Contacts of the strand formed by residues 73 - 80 (chain A) in PDB entry 4XDO
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 73 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A ALA* 3.4 19.1 - - + +
72A PRO* 1.3 77.0 - - - +
74A GLN* 1.3 65.7 + - - +
75A GLN* 3.8 6.4 + - + +
88A ASN* 3.3 47.6 - - + +
89A ILE 3.5 2.0 - - - +
90A GLN* 4.4 17.0 - - + +
132A PRO 3.8 0.5 - - - +
133A ILE* 3.2 5.1 - - - -
134A TYR* 2.8 49.1 + - + +
136A ALA* 5.6 8.7 - - + +
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Residues in contact with GLN 74 (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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72A PRO 4.2 0.4 + - - -
73A ILE* 1.3 73.2 - - - +
75A GLN* 1.3 59.5 + - - +
76A MET* 3.4 25.8 + - - +
88A ASN* 3.6 3.5 - - - -
89A ILE* 2.8 53.3 + - + +
91A LYS* 2.9 36.3 + - + +
108A TYR* 4.9 4.0 + - - -
131A ALA* 3.6 28.7 - - + +
132A PRO 3.4 7.9 - - - +
133A ILE* 4.1 14.3 - - + +
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Residues in contact with GLN 75 (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 ILE* 4.5 8.7 - - + +
74A GLN* 1.3 71.8 - - - +
76A MET* 1.3 62.0 + - - +
77A VAL* 3.7 6.7 + - + +
86A GLN* 3.7 27.5 + - - +
87A TYR 3.8 4.0 - - - -
88A ASN* 4.2 12.0 + - - +
131A ALA* 3.4 18.0 - - - +
132A PRO* 2.9 29.6 + - + +
134A TYR* 3.9 18.2 - - + +
185A THR* 3.4 13.1 - - - -
186A THR* 2.8 50.3 + - - +
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Residues in contact with MET 76 (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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74A GLN* 3.4 33.0 - - - +
75A GLN* 1.3 73.1 - - - +
77A VAL* 1.3 60.5 + - - +
78A THR* 4.0 0.8 + - - -
85A THR 3.8 0.7 - - - +
86A GLN* 3.2 1.8 - - - -
87A TYR* 2.8 81.9 + - + +
89A ILE* 3.6 22.4 - - + -
131A ALA* 3.6 19.3 - - + -
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Residues in contact with VAL 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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75A GLN* 3.7 9.7 + - + +
76A MET* 1.3 73.3 - - - +
78A THR* 1.3 62.4 + - - +
84A PHE* 3.7 36.3 - - + -
85A THR 3.4 4.3 - - - +
86A GLN* 3.6 30.3 - - + +
127A LEU* 3.8 42.8 + - + +
128A THR* 3.6 16.8 - - + +
132A PRO* 5.9 3.1 - - + -
186A THR* 4.9 0.4 - - - +
246A LEU* 4.3 4.9 - - + -
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Residues in contact with THR 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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76A MET 4.0 2.5 + - - -
77A VAL* 1.3 76.6 + - - +
79A GLY* 1.3 64.3 + - - +
84A PHE* 3.1 8.6 - - - -
85A THR* 2.7 43.5 + - - -
87A TYR* 5.1 9.7 - - - -
128A THR* 4.6 1.3 - - - -
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Residues in contact with GLY 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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78A THR* 1.3 84.0 - - - +
80A GLN* 1.3 79.5 + - - +
83A LEU 3.5 9.9 - - - -
84A PHE* 3.5 10.8 - - - -
128A THR* 4.0 10.8 + - - +
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Residues in contact with GLN 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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79A GLY* 1.3 84.0 - - - +
81A SER* 1.3 85.7 + - - +
82A GLY 3.3 2.9 - - - -
83A LEU* 3.1 23.3 + - - +
84A PHE* 3.7 9.4 - - - -
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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