Contacts of the helix formed by residues 74 - 84 (chain H) in PDB entry 4XLN
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 ASP 74 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65H PHE 4.3 4.8 - - - +
67H THR* 4.3 23.1 - - - +
68H ILE* 4.5 3.1 - - - -
72H LYS 3.7 1.6 + - - -
73H GLU* 1.3 78.0 - - - +
75H VAL* 1.3 70.0 + - + +
76H VAL* 3.3 26.2 + - - +
77H GLU* 3.4 15.1 + - - +
78H ILE* 3.1 17.9 + - - +
872J ARG* 3.5 20.5 + - - -
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Residues in contact with VAL 75 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58H ILE* 5.3 5.2 - - + -
61H VAL* 4.7 10.3 - - + -
63H HIS 4.7 1.6 - - - +
64H GLU 3.1 31.2 - - - +
65H PHE 3.2 22.9 - - - +
66H SER 3.6 15.3 - - - +
68H ILE* 4.3 11.3 - - + +
74H ASP* 1.3 74.3 - - + +
76H VAL* 1.3 64.7 + - - +
78H ILE* 3.0 12.2 + - + +
79H ILE* 2.9 39.7 + - + +
165H ILE* 4.2 14.1 - - + -
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Residues in contact with VAL 76 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64H GLU* 3.9 27.4 - - - +
65H PHE* 5.1 11.2 - - + -
74H ASP* 3.3 18.4 - - - +
75H VAL* 1.3 74.9 - - - +
77H GLU* 1.3 65.2 + - - +
79H ILE* 2.9 15.4 + - + +
80H LEU* 2.9 43.2 + - + +
842J VAL* 4.9 8.3 - - + -
872J ARG* 4.1 17.7 - - - +
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Residues in contact with GLU 77 (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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73H GLU* 3.7 33.9 - - + +
74H ASP* 3.4 6.9 + - - +
75H VAL 3.4 0.2 - - - -
76H VAL* 1.3 78.2 - - - +
78H ILE* 1.3 53.3 + - - +
80H LEU* 3.3 6.1 + - - +
81H ASN* 2.5 54.4 + - - +
867J ARG* 3.2 33.1 + - - +
872J ARG* 3.4 27.0 + - - +
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Residues in contact with ILE 78 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58H ILE* 6.1 0.4 - - + -
68H ILE* 5.4 3.1 - - + -
71H VAL* 4.7 2.9 - - + -
73H GLU* 3.7 26.5 - - + +
74H ASP 3.1 17.0 - - - +
75H VAL* 3.0 10.0 + - - +
77H GLU* 1.3 74.0 - - - +
79H ILE* 1.3 66.4 + - + +
81H ASN* 3.1 4.2 + - - +
82H LEU* 2.9 32.1 + - + +
129H ILE* 3.2 35.2 - - + +
130H ALA* 3.6 19.3 - - + -
140H MET* 3.8 29.6 - - + -
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Residues in contact with ILE 79 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56H VAL* 6.1 3.4 - - + -
64H GLU* 3.5 37.5 - - + +
75H VAL* 2.9 28.0 + - + +
76H VAL* 2.9 13.7 + - + +
78H ILE* 1.3 74.1 - - + +
80H LEU* 1.3 65.6 + - + +
82H LEU* 3.1 15.0 + - + +
83H LYS* 2.9 28.5 + - + +
165H ILE* 4.3 10.5 - - + -
166H PRO 5.8 0.2 - - - +
167H VAL* 3.5 37.2 - - + +
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Residues in contact with LEU 80 (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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76H VAL* 2.9 31.2 + - + +
77H GLU* 3.5 12.6 - - - +
78H ILE 3.2 0.2 - - - -
79H ILE* 1.3 84.7 - - + +
81H ASN* 1.3 61.0 + - - +
83H LYS* 3.1 27.8 + - - +
84H GLU* 3.4 5.7 + - - +
842J VAL* 3.7 27.4 - - + -
843J PHE 3.9 12.3 - - - +
844J ALA* 3.2 27.4 - - + +
866J VAL 5.8 0.4 - - - -
867J ARG* 3.5 37.8 + - + +
872J ARG* 5.1 5.2 - - - +
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Residues in contact with ASN 81 (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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73H GLU* 5.1 2.2 + - - -
77H GLU* 2.5 55.0 + - - +
78H ILE 3.1 5.1 + - - +
80H LEU* 1.3 75.9 - - - +
82H LEU* 1.3 61.4 + - - +
84H GLU* 3.5 8.6 + - - +
127H LEU* 3.3 30.3 - - - +
128H HIS* 2.9 34.1 - - - +
129H ILE* 3.8 20.8 + - + +
867J ARG* 3.5 18.6 + - - +
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Residues in contact with LEU 82 (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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53H VAL* 3.6 21.0 - - + +
56H VAL* 3.6 41.1 - - + -
78H ILE* 2.9 33.1 + - + +
79H ILE* 3.1 15.5 + - + +
81H ASN* 1.3 75.6 - - - +
83H LYS* 1.3 64.5 + - - +
85H LEU* 3.3 21.9 - - + +
114H PHE* 4.1 24.2 - - + -
129H ILE* 4.0 22.9 - - + -
140H MET* 4.3 10.5 - - + -
142H VAL* 4.4 5.8 - - + -
167H VAL* 5.9 2.0 - - + -
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Residues in contact with LYS 83 (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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53H VAL* 5.2 4.3 - - - +
79H ILE* 2.9 14.5 + - + +
80H LEU* 3.1 39.0 + - - +
82H LEU* 1.3 79.1 - - - +
84H GLU* 1.3 58.5 - - + +
85H LEU 3.1 6.8 + - - +
167H VAL* 3.5 22.2 - - + -
168H ASP* 3.5 27.5 + - - +
170H ILE* 3.5 27.3 - - + +
842J VAL* 2.6 35.6 + - - +
843J PHE* 3.7 2.8 - - - +
844J ALA* 3.7 9.3 - - + +
848J GLU* 3.4 25.1 + - - +
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Residues in contact with GLU 84 (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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80H LEU 3.4 10.4 + - - +
81H ASN* 3.5 8.7 + - - +
82H LEU 3.3 0.6 - - - -
83H LYS* 1.3 74.7 - - - +
85H LEU* 1.3 63.4 + - - +
86H VAL* 4.4 1.6 - - - +
124H ASN* 3.3 13.2 + - - -
127H LEU* 4.0 19.6 - - + +
175H ARG* 4.1 22.8 + - - +
844J ALA* 3.2 24.4 - - + +
845J ASN* 3.4 22.1 - - - +
867J ARG* 2.7 29.1 + - - -
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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