Contacts of the strand formed by residues 95 - 106 (chain C) in PDB entry 2VKM
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 VAL 95 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C ASP 3.5 0.5 - - - +
84C LEU* 3.4 5.0 - - - -
85C VAL* 2.8 40.2 + - - +
93C VAL* 4.3 3.4 - - + -
94C THR* 1.3 79.5 - - - +
96C ARG* 1.3 60.2 + - - +
97C ALA* 3.6 8.6 + - + -
136C PHE* 3.6 33.7 - - + -
139C SER* 4.9 0.4 - - - -
140C LEU* 3.7 37.0 - - + +
143C GLN* 3.3 18.6 - - + +
144C THR* 3.7 18.4 - - + -
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Residues in contact with ARG 96 (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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59C THR* 2.9 45.4 + - - +
61C ARG* 3.3 46.9 - - - +
82C THR* 2.8 48.8 + - + +
83C ASP* 3.3 7.3 - - - +
84C LEU* 4.0 23.6 - - + +
95C VAL* 1.3 70.2 - - - +
97C ALA* 1.3 60.3 + - - +
139C SER* 4.0 4.2 + - - -
143C GLN* 2.9 32.4 + - - +
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Residues in contact with ALA 97 (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 PHE* 4.7 0.7 - - + -
82C THR* 3.1 24.4 - - - -
83C ASP 3.0 12.0 + - - -
85C VAL* 4.2 13.0 - - + -
95C VAL* 3.6 4.2 + - + -
96C ARG* 1.3 75.9 - - - +
98C ASN* 1.3 71.9 + - - +
99C ILE* 3.6 2.9 + - - +
136C PHE* 3.7 34.1 - - + -
139C SER* 4.4 11.4 - - - +
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Residues in contact with ASN 98 (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 PHE* 3.4 21.9 - - - +
63C LEU* 4.0 7.8 - - - +
80C LEU* 5.4 0.9 - - + -
81C GLY 3.5 5.2 - - - +
82C THR* 3.5 17.4 - - - +
97C ALA* 1.3 77.1 - - - +
99C ILE* 1.3 63.7 + - - +
133C LEU* 3.6 35.9 - - + +
134C GLU* 2.9 51.0 + - - +
136C PHE* 5.7 1.1 - - - +
139C SER* 5.0 1.4 + - - -
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Residues in contact with ILE 99 (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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20C VAL* 4.0 24.0 - - + -
38C PHE* 3.7 17.7 - - + +
40C VAL* 3.8 34.1 - - + -
52C TYR* 4.0 18.3 - - + +
60C TYR* 6.1 0.2 - - - -
79C GLU 3.6 0.5 - - - +
80C LEU* 3.8 3.5 - - - +
81C GLY 2.9 33.0 + - - +
82C THR* 5.0 0.2 - - - -
83C ASP* 3.6 30.7 - - + +
85C VAL* 4.0 9.0 - - + -
97C ALA 3.6 8.3 - - - +
98C ASN* 1.3 81.3 - - - +
100C ALA* 1.3 65.3 + - - +
101C ALA* 3.6 2.9 + - - +
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Residues in contact with ALA 100 (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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37C ASN* 5.2 3.6 - - - +
38C PHE 3.0 16.0 + - - +
39C ALA* 3.3 1.5 - - + +
40C VAL 3.1 24.3 + - - -
67C VAL* 4.0 11.9 - - + -
76C TRP* 3.5 36.8 - - + -
79C GLU 3.6 5.4 - - - -
80C LEU* 4.2 10.0 - - + +
99C ILE* 1.3 73.1 - - - +
101C ALA* 1.3 59.3 + - - +
102C ILE 3.3 3.2 + - - -
133C LEU* 6.1 0.2 - - + -
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Residues in contact with ALA 101 (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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40C VAL* 3.8 8.5 - - - -
42C ALA* 3.4 20.4 - - + -
52C TYR* 4.4 5.6 - - + -
54C ARG* 3.6 33.7 - - - +
78C GLY* 3.0 3.6 - - - -
79C GLU 2.8 38.9 + - - +
99C ILE 3.6 2.2 + - - +
100C ALA* 1.3 69.7 - - - +
102C ILE* 1.3 61.4 + - - +
103C THR* 3.3 4.7 + - - +
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Residues in contact with ILE 102 (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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39C ALA* 3.8 22.7 - - + -
40C VAL 2.8 23.9 + - - +
41C GLY* 4.0 3.9 - - - -
42C ALA* 2.9 27.5 + - - -
43C ALA* 3.8 3.1 + - - +
76C TRP* 3.6 41.7 - - + -
77C GLU 3.5 5.4 - - - +
78C GLY* 4.0 0.7 - - - -
100C ALA 3.3 0.2 + - - -
101C ALA* 1.3 69.3 - - - +
103C THR* 1.3 62.1 + - - +
104C GLU 3.6 24.9 - - - +
105C SER* 4.2 6.5 - - - +
108C PHE* 3.9 11.4 - - + -
109C PHE* 3.8 28.5 - - + -
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Residues in contact with THR 103 (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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42C ALA* 5.1 2.9 - - + +
43C ALA* 4.5 19.9 - - + +
54C ARG* 4.2 11.2 - - - +
77C GLU* 2.9 12.3 + - - +
78C GLY* 3.9 6.2 - - - -
79C GLU* 4.0 29.5 + - + +
101C ALA 3.3 13.7 + - - +
102C ILE* 1.3 75.7 - - - +
104C GLU* 1.3 76.7 + - - +
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Residues in contact with GLU 104 (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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76C TRP* 3.3 2.8 - - - +
77C GLU* 2.8 53.5 + - + +
102C ILE* 3.6 2.8 - - - +
103C THR* 1.3 90.7 + - - +
105C SER* 1.3 75.6 + - - +
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Residues in contact with SER 105 (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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45C HIS* 3.6 21.0 + - - -
75C LYS 3.4 11.9 - - - -
76C TRP* 3.9 10.3 - - - +
102C ILE* 4.2 7.2 - - - -
104C GLU* 1.3 88.0 + - - +
106C ASP* 1.3 63.2 + - - +
107C LYS 4.3 0.4 + - - -
108C PHE* 4.2 12.6 + - - +
109C PHE* 3.6 21.9 + - - -
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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 GLY* 3.3 1.4 - - - -
75C LYS* 2.8 61.6 + - + +
105C SER* 1.3 76.0 - - - +
107C LYS* 1.3 94.5 + - - +
108C PHE 3.2 0.7 - - - -
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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