Contacts of the strand formed by residues 101 - 108 (chain C) in PDB entry 2VM8
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 THR 101 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69C GLY 3.4 9.4 - - - +
71C ASP* 3.8 20.4 - - + -
96C ALA* 3.2 29.0 + - + +
97C LEU* 3.3 25.3 + - - +
99C GLY 4.6 0.9 + - - -
100C GLY* 1.3 75.2 - - - +
102C THR* 1.3 59.7 + - - +
103C MET 3.2 24.6 + - - +
104C ILE* 4.3 0.7 - - + -
133C CYS* 4.8 0.7 - - - -
358C THR* 4.3 8.7 + - - +
361C ARG* 3.1 21.7 + - - +
362C MET* 3.6 11.4 - - - +
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Residues in contact with THR 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C GLY* 3.2 31.7 - - - -
69C GLY 3.1 4.9 + - - +
97C LEU* 3.9 11.4 - - + -
100C GLY 4.5 1.6 - - - +
101C THR* 1.3 74.2 - - - +
103C MET* 1.3 60.3 + - - +
133C CYS* 3.1 22.2 - - - +
134C ASP* 3.7 6.6 + - - +
408C ASP* 3.5 28.4 + - - +
409C LEU 4.6 1.1 - - - +
410C VAL* 4.7 0.2 - - + -
446C VAL* 3.5 32.3 - - + -
447C ILE 3.5 14.4 - - - +
448C SER* 4.2 5.4 + - - -
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Residues in contact with MET 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C GLY 3.3 3.0 + - - +
70C ILE* 4.1 25.4 - - + -
71C ASP 3.2 11.7 + - - -
101C THR* 3.2 20.9 + - - +
102C THR* 1.3 80.8 - - - +
104C ILE* 1.3 66.5 + - - +
105C ILE* 4.9 2.2 - - + -
133C CYS* 4.1 0.6 - - - -
134C ASP* 3.2 21.8 - - + +
135C TYR 4.1 4.7 - - - -
136C SER* 4.0 19.3 - - - -
394C LEU* 4.0 24.5 - - + -
398C LYS* 3.8 29.8 - - + -
408C ASP* 5.0 5.4 - - - +
469C ILE* 3.6 32.8 - - + -
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Residues in contact with ILE 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C ASP* 3.7 6.7 - - + -
74C THR* 3.3 37.9 - - + +
76C PHE* 4.0 17.9 - - + -
89C PHE* 4.3 7.9 - - + -
93C THR* 3.9 16.2 - - + -
96C ALA* 4.1 21.5 - - + -
101C THR* 4.3 3.8 - - + -
103C MET* 1.3 81.6 - - - +
105C ILE* 1.3 65.3 + - - +
106C ASP* 4.1 14.6 - - + +
133C CYS* 4.1 13.0 - - - -
134C ASP 3.2 2.2 + - - -
135C TYR* 3.1 28.6 - - + -
136C SER 3.0 21.2 + - - +
358C THR* 4.8 0.2 - - - +
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Residues in contact with ILE 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C ILE* 3.9 26.2 - - + -
71C ASP 3.2 5.9 + - - -
72C VAL* 3.5 18.5 - - - +
73C HIS* 3.6 0.3 - - - -
74C THR* 3.2 20.4 + - - -
103C MET* 4.9 3.6 - - + -
104C ILE* 1.3 78.8 - - - +
106C ASP* 1.3 61.9 + - - +
136C SER* 3.2 26.2 - - - +
137C LEU 3.9 1.6 - - - +
138C HIS* 3.1 35.7 - - + +
392C PHE* 3.8 36.1 - - + -
394C LEU* 4.7 11.2 - - + -
471C ARG* 4.6 5.6 - - - +
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Residues in contact with ASP 106 (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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74C THR* 2.9 29.9 + - - +
75C ARG* 3.5 8.8 - - - -
76C PHE* 2.9 31.1 + - - +
78C MET* 6.0 0.2 - - - +
89C PHE* 3.8 18.1 - - + -
104C ILE* 4.1 4.0 - - + -
105C ILE* 1.3 72.1 - - - +
107C HIS* 1.3 73.0 + - - +
123C TRP* 3.4 16.5 + - - -
136C SER 3.0 7.9 + - - +
137C LEU* 3.5 19.2 - - + -
138C HIS* 2.8 30.7 + - - -
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Residues in contact with HIS 107 (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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72C VAL 4.3 0.6 + - - -
73C HIS* 3.7 38.9 + + - -
74C THR 3.8 3.8 - - - -
75C ARG* 3.6 32.9 + - + +
78C MET* 5.9 0.3 - - - +
105C ILE 4.4 1.3 - - - -
106C ASP* 1.3 85.8 + - - +
108C VAL* 1.3 63.7 + - - +
109C VAL* 3.5 4.0 + - - +
123C TRP* 3.1 25.1 + - - -
138C HIS* 3.0 30.7 + + + +
140C ASP* 2.8 21.4 + - - +
165C LEU* 4.0 11.9 - - + -
196C GLN* 3.1 29.0 + - - -
253C THR* 5.0 0.9 - - + +
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Residues in contact with VAL 108 (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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107C HIS* 1.3 68.8 - - - +
109C VAL* 1.3 61.8 + - - +
110C PRO* 3.2 9.0 - - + +
116C LEU 4.6 0.2 - - - +
119C ALA* 3.5 33.0 - - + -
120C PHE* 3.7 17.0 - - + +
123C TRP* 3.9 28.9 - - + -
137C LEU* 4.1 13.5 - - + -
138C HIS 2.8 21.1 + - - +
139C VAL* 3.9 24.2 - - + -
140C ASP* 2.8 33.6 + - - +
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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