Contacts of the strand formed by residues 84 - 89 (chain Q) 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 Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46Q THR* 4.0 6.2 + - - -
79Q ASN* 3.7 8.0 - - - +
80Q ASN* 2.9 41.2 + - - +
82Q GLY 3.4 0.2 - - - -
83Q LYS* 1.3 81.0 - - - +
85Q LEU* 1.3 62.9 + - - +
106Q ILE* 4.9 0.2 - - - -
291Q LEU 3.5 9.9 - - - -
292Q VAL* 4.8 6.5 - - - -
293Q ASP 5.6 0.2 - - - -
303Q THR* 4.5 3.1 - - - +
308Q LYS* 5.0 0.7 - - - -
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Residues in contact with LEU 85 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46Q THR* 4.2 10.8 - - - +
49Q ILE* 3.4 34.8 - - + -
50Q LYS* 3.4 31.0 - - - +
77Q TYR* 3.9 16.6 - - + -
78Q ALA 3.6 12.6 - - - +
84Q GLY* 1.3 75.4 - - - +
86Q ILE* 1.3 81.4 + - - +
87Q MET* 4.2 13.7 - - + -
106Q ILE* 5.5 0.9 - - + +
289Q THR 3.9 0.7 - - - +
290Q ILE* 3.7 1.4 - - - +
291Q LEU* 2.8 56.5 + - + +
292Q VAL* 5.6 0.6 - - - +
308Q LYS* 5.1 1.7 - - - +
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Residues in contact with ILE 86 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76Q VAL 4.1 0.3 - - - +
77Q TYR* 3.3 3.5 - - - -
78Q ALA* 2.9 52.1 + - + +
85Q LEU* 1.3 79.4 - - - +
87Q MET* 1.3 67.0 + - - +
88Q PHE* 3.5 33.1 - - + -
288Q ILE* 4.9 2.9 - - + -
289Q THR 3.2 11.4 - - - +
290Q ILE* 4.3 13.0 - - + -
308Q LYS* 3.7 17.7 - - + -
309Q PHE* 3.6 40.6 - - + +
312Q ASN* 4.4 5.6 - - - +
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Residues in contact with MET 87 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49Q ILE* 5.4 0.2 - - + -
53Q GLU* 3.2 44.4 - - - +
57Q TYR* 4.1 14.8 - - + -
76Q VAL 3.5 3.1 - - - -
77Q TYR* 4.3 7.2 - - + -
85Q LEU* 4.2 22.9 - - + -
86Q ILE* 1.3 75.5 - - - +
88Q PHE* 1.3 64.0 + - - +
274Q PHE* 3.4 25.1 - - + -
277Q MET* 3.2 26.4 - - + +
288Q ILE* 3.1 9.5 - - - +
289Q THR* 2.8 53.7 + - + +
291Q LEU* 5.5 1.3 - - + -
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Residues in contact with PHE 88 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57Q TYR* 3.1 23.9 - - - -
59Q ASN* 5.9 1.3 - - - -
75Q LYS* 3.5 7.0 - - - -
76Q VAL* 2.8 30.5 + - + +
77Q TYR* 5.3 0.9 - - - -
78Q ALA* 5.4 1.8 - - + -
86Q ILE* 3.5 34.3 - - + -
87Q MET* 1.3 78.6 - - - +
89Q LEU* 1.3 62.4 + - - +
90Q ILE* 4.3 7.2 - - + -
95Q LEU* 6.0 0.7 - - + -
99Q PHE* 4.6 6.5 - + - -
277Q MET* 3.9 0.9 - - - -
286Q THR* 5.0 5.6 - - + -
287Q CYS 3.8 1.1 - - - -
288Q ILE* 3.0 32.1 - - + -
312Q ASN* 3.4 25.8 - - - -
313Q THR* 4.1 25.4 - - + -
316Q ASP* 4.0 28.9 - - + +
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Residues in contact with LEU 89 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57Q TYR* 4.8 4.7 - - - +
73Q GLY* 4.8 6.1 - - - +
74Q ASP 3.4 14.4 - - - +
75Q LYS* 4.4 19.7 - - + -
88Q PHE* 1.3 79.0 - - - +
90Q ILE* 1.3 69.0 + - - +
277Q MET* 4.2 10.1 - - + +
280Q MET* 3.2 35.7 - - + +
281Q LYS* 5.3 1.1 - - - -
282Q ASN 6.1 0.7 - - - +
283Q ALA* 4.0 19.4 - - + +
286Q THR* 3.1 16.0 - - - +
287Q CYS* 3.2 42.2 + - - +
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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