Contacts of the strand formed by residues 63 - 67 (chain G) 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 63 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46G LEU* 4.1 16.6 - - + +
48G ALA* 4.3 9.2 - - + -
61G LYS* 4.8 10.2 - - - +
62G LYS* 1.3 85.1 + - - +
64G LEU* 1.3 66.6 + - - +
72G ILE 3.2 14.6 - - - +
73G SER* 4.8 3.4 - - - +
211G SER* 3.6 31.8 - - - +
212G ILE 3.5 33.0 - - - +
213G GLY* 3.7 2.7 - - - +
221G PHE* 3.6 32.3 - - + -
223G ILE* 3.5 24.3 - - + +
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Residues in contact with LEU 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61G LYS* 5.3 9.6 - - + +
63G ILE* 1.3 83.8 - - - +
65G HIS* 1.3 63.0 + - - +
66G VAL 3.7 0.2 + - - -
71G GLY* 3.4 4.9 - - - -
72G ILE* 2.9 44.6 + - + +
74G ILE* 3.8 40.8 - - + -
81G ALA* 4.6 7.0 - - + +
82G ARG* 5.2 10.5 - - + -
85G CYS* 3.8 30.5 - - + -
89G ARG* 5.1 2.9 - - - +
221G PHE* 4.1 1.7 - - - -
223G ILE* 4.6 4.5 - - - -
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Residues in contact with HIS 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64G LEU* 1.3 74.5 - - - +
66G VAL* 1.3 67.0 + - - +
67G ASP* 2.8 36.3 + - - -
68G ASN* 3.6 20.4 + - - -
70G ILE 3.8 3.6 - - - -
71G GLY* 4.8 0.7 - - - -
85G CYS* 4.1 1.0 - - - -
89G ARG* 3.0 32.2 + - - +
221G PHE* 4.0 27.4 + + + +
223G ILE* 4.7 7.4 - - + +
76f LYS* 3.7 28.2 + - + +
77f HIS* 3.5 16.9 - + + +
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Residues in contact with VAL 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64G LEU 3.7 1.3 + - - +
65G HIS* 1.3 75.9 - - - +
67G ASP* 1.3 64.4 + - - +
70G ILE* 3.0 26.5 + - + +
72G ILE* 3.9 38.1 - - + -
85G CYS* 4.7 5.8 - - - +
88G MET* 3.7 47.6 - - + +
89G ARG* 3.7 9.1 - - - +
92G CYS* 3.9 14.0 - - - +
93G LEU* 6.2 0.2 - - - +
108G LEU* 4.2 0.9 - - + -
77f HIS* 3.0 25.3 + - - -
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Residues in contact with ASP 67 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65G HIS* 2.8 18.5 + - - -
66G VAL* 1.3 77.9 - - + +
68G ASN* 1.3 81.1 + - - +
69G HIS* 2.9 29.1 + - + +
70G ILE* 2.9 18.3 + - + +
92G CYS* 3.2 31.4 - - + +
93G LEU* 5.1 4.4 - - - +
96G ARG* 2.9 42.7 + - - +
102G PRO* 5.1 0.7 - - - +
221G PHE* 4.1 0.7 - - - +
73f LYS* 3.9 7.9 + - - +
77f HIS* 5.2 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