Contacts of the strand formed by residues 64 - 72 (chain C) in PDB entry 2W7U
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 ASN 64 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ILE 3.2 26.5 + - - +
47B PHE* 3.2 32.2 + - - +
48B LYS* 3.7 9.8 - - + +
50C ARG* 4.6 5.6 - - - -
51C VAL 3.3 12.7 - - - +
52C SER* 3.4 10.5 + - - -
63C GLY* 1.3 74.3 - - - -
65C TYR* 1.3 63.4 + - - +
88C SER* 3.4 3.5 - - - -
89C THR* 3.1 35.1 + - - +
90C GLU* 3.1 27.6 + - - +
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Residues in contact with TYR 65 (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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50C ARG* 3.3 7.4 - - - +
51C VAL* 3.0 48.8 + - + +
53C ALA* 4.0 10.5 - - + -
62C GLY 2.6 28.7 + - - -
63C GLY 3.6 15.0 - - - -
64C ASN* 1.3 74.9 - - - +
66C ASP* 1.3 62.4 + - - +
84C VAL* 4.2 13.2 - - + -
85C HIS 3.6 17.9 - - - +
86C GLU 3.5 17.7 - - - -
87C THR 4.1 0.9 - - - -
88C SER* 3.5 28.0 - - - +
92C LEU* 3.7 5.7 - - - +
93C ASN 3.2 19.9 + - - -
94C PHE* 3.4 34.8 - + - -
97C ASN* 4.0 1.8 - - + +
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Residues in contact with ASP 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ARG* 4.4 7.6 + - - -
48C LYS* 4.9 5.5 - - - +
49C ASN 4.8 1.5 - - - +
50C ARG* 2.9 45.7 + - - +
64C ASN 4.4 0.2 + - - -
65C TYR* 1.3 74.1 - - - +
67C VAL* 1.3 64.2 + - - +
84C VAL* 3.4 5.8 - - - -
85C HIS* 3.2 46.8 + - + +
87C THR 5.3 3.2 + - - +
88C SER 6.1 0.2 - - - -
89C THR* 4.3 7.1 - - - +
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Residues in contact with VAL 67 (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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21C PHE* 5.1 1.1 - - + -
44C ASN* 3.4 28.0 - - + +
49C ASN 3.6 13.7 + - - +
51C VAL* 4.4 16.2 - - + -
65C TYR 4.8 0.4 - - - +
66C ASP* 1.3 74.0 - - - +
68C LYS* 1.3 66.5 + - - +
69C ASP* 4.1 11.9 - - - +
70C ILE* 4.2 19.5 - - + -
82C VAL* 3.8 30.7 - - + -
83C HIS 3.8 4.7 - - - +
84C VAL* 4.4 1.8 - - + -
85C HIS* 4.4 4.1 + - - -
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Residues in contact with LYS 68 (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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32C ASN* 5.8 0.2 + - - -
66C ASP 3.6 3.0 + - - -
67C VAL* 1.3 75.1 - - - +
69C ASP* 1.3 75.9 + - + +
83C HIS* 2.7 19.9 + - - +
84C VAL 4.3 8.2 + - - +
85C HIS* 3.7 39.4 - - + +
199C GLU* 2.9 30.3 + - - -
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Residues in contact with ASP 69 (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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67C VAL* 3.8 2.8 - - - +
68C LYS* 1.3 99.5 - - + +
70C ILE* 1.3 71.2 + - - +
71C VAL* 4.1 9.9 - - - +
82C VAL* 3.9 0.2 - - - -
83C HIS* 2.8 65.3 + - - +
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Residues in contact with ILE 70 (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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41C ALA* 3.4 48.7 - - + +
42C LYS* 4.9 9.4 - - + +
44C ASN* 5.1 3.8 - - + -
45C ASP* 6.1 3.8 - - + +
67C VAL* 4.2 21.1 - - + -
69C ASP* 1.3 81.5 - - - +
71C VAL* 1.3 73.0 + - - +
72C GLU* 4.0 11.8 + - + +
80C ALA* 4.5 4.5 - - + -
81C ILE 3.5 8.1 - - - +
82C VAL* 4.5 6.1 - - + -
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Residues in contact with VAL 71 (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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69C ASP* 4.1 14.6 - - - +
70C ILE* 1.3 77.1 - - - +
72C GLU* 1.3 72.1 + - - +
80C ALA* 3.5 0.7 - - - -
81C ILE* 2.8 48.7 + - + +
83C HIS* 4.1 13.0 - - + -
193C PHE* 3.8 17.9 - - + -
197C ASN* 3.8 25.6 - - - +
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Residues in contact with GLU 72 (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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38C LYS* 3.9 33.6 + - + +
42C LYS* 3.3 27.1 - - + +
70C ILE* 4.0 15.0 + - + -
71C VAL* 1.3 77.2 - - - +
73C TYR* 1.3 66.7 + - - +
74C PRO* 3.7 4.4 - - + +
79C LEU 4.1 3.8 - - - -
80C ALA* 4.5 2.7 - - + +
193C PHE* 3.3 16.3 - - - -
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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