Contacts of the strand formed by residues 64 - 70 (chain C) in PDB entry 6VSU
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 SER 64 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55C VAL* 3.3 12.9 - - - +
61C ALA* 3.3 17.5 - - - +
63C ALA* 1.3 75.6 + - - +
65C THR* 1.3 65.5 + - - +
66C SER 3.3 0.5 + - - -
111C PRO 4.1 5.6 - - - -
112C ARG 2.8 26.3 + - - -
151C PRO* 3.1 8.7 + - - +
152C LEU* 3.1 25.6 - - - +
153C ARG* 2.9 26.1 + - - +
341C SER* 4.1 0.4 - - - -
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Residues in contact with THR 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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64C SER* 1.3 72.4 - - - +
66C SER* 1.3 61.1 + - - +
67C LEU* 4.3 0.9 - - + -
111C PRO 4.6 0.5 - - - +
113C VAL 3.6 5.8 + - - -
114C LEU* 3.2 16.4 + - + -
115C THR* 2.9 25.3 + - - -
153C ARG 3.5 6.7 - - - -
155C LEU* 3.7 30.3 - - + -
337C ALA* 3.4 24.0 + - + -
340C ILE* 3.0 31.5 - - + +
341C SER* 3.1 21.0 + - - +
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Residues in contact with SER 66 (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 SER 3.3 0.2 + - - -
65C THR* 1.3 72.8 - - - +
67C LEU* 1.3 64.7 + - - +
68C LEU* 3.7 0.7 + - - +
115C THR* 2.8 27.2 + - - -
117C VAL* 3.3 25.2 - - - +
146C VAL* 3.9 22.8 - - - +
152C LEU* 3.9 14.9 - - - +
153C ARG 3.1 6.6 + - - -
154C PRO* 3.6 6.2 - - - +
155C LEU 3.1 20.1 + - - -
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Residues in contact with LEU 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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65C THR* 4.3 0.2 - - + -
66C SER* 1.3 73.1 - - - +
68C LEU* 1.3 59.2 + - - +
90C ARG* 4.7 2.9 - - + +
93C ILE* 3.9 27.6 - - + -
114C LEU* 3.7 25.1 - - + -
115C THR 2.8 8.7 + - - +
116C ASP* 3.5 29.0 - - + +
117C VAL* 2.9 33.7 + - - +
155C LEU* 3.2 28.0 - - + +
157C LEU* 3.9 23.8 - - + -
333C VAL* 3.7 20.9 - - + -
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Residues in contact with LEU 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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44C ILE* 4.3 16.8 - - + -
66C SER 4.7 2.2 - - - +
67C LEU* 1.3 73.4 - - - +
69C GLY* 1.3 63.2 - - - +
70C VAL* 4.6 3.8 - - + -
90C ARG* 4.5 0.4 - - - -
117C VAL* 3.8 21.1 - - + -
118C GLY 3.4 8.7 - - - +
120C VAL* 3.8 25.1 - - + -
139C ILE 5.1 0.2 - - - +
142C SER* 4.2 4.9 - - - +
143C VAL* 3.8 44.0 - - + +
146C VAL* 4.3 8.3 - - + -
154C PRO* 5.3 3.8 - - + -
155C LEU 3.0 8.5 + - - +
156C VAL* 3.1 20.8 - - + +
157C LEU* 3.0 20.0 + - - -
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Residues in contact with GLY 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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68C LEU* 1.3 72.8 - - - +
70C VAL* 1.3 65.1 + - - +
71C PRO* 3.6 5.8 - - - -
86C PRO* 4.2 2.0 - - - -
90C ARG* 3.6 5.9 - - - +
118C GLY 3.0 11.9 + - - -
119C ASP* 3.1 18.8 + - - -
120C VAL* 3.0 26.0 + - - +
157C LEU* 3.4 14.1 - - - -
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Residues in contact with VAL 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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68C LEU* 4.3 8.3 - - + +
69C GLY* 1.3 79.1 - - - +
71C PRO* 1.4 53.2 - - - +
72C LEU* 2.5 24.7 + - + -
86C PRO* 4.2 1.2 - - - +
120C VAL* 4.4 11.0 - - + -
122C VAL* 4.2 6.3 - - + -
139C ILE* 3.6 37.2 - - + -
156C VAL* 3.9 18.8 - - + -
157C LEU 2.8 15.3 + - - +
159C GLY* 3.3 17.0 - - - -
163C ILE* 3.4 32.1 - - + -
167C VAL* 5.5 0.2 - - + -
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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