Contacts of the strand formed by residues 76 - 83 (chain A) in PDB entry 4UAL
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 PHE 76 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A LEU* 4.1 15.0 - - + -
72A HIS 3.7 18.2 - - - -
73A ARG 3.2 15.1 + - - +
74A GLU* 3.2 1.6 - - - -
75A ASP* 1.3 88.9 - - + +
77A GLU* 1.3 61.0 + - - +
78A ILE* 4.0 10.4 + - + +
93A VAL* 3.9 26.0 - - + -
94A LYS 3.4 4.7 - - - +
95A MET* 3.8 43.1 - - + -
96A LYS* 4.1 10.5 + - - -
102A TYR* 3.9 17.3 - + - -
104A MET* 3.6 23.6 - - + -
141A TYR* 4.5 0.9 - + - -
143A PHE* 4.0 18.4 - + - -
152A VAL* 4.0 20.6 - - + -
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Residues in contact with GLU 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A PHE* 1.3 72.5 - - - +
78A ILE* 1.3 74.3 + - - +
79A ILE* 4.0 6.1 - - + +
93A VAL* 3.0 6.8 - - - -
94A LYS* 2.8 61.2 + - + +
96A LYS* 4.3 19.8 - - + +
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Residues in contact with ILE 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A ARG* 5.7 8.1 - - + +
76A PHE* 4.1 12.3 - - + +
77A GLU* 1.3 85.4 - - - +
79A ILE* 1.3 64.9 + - - +
80A LYS* 3.8 15.3 - - - +
81A VAL* 4.7 8.3 - - + +
91A ALA* 4.2 16.6 - - + -
92A VAL 3.9 6.3 - - - +
93A VAL* 3.9 10.8 - - + -
104A MET* 6.0 3.6 - - - -
106A ILE* 5.9 7.4 - - + -
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Residues in contact with ILE 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A GLU* 4.0 14.8 - - - +
78A ILE* 1.3 79.7 - - - +
80A LYS* 1.3 68.0 + - + +
92A VAL* 2.8 29.6 + - + +
93A VAL 3.9 11.4 - - - -
94A LYS* 4.0 9.6 - - + +
101A ILE* 3.6 31.4 - - + -
365A SER* 4.2 15.5 - - - +
367A THR* 6.3 0.2 - - + -
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Residues in contact with LYS 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ILE* 3.8 3.8 - - - +
79A ILE* 1.3 90.9 - - + +
81A VAL* 1.3 72.2 + - - +
82A ILE* 3.5 1.4 + - - +
91A ALA* 3.3 2.8 - - - -
92A VAL* 2.6 34.5 + - + -
367A THR* 3.0 46.9 + - + +
372A VAL* 4.1 18.8 - - + +
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Residues in contact with VAL 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ILE* 4.7 9.1 - - + +
80A LYS* 1.3 82.5 - - - +
82A ILE* 1.3 62.5 + - - +
83A GLY* 3.9 13.9 - - - +
84A ARG* 5.5 5.2 - - + +
89A GLU* 4.0 31.0 - - + +
90A VAL 3.7 11.7 - - - +
91A ALA* 4.0 9.9 - - + -
372A VAL* 3.5 19.6 - - + +
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Residues in contact with ILE 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A LYS* 3.5 6.3 + - + +
81A VAL* 1.3 78.4 - - - +
83A GLY* 1.3 61.8 + - - +
90A VAL* 2.9 37.3 + - + +
91A ALA 4.2 5.2 - - - +
92A VAL* 3.6 33.7 - - + -
103A ALA* 5.0 1.1 - - + -
155A TYR* 4.1 15.3 - - + -
367A THR* 3.9 9.9 - - + -
370A PHE* 3.6 31.0 - - + -
371A ASP 4.4 2.1 - - - +
372A VAL* 3.9 27.9 - - + +
501A 3FV 4.2 20.2 - - + +
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Residues in contact with GLY 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A VAL* 3.6 7.3 - - - +
82A ILE* 1.3 82.0 - - - +
84A ARG* 1.3 68.5 + - - +
89A GLU* 3.4 1.7 - - - +
90A VAL* 2.8 34.1 + - - +
372A VAL* 5.4 4.0 - - - -
501A 3FV 4.3 17.5 - - - -
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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