - -
100G MET* 3.1 20.9 - - + -
225G ILE* 3.9 11.7 - - + -
226G LEU 3.3 6.7 - - - -
227G LYS* 4.3 33.9 + - + +
245G VAL* 4.3 6.1 - - + -
248G THR* 3.4 35.2 - - + -
249G HIS* 2.9 40.5 + + - +
482G GLU 3.7 23.1 - - - -
483G LEU* 2.8 12.1 + - + +
484G TYR 3.5 0.9 - - - +
485G LYS* 1.3 104.0 - - + +
487G LYS* 1.3 63.6 + - - +
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Residues in contact with LYS 487 (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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91G GLU* 3.8 20.1 + - - +
92G ASN* 3.0 30.9 + - - +
93G PHE* 3.4 35.0 - - + +
94G ASN 6.1 0.7 - - - +
98G ASN* 4.1 5.4 - - - +
100G MET* 3.0 8.2 - - - +
225G ILE* 4.5 1.3 - - - +
226G LEU* 2.8 32.8 + - + +
486G TYR* 1.3 79.3 - - - +
488G VAL* 1.3 69.9 + - - +
489G VAL* 3.7 11.7 + - - +
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Residues in contact with VAL 488 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98G ASN* 5.4 0.7 - - - +
99G ASN* 5.7 5.4 - - + -
100G MET* 3.3 34.5 - - + +
219G ALA* 5.0 3.1 - - + -
220G PRO* 6.3 0.4 - - + -
223G PHE* 3.7 33.2 - - + -
224G ALA 3.5 10.5 - - - +
225G ILE* 4.1 13.5 - - + +
487G LYS* 1.3 78.2 - - - +
489G VAL* 1.3 62.4 + - - +
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Residues in contact with VAL 489 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91G GLU* 5.2 7.2 - - - +
223G PHE* 3.4 7.1 - - - -
224G ALA* 2.6 55.4 + - + +
226G LEU* 3.8 31.6 - - + -
487G LYS* 3.7 10.5 + - - +
488G VAL* 1.3 76.5 - - - +
490G LYS* 1.3 74.4 + - + +
492G GLU* 6.3 0.2 - - + -
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Residues in contact with LYS 490 (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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222G GLY 3.3 11.9 - - - +
223G PHE* 4.3 18.1 - - + -
224G ALA* 5.8 0.2 - - - -
489G VAL* 1.3 90.3 - - + +
491G ILE* 1.3 88.3 + - + +
492G GLU* 3.6 22.8 + - - +
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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