Contacts of the strand formed by residues 71 - 77 (chain C) 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 ILE 71 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C PRO* 3.7 3.3 - - - +
67C ILE* 2.9 30.3 + - + -
68C THR* 3.5 13.7 + - - +
69C LYS 3.8 0.6 - - - -
70C HIS* 1.3 114.2 - - + +
72C GLY* 1.3 61.6 + - - +
104C ILE* 3.6 15.9 - - + +
106C THR* 3.7 28.3 - - - +
109C LEU* 3.6 32.8 - - + -
135C ILE* 3.7 13.5 - - + -
136C CYS 3.2 12.1 - - - +
217C PHE* 3.9 7.5 - - - +
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Residues in contact with GLY 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C LEU* 4.0 4.7 - - - -
65C GLU 3.4 8.5 - - - -
67C ILE* 4.5 1.1 - - - -
71C ILE* 1.3 75.2 - - - +
73C LEU* 1.3 61.4 + - - -
135C ILE* 3.3 8.7 - - - +
136C CYS* 2.9 36.8 + - - +
217C PHE* 3.6 23.8 - - - -
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Residues in contact with LEU 73 (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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45C LEU* 4.1 3.4 - - - +
64C VAL* 3.3 2.3 - - - +
65C GLU* 2.8 37.2 + - + +
67C ILE* 3.7 29.8 - - + -
72C GLY* 1.3 73.7 - - - +
74C VAL* 1.3 71.2 + - - +
82C TYR* 3.2 13.8 + - + +
85C LEU 4.9 1.1 - - - +
86C VAL* 3.8 24.7 - - + +
89C ALA* 4.8 6.7 - - + -
133C LEU* 3.9 26.5 - - + -
134C LEU 3.3 17.5 - - - +
135C ILE* 3.5 27.6 - - + -
217C PHE* 4.7 0.6 - - - -
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Residues in contact with VAL 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C SER* 4.6 12.6 - - - +
45C LEU* 3.7 25.8 - - + -
46C ALA 5.0 2.5 - - - +
47C THR* 4.4 12.6 - - + -
63C LYS* 3.6 11.7 - - + +
64C VAL* 3.5 34.5 - - + -
73C LEU* 1.3 83.2 - - - +
75C TYR* 1.3 64.0 + - - +
82C TYR* 3.9 3.4 - - - -
133C LEU* 3.5 3.6 - - - -
134C LEU* 2.9 53.8 + - + +
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Residues in contact with TYR 75 (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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32C ALA 4.3 0.2 - - - +
34C SER* 3.0 20.6 + - - -
63C LYS* 3.6 52.5 + - + +
74C VAL* 1.3 75.6 - - - +
76C SER* 1.3 66.6 + - - +
77C GLY 3.5 29.1 + - - -
78C MET 3.8 13.0 - - - -
79C GLY* 3.9 15.6 + - - -
82C TYR* 3.3 57.4 - + + -
131C VAL* 4.0 7.2 - - + -
132C SER 3.2 11.0 - - - +
133C LEU* 4.1 0.7 - - + -
134C LEU* 4.9 0.4 - - - +
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Residues in contact with SER 76 (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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28C VAL* 3.3 15.7 - - - +
31C GLY 5.2 0.4 - - - -
32C ALA 3.1 22.3 + - - -
34C SER* 3.4 9.7 + - - -
75C TYR* 1.3 81.0 + - - +
77C GLY* 1.3 58.8 + - - +
131C VAL* 3.5 0.7 - - - -
132C SER 2.9 32.5 + - - -
162C MET* 3.6 20.6 + - - +
163C GLY* 3.8 22.0 - - - -
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Residues in contact with GLY 77 (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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27C ALA 3.9 17.9 - - - -
28C VAL* 4.0 1.3 - - - -
31C GLY* 4.2 17.2 - - - -
75C TYR* 3.5 12.3 + - - -
76C SER* 1.3 76.5 - - - +
78C MET* 1.3 65.0 + - - -
79C GLY 3.7 0.9 + - - -
130C GLY 3.3 9.4 - - - -
131C VAL* 4.4 0.4 - - - -
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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