Contacts of the strand formed by residues 77 - 80 (chain G) in PDB entry 2GLJ
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 77 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50G LYS* 3.3 56.2 - - + +
53G GLU* 5.4 5.4 - - + -
56G GLY 5.3 0.2 - - - -
57G TYR* 3.6 27.8 - - + -
58G ARG* 3.1 50.2 + - - +
59G ASN* 3.1 21.4 - - - +
60G ILE* 3.2 23.8 + - + +
76G VAL* 1.3 77.1 - - - +
78G ALA* 1.3 66.7 + - - +
79G ASN* 4.6 1.6 - - + -
85G LEU* 3.9 10.1 - - + -
86G ILE 3.3 10.3 - - - +
87G MET* 4.3 10.1 - - + -
88G PHE* 5.3 1.3 - - - -
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Residues in contact with ALA 78 (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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59G ASN* 5.2 8.1 - - - +
60G ILE* 4.9 4.7 - - - +
77G TYR* 1.3 79.1 - - - +
79G ASN* 1.3 62.5 + - - +
85G LEU* 3.6 4.1 - - - +
86G ILE* 2.9 42.2 + - + +
88G PHE* 5.3 2.0 - - + -
308G LYS* 3.6 7.0 - - - +
312G ASN* 3.4 31.2 - - - +
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Residues in contact with ASN 79 (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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46G THR* 3.5 14.3 - - - +
50G LYS* 3.3 34.6 - - + +
60G ILE* 3.9 28.2 - - + +
77G TYR* 4.2 1.8 - - + -
78G ALA* 1.3 73.0 - - - +
80G ASN* 1.3 69.2 + - - +
81G ARG 3.5 3.5 + - - -
82G GLY* 2.5 37.0 + - - -
84G GLY 3.7 6.4 - - - +
308G LYS* 3.5 6.3 + - - -
334H TYR* 4.8 4.0 + - - -
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Residues in contact with ASN 80 (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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79G ASN* 1.3 73.9 + - - +
81G ARG* 1.3 74.6 + - - +
82G GLY 2.8 1.6 + - - -
83G LYS* 2.9 15.6 + - - +
84G GLY* 2.9 22.4 + - - +
302G ALA 3.5 10.3 + - - +
303G THR* 3.4 20.5 - - - +
306G GLN* 3.5 5.8 + - - +
308G LYS* 3.1 44.4 - - + +
334H TYR* 3.4 24.7 + - - -
427H GLY* 6.0 0.2 - - - -
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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