Contacts of the strand formed by residues 77 - 80 (chain X) 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 X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50X LYS* 3.3 57.4 - - + +
53X GLU* 5.5 5.6 - - + -
56X GLY 5.3 0.2 - - - -
57X TYR* 3.6 27.4 - - + -
58X ARG* 3.1 44.3 + - - +
59X ASN* 3.1 22.0 - - - +
60X ILE* 3.2 23.8 + - + +
76X VAL* 1.3 76.4 - - - +
78X ALA* 1.3 65.4 + - - +
79X ASN* 4.7 2.0 - - + -
85X LEU* 3.9 9.9 - - + -
86X ILE 3.3 10.8 - - - +
87X MET* 4.3 10.5 - - + -
88X PHE* 5.7 1.1 - - - -
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Residues in contact with ALA 78 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59X ASN* 5.2 7.9 - - - +
60X ILE* 4.9 5.2 - - - +
77X TYR* 1.3 79.1 - - - +
79X ASN* 1.3 62.2 + - - +
85X LEU* 3.6 4.0 - - - +
86X ILE* 2.9 43.1 + - + +
88X PHE* 5.3 1.6 - - + -
308X LYS* 3.6 7.2 - - - +
312X ASN* 3.4 32.5 - - - +
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Residues in contact with ASN 79 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334V TYR* 4.9 3.8 + - - -
46X THR* 3.5 13.3 - - - +
50X LYS* 3.3 34.9 - - + +
60X ILE* 3.9 28.3 - - + +
77X TYR* 4.2 1.6 - - + -
78X ALA* 1.3 72.9 - - - +
80X ASN* 1.3 68.1 + - - +
81X ARG* 3.5 4.4 + - - -
82X GLY* 2.5 37.8 + - - -
84X GLY 3.7 6.8 - - - +
308X LYS* 3.5 7.6 + - - -
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Residues in contact with ASN 80 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334V TYR* 3.5 24.2 + - - -
427V GLY* 6.1 0.2 - - - -
79X ASN* 1.3 70.8 + - - +
81X ARG* 1.3 76.3 + - - +
82X GLY 2.8 2.3 + - - -
83X LYS* 2.9 15.8 + - - +
84X GLY* 2.9 22.2 + - - +
302X ALA 3.5 11.1 + - - +
303X THR* 3.4 20.5 - - - +
306X GLN* 3.5 5.6 + - - +
308X LYS* 3.1 45.6 - - + +
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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