Contacts of the strand formed by residues 64 - 71 (chain H) in PDB entry 3J8B
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 GLN 64 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62H VAL 4.2 1.2 + - - +
63H VAL* 1.3 76.9 - - - +
65H GLY* 1.3 59.6 + - - +
83H PRO* 3.9 3.2 - - - +
84H PHE* 2.9 34.0 + - + +
94H PHE* 5.8 8.3 - - + -
119H TRP* 6.4 0.4 - - + -
120H TYR 3.2 12.1 - - - +
121H GLN* 4.5 7.6 - - + -
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Residues in contact with GLY 65 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64H GLN* 1.3 77.2 - - - +
66H VAL* 1.3 60.1 + - - -
81H CYS* 5.9 1.1 - - - -
82H PHE 3.1 15.3 - - - -
83H PRO* 4.2 0.7 - - - -
84H PHE* 3.8 9.4 - - - -
119H TRP* 3.3 9.4 - - - +
120H TYR* 3.0 32.1 + - - +
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Residues in contact with VAL 66 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65H GLY* 1.3 73.5 - - - -
67H LEU* 1.3 63.1 + - - +
68H LEU 4.2 0.2 + - - -
81H CYS* 3.1 8.2 - - - +
82H PHE* 2.9 34.6 + - + +
84H PHE* 5.7 0.2 - - - +
116H HIS* 5.3 8.7 - - + -
118H GLY 3.7 9.0 - - - +
119H TRP* 4.3 1.8 - - + +
120H TYR* 5.1 1.3 - - - -
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Residues in contact with LEU 67 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66H VAL* 1.3 74.5 - - - +
68H LEU* 1.3 59.6 + - - +
78H ILE* 4.9 14.1 - - + -
80H ASN 3.7 6.3 - - - +
81H CYS* 4.3 5.4 - - + +
116H HIS* 3.4 7.3 - - - +
117H VAL* 2.9 27.7 + - + -
118H GLY* 3.0 24.1 + - - +
119H TRP* 4.2 7.4 - - - +
120H TYR* 5.3 2.7 - - + +
150H LEU* 6.5 1.1 - - + -
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Residues in contact with LEU 68 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66H VAL 4.2 0.6 + - - +
67H LEU* 1.3 73.3 - - - +
69H GLY* 1.3 60.4 + - - +
77H GLU 4.5 0.4 - - - -
78H ILE* 3.6 4.0 - - - -
79H THR* 2.8 22.6 + - - -
80H ASN* 2.7 29.2 + - + +
81H CYS* 5.2 2.0 - - - -
112H ILE* 6.5 0.4 - - + -
114H HIS* 3.7 22.9 - - + +
115H LEU 3.3 5.4 - - - -
116H HIS* 4.6 0.9 - - - +
117H VAL* 4.8 1.8 - - - -
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Residues in contact with GLY 69 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68H LEU* 1.3 76.6 - - - +
70H LEU* 1.3 62.7 + - - +
77H GLU 3.1 11.2 - - - -
79H THR* 4.1 8.7 - - - -
114H HIS* 3.4 14.8 - - - +
115H LEU* 2.8 36.8 + - - +
117H VAL* 4.5 7.0 - - - +
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Residues in contact with LEU 70 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69H GLY* 1.3 75.6 - - - +
71H VAL* 1.3 66.2 - - - +
72H VAL* 3.4 6.1 + - + +
76H LEU* 3.5 2.9 - - - +
77H GLU* 2.8 47.1 + - + +
115H LEU* 5.5 1.6 - - - -
117H VAL* 4.8 4.2 - - - +
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Residues in contact with VAL 71 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70H LEU* 1.3 73.2 - - - +
72H VAL* 1.3 59.3 + - - +
73H GLU 4.1 6.1 + - - +
74H ASP 6.0 0.7 - - - +
75H ARG 3.9 4.5 - - - +
76H LEU* 4.5 6.7 - - + +
115H LEU* 6.0 0.8 - - - +
117H VAL* 5.5 3.9 - - + +
146H GLU* 5.0 16.6 - - + -
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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