Contacts of the helix formed by residues 88 - 103 (chain V) in PDB entry 5LN3
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 88 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75V MET* 3.0 28.4 - - + +
76V PRO* 4.6 16.1 - - + +
86V ALA 3.8 4.2 + - - +
87V VAL* 1.4 72.7 - - - +
89V PRO* 1.4 70.7 - - - +
90V VAL* 3.7 24.5 + - - +
91V PHE* 3.7 20.5 + - + +
92V GLN* 3.2 6.5 - - - +
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Residues in contact with PRO 89 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87V VAL* 4.0 6.0 - - - +
88V ASP* 1.4 89.2 - - - +
90V VAL* 1.3 69.6 + - + +
91V PHE 3.3 0.2 - - - -
92V GLN* 3.4 11.8 - - + +
93V ALA* 3.1 25.1 + - - +
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Residues in contact with VAL 90 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88V ASP* 3.7 21.8 - - - +
89V PRO* 1.3 81.2 - - + +
91V PHE* 1.4 62.8 - - + +
93V ALA* 3.6 4.3 - - - +
94V LYS* 2.9 59.4 + - + +
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Residues in contact with PHE 91 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81U MET* 3.6 48.7 - - + +
84U LYS* 5.6 7.2 - - + -
85U VAL* 4.9 10.8 - - + -
73V PHE* 4.3 14.8 - + - -
74V ALA 3.6 24.0 - - - -
75V MET* 4.3 8.3 - - + -
76V PRO* 4.1 23.3 - - + -
88V ASP* 3.7 26.8 + - + +
89V PRO 3.3 0.6 - - - -
90V VAL* 1.4 82.6 - - + +
92V GLN* 1.4 62.8 + - - +
94V LYS* 3.7 11.5 - - - +
95V MET* 3.0 30.6 + - - +
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Residues in contact with GLN 92 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56V LEU* 4.2 15.9 - - + +
73V PHE* 3.8 30.4 - - + -
75V MET* 3.2 19.1 - - + +
87V VAL* 4.2 10.7 - - - +
88V ASP 3.2 23.8 + - - +
89V PRO* 3.4 13.2 - - - +
91V PHE* 1.4 77.6 - - - +
93V ALA* 1.4 64.7 + - - +
95V MET* 3.5 2.1 + - - +
96V LEU* 3.2 24.0 + - - +
108V VAL* 6.1 2.8 - - - +
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Residues in contact with ALA 93 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89V PRO 3.1 18.4 + - - +
90V VAL* 3.6 5.6 - - - +
91V PHE 3.3 0.6 - - - -
92V GLN* 1.4 78.6 - - + +
94V LYS* 1.4 61.2 - - + +
96V LEU* 3.4 11.6 + - - +
97V ASP* 2.8 33.7 + - - +
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Residues in contact with LYS 94 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81U MET* 4.0 26.2 - - + -
90V VAL* 2.9 50.1 + - + +
91V PHE* 3.7 11.3 - - - +
93V ALA* 1.4 76.3 - - + +
95V MET* 1.3 63.3 + - - +
97V ASP* 3.3 19.9 + - - +
98V MET* 3.3 23.0 + - + +
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Residues in contact with MET 95 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54U PHE* 4.2 18.2 - - + -
78U MET* 3.7 37.5 - - + +
81U MET* 3.8 18.6 - - - +
82U PHE* 5.0 8.1 - - + -
73V PHE* 4.4 39.3 - - + -
91V PHE* 3.0 25.8 + - + +
92V GLN 3.8 5.2 - - - +
93V ALA 3.4 0.2 - - - -
94V LYS* 1.3 76.0 - - - +
96V LEU* 1.3 56.8 + - - +
98V MET* 3.1 6.0 + - - +
99V LEU* 2.8 46.4 + - + +
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Residues in contact with LEU 96 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58V LEU* 5.1 11.2 - - + -
73V PHE* 6.1 4.0 - - + -
92V GLN 3.2 12.1 + - - +
93V ALA* 3.4 13.7 - - - +
94V LYS 3.2 0.2 - - - -
95V MET* 1.3 78.8 - - - +
97V ASP* 1.4 55.8 + - - +
99V LEU* 3.4 14.1 + - + +
100V LYS* 2.8 39.9 + - + +
105V PRO* 5.0 7.9 - - + -
106V GLU 3.6 30.7 - - - +
107V MET* 6.3 0.2 - - - -
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Residues in contact with ASP 97 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93V ALA* 2.8 24.0 - - - +
94V LYS* 3.5 11.4 - - - +
95V MET 3.2 0.2 - - - -
96V LEU* 1.4 77.4 - - - +
98V MET* 1.4 68.6 + - + +
100V LYS* 3.3 26.4 + - - +
101V GLN* 2.9 29.8 + - - +
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Residues in contact with MET 98 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74U TYR* 3.1 36.6 + - + +
77U ASN* 3.7 28.0 - - + +
78U MET* 3.8 24.2 - - + -
81U MET* 5.4 5.8 - - + -
94V LYS* 3.6 19.3 - - + +
95V MET* 3.1 7.7 + - - +
97V ASP* 1.4 83.2 - - + +
99V LEU* 1.4 59.5 + - - +
101V GLN* 3.2 8.7 + - - +
102V THR* 2.9 24.8 + - - -
101W GLN* 3.8 25.1 - - - +
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Residues in contact with LEU 99 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54U PHE* 3.9 29.8 - - + -
58V LEU* 3.9 28.3 - - + -
71V ASP* 6.1 2.0 - - + +
73V PHE* 4.8 8.3 - - + -
95V MET* 2.8 39.2 + - + +
96V LEU* 3.5 16.4 - - + +
98V MET* 1.4 72.2 - - + +
100V LYS* 1.3 56.0 + - - +
102V THR* 3.0 18.7 + - - +
103V GLY 3.2 8.5 + - - -
104V ARG* 3.2 44.1 + - + +
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Residues in contact with LYS 100 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96V LEU* 2.8 23.3 + - + +
97V ASP* 3.3 30.2 + - - +
99V LEU* 1.3 67.9 - - - +
101V GLN* 1.3 64.8 + - - +
103V GLY* 3.3 12.0 + - - -
104V ARG 4.4 0.3 + - - -
105V PRO* 4.1 35.5 - - + +
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Residues in contact with GLN 101 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28U LYS* 5.6 1.9 + - - -
57U PRO* 3.7 26.2 - - + +
71U ASP* 5.7 3.4 - - - +
74U TYR* 3.4 32.6 - - - +
97V ASP 2.9 12.1 + - - +
98V MET* 3.2 14.6 + - - +
100V LYS* 1.3 78.4 - - - +
102V THR* 1.3 59.6 + - - +
103V GLY* 3.1 1.4 + - - -
99W HIS* 6.4 1.8 - - + -
100W ARG 4.2 20.0 - - - +
101W GLN* 3.4 31.4 + - - +
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Residues in contact with THR 102 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26U ILE* 3.5 18.5 - - + +
28U LYS* 4.9 8.2 + - - +
54U PHE* 5.4 2.5 - - + -
55U ALA* 4.3 14.0 + - + +
56U VAL 5.4 0.7 - - - -
57U PRO* 3.8 18.6 - - + +
74U TYR* 2.9 15.8 + - - -
98V MET 2.9 13.7 + - - -
99V LEU* 3.0 14.0 + - + +
101V GLN* 1.3 76.5 - - - +
103V GLY* 1.4 63.6 + - - +
104V ARG* 3.3 39.7 - - - +
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Residues in contact with GLY 103 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25U ARG 3.3 19.9 - - - +
26U ILE* 3.6 13.4 - - - +
28U LYS* 6.0 1.6 - - - -
99V LEU 3.2 1.6 + - - -
100V LYS 3.3 8.7 + - - -
101V GLN 3.1 4.7 - - - -
102V THR* 1.4 82.2 - - - +
104V ARG* 1.3 66.8 + - - +
105V PRO* 3.8 5.2 - - - -
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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