Contacts of the strand formed by residues 72 - 78 (chain j) in PDB entry 5GJQ
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 MET 72 (chain j).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68j LEU* 3.0 11.4 + - + -
69j ASN* 2.9 45.6 + - + +
70j GLU 3.6 0.2 - - - -
71j ASP* 1.3 81.1 - - + +
73j ALA* 1.3 69.4 + - - +
105j ILE* 3.4 28.9 - - + +
106j PRO 4.3 0.2 - - - -
107j CYS* 3.6 40.2 - - - +
110j LEU* 3.4 32.3 - - + -
136j TYR* 5.4 8.1 - - + -
137j ILE 3.3 17.3 - - - +
138j GLY* 4.1 4.7 - - - -
139j TRP 5.1 2.0 - - - +
216j LEU* 4.3 1.3 - - - -
225j ILE* 3.8 3.1 - - - +
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Residues in contact with ALA 73 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65j ILE* 4.7 7.0 - - + -
66j TYR 3.3 13.9 - - - +
67j LYS* 4.3 3.4 - - - -
68j LEU* 4.2 4.7 - - - +
72j MET* 1.3 79.9 - - - +
74j CYS* 1.3 64.6 + - - +
136j TYR* 3.8 1.2 - - - +
137j ILE* 2.9 47.5 + - + +
216j LEU* 4.6 0.2 - - + -
225j ILE* 3.8 30.1 - - + -
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Residues in contact with CYS 74 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45j LEU* 3.9 5.4 - - - -
65j ILE* 3.4 2.9 - - - +
66j TYR* 2.7 51.0 + - - -
68j LEU* 3.6 35.2 - - + -
73j ALA* 1.3 78.9 - - - +
75j SER* 1.3 61.6 + - - +
76j VAL* 5.4 0.4 - - - -
87j THR* 4.0 12.3 - - - -
90j LEU* 4.6 0.2 - - - -
134j LEU* 4.1 16.2 - - + -
135j LEU 3.2 11.9 - - - +
136j TYR* 4.0 12.1 - - + -
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Residues in contact with SER 75 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34j CYS* 2.9 31.8 - - - -
45j LEU* 3.6 21.0 - - - +
47j ALA* 4.2 0.7 - - - +
64j LYS* 2.7 23.0 + - - +
65j ILE* 3.6 8.8 - - - +
74j CYS* 1.3 76.3 - - - +
76j VAL* 1.3 68.4 + - - +
134j LEU* 3.4 8.5 - - - +
135j LEU* 2.9 30.2 + - - +
164j ILE* 6.2 0.2 - - - +
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Residues in contact with VAL 76 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34j CYS* 4.4 3.1 - - - +
63j GLU 5.7 0.4 - - - +
64j LYS* 3.4 33.6 + - + +
66j TYR* 4.0 23.3 - - + +
74j CYS* 5.4 0.4 - - - -
75j SER* 1.3 85.3 + - - +
77j ALA* 1.3 70.4 + - - +
79j ILE 6.5 0.2 - - - -
80j THR* 5.7 6.3 - - + -
83j ALA* 3.5 35.0 - - + +
87j THR* 5.5 0.9 - - + -
132j VAL* 3.6 14.4 - - + -
133j SER 3.5 13.2 - - - +
134j LEU* 4.0 15.0 - - + -
164j ILE* 5.5 0.4 - - - -
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Residues in contact with ALA 77 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28j ILE* 3.8 8.8 - - + +
31j ALA* 4.1 7.6 - - + -
32j GLY 4.1 16.2 - - - +
34j CYS* 4.6 2.5 - - + -
64j LYS* 4.9 3.6 - - - +
76j VAL* 1.3 82.9 - - - +
78j GLY* 1.3 59.8 + - - +
132j VAL* 3.6 3.1 - - - -
133j SER* 2.9 33.8 + - - +
164j ILE* 3.5 31.6 - - + +
165j GLY* 4.7 2.9 - - - -
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Residues in contact with GLY 78 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27j ALA 4.8 1.6 - - - -
28j ILE* 4.4 10.3 - - - -
31j ALA* 3.5 23.0 - - - +
76j VAL* 5.5 0.6 - - - +
77j ALA* 1.3 76.2 - - - +
79j ILE* 1.3 67.7 + - - -
80j THR* 3.5 10.9 + - - +
131j GLY 3.4 9.0 - - - -
132j VAL* 4.5 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