Contacts of the strand formed by residues 84 - 89 (chain C) 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 GLY 84 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46C THR* 4.1 5.0 + - - -
79C ASN* 3.6 8.1 - - - +
80C ASN* 2.9 42.0 + - - +
82C GLY 3.4 0.2 - - - -
83C LYS* 1.3 81.6 - - - +
85C LEU* 1.3 63.2 + - - +
106C ILE* 4.9 0.4 - - - -
291C LEU 3.5 9.4 - - - -
292C VAL* 4.8 6.5 - - - -
303C THR* 4.4 3.8 - - - +
308C LYS* 5.0 0.9 - - - -
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Residues in contact with LEU 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C THR* 4.3 10.5 - - - +
49C ILE* 3.4 35.0 - - + -
50C LYS* 3.3 32.1 - - - +
77C TYR* 3.9 17.0 - - + -
78C ALA 3.6 12.6 - - - +
84C GLY* 1.3 75.5 - - - +
86C ILE* 1.3 76.8 + - - +
87C MET* 4.3 12.1 - - + -
106C ILE* 5.9 0.9 - - + -
289C THR 4.0 0.4 - - - +
290C ILE* 3.7 1.7 - - - +
291C LEU* 2.8 58.6 + - + +
292C VAL* 5.6 0.6 - - - +
308C LYS* 5.1 1.3 - - - +
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Residues in contact with ILE 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C TYR* 3.3 3.3 - - - +
78C ALA* 2.9 53.9 + - + +
85C LEU* 1.3 78.3 - - - +
87C MET* 1.3 66.7 + - - +
88C PHE* 3.5 32.7 - - + -
288C ILE* 4.9 2.7 - - + -
289C THR 3.1 14.1 - - - +
290C ILE* 4.4 11.0 - - + -
308C LYS* 3.7 17.9 - - + -
309C PHE* 3.6 41.3 - - + +
312C ASN* 4.4 4.9 - - - +
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Residues in contact with MET 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C GLU* 3.1 44.9 - - - +
57C TYR* 4.1 14.6 - - + -
76C VAL 3.5 3.6 - - - -
77C TYR* 4.3 7.4 - - + -
85C LEU* 4.3 22.2 - - + -
86C ILE* 1.3 76.7 - - - +
88C PHE* 1.3 64.8 + - - +
274C PHE* 3.4 24.7 - - + -
277C MET* 3.2 26.6 - - + +
288C ILE* 3.1 8.5 - - - +
289C THR* 2.8 53.2 + - + +
291C LEU* 5.5 1.3 - - + -
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Residues in contact with PHE 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C TYR* 3.1 24.6 - - - -
59C ASN* 5.9 1.1 - - - -
75C LYS* 3.5 6.7 - - - -
76C VAL* 2.8 31.6 + - + +
77C TYR* 5.3 0.9 - - - -
78C ALA* 5.3 1.8 - - + -
86C ILE* 3.5 33.4 - - + -
87C MET* 1.3 79.0 - - - +
89C LEU* 1.3 62.7 + - - +
90C ILE* 4.8 7.2 - - + -
95C LEU* 6.1 0.7 - - + -
99C PHE* 4.6 6.1 - + - -
277C MET* 3.9 1.1 - - - -
286C THR* 5.0 4.9 - - + -
287C CYS 3.7 0.9 - - - -
288C ILE* 3.0 30.5 - - + -
312C ASN* 3.4 27.1 - - - -
313C THR* 4.1 25.6 - - + -
316C ASP* 4.0 28.3 - - + +
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Residues in contact with LEU 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C TYR* 4.7 4.7 - - - +
73C GLY* 4.8 7.0 - - - +
74C ASP 3.4 13.5 - - - +
75C LYS* 4.4 20.0 - - + -
88C PHE* 1.3 80.3 - - - +
90C ILE* 1.3 70.0 + - - +
277C MET* 4.2 11.2 - - + +
280C MET* 3.2 35.9 - - + +
281C LYS* 6.0 0.9 - - - -
282C ASN 6.1 1.1 - - - +
283C ALA* 4.0 19.5 - - + +
286C THR* 3.1 15.6 - - - +
287C CYS* 3.1 41.8 + - - +
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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