Contacts of the strand formed by residues 85 - 93 (chain C) in PDB entry 4LML
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 85 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82B ASN* 6.1 2.5 - - + +
83B ALA* 4.7 14.5 - - - +
83C ALA 3.8 2.2 + - - +
84C ARG* 1.3 72.8 - - - +
86C ALA* 1.3 74.9 + - - +
87C ASP* 4.0 7.4 - - - +
104C ARG 4.2 0.2 - - - +
105C PHE* 3.2 3.1 - - - +
106C SER* 2.8 48.7 + - - +
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Residues in contact with ALA 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C ARG* 3.5 33.3 + - - +
85C ASP* 1.3 81.4 + - - +
87C ASP* 1.3 73.9 + - - +
88C VAL* 5.8 1.0 - - - +
103C GLU* 3.8 15.9 - - - +
104C ARG 3.5 4.9 - - - -
105C PHE* 4.0 2.7 - - + -
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Residues in contact with ASP 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B ARG* 6.3 2.5 - - - -
83B ALA* 3.4 27.4 - - - +
85C ASP* 4.0 7.2 - - - +
86C ALA* 1.3 84.1 - - - +
88C VAL* 1.3 64.6 + - - +
89C VAL* 3.2 3.5 + - + +
103C GLU* 3.2 3.3 - - - +
104C ARG* 2.8 42.7 + - + +
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Residues in contact with VAL 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B GLU* 3.9 8.5 - - - +
67C PRO* 4.0 26.9 - - + -
86C ALA 5.8 1.1 - - - +
87C ASP* 1.3 71.7 - - - +
89C VAL* 1.3 64.1 + - - +
90C ASP 4.2 3.6 - - - +
91C ILE* 4.1 18.4 - - + -
101C TYR* 3.5 37.7 - - + +
102C LEU 4.1 5.6 - - - +
103C GLU* 3.9 6.7 - - - +
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Residues in contact with VAL 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B GLU* 3.5 24.7 - - - +
76B ARG* 4.2 20.6 - - - +
132B ARG* 3.8 32.1 - - + -
41C PHE* 3.8 22.9 - - + -
87C ASP* 3.2 4.3 + - + +
88C VAL* 1.3 73.4 - - - +
90C ASP* 1.3 66.7 + - + +
102C LEU* 2.7 27.1 + - + +
103C GLU 4.1 0.2 - - - -
104C ARG* 4.0 17.9 - - + +
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Residues in contact with ASP 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B ARG* 5.3 5.4 - - - +
133B SER 4.8 0.6 - - - +
134B VAL* 3.2 33.1 - - - +
178B ARG* 3.9 11.4 + - - -
64C THR* 3.9 14.6 - - - +
88C VAL* 3.7 2.7 - - - +
89C VAL* 1.3 89.6 - - + +
91C ILE* 1.3 72.3 + - - +
92C SER* 3.4 17.8 + - - -
100C GLN 3.6 2.1 - - - +
102C LEU* 2.9 36.0 + - + +
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Residues in contact with ILE 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C THR* 3.2 11.5 - - - +
65C TYR* 3.2 50.2 + - + +
66C GLU 4.7 0.4 - - - -
67C PRO* 4.1 20.2 - - + -
70C ILE* 4.8 6.7 - - + -
72C ILE* 3.7 19.3 - - + -
88C VAL* 4.1 10.8 - - + -
90C ASP* 1.3 81.9 + - - +
92C SER* 1.3 63.1 + - - +
93C VAL* 4.8 2.7 - - + -
99C VAL* 3.9 25.6 - - + -
100C GLN 3.2 3.4 - - - +
101C TYR* 3.6 30.1 - - + -
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Residues in contact with SER 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B ARG* 3.7 13.7 + - - -
62C VAL* 3.5 23.8 - - - +
63C LYS 3.8 4.0 - - - -
64C THR* 3.7 9.4 + - - -
90C ASP* 3.4 19.3 + - - -
91C ILE* 1.3 72.4 - - - +
93C VAL* 1.3 63.1 + - - +
94C SER* 3.7 0.9 + - - -
98C THR 3.6 0.5 - - - +
100C GLN* 2.9 51.1 + - - +
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Residues in contact with VAL 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C LEU* 3.9 35.7 - - + +
53C PHE* 4.9 4.5 - - + -
62C VAL* 3.9 3.5 - - - -
63C LYS* 2.8 38.6 + - + +
65C TYR* 3.4 30.7 - - + -
70C ILE* 5.0 1.6 - - + -
91C ILE* 4.8 3.1 - - + -
92C SER* 1.3 71.3 - - - +
94C SER* 1.3 76.6 + - - +
97C GLY* 4.3 6.1 - - - -
98C THR 3.2 7.6 - - - +
99C VAL* 3.7 26.7 - - + -
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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