Contacts of the strand formed by residues 45 - 52 (chain H) in PDB entry 2VTX
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 LEU 45 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H TRP* 3.6 50.3 - - + -
32H PHE* 4.0 32.9 - - + -
43H HIS 4.4 0.4 + - - -
44H GLN* 1.3 71.3 - - - +
46H ALA* 1.3 65.0 + - - +
47H LEU* 4.0 13.5 + - + -
94H ILE 3.8 0.9 - - - +
95H GLU* 3.4 1.8 - - - -
96H LEU* 2.8 43.2 + - + +
98H PRO* 4.8 1.2 - - - +
100H VAL* 5.1 2.0 - - + -
102H PHE* 4.2 12.3 - - + -
115H GLY* 3.9 2.9 - - - -
116H GLN 3.2 34.3 - - - +
117H HIS* 4.1 4.7 - - - +
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Residues in contact with ALA 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44H GLN 3.8 1.7 + - - +
45H LEU* 1.3 72.6 - - - +
47H LEU* 1.3 66.1 + - - +
48H ARG* 3.8 27.6 - - - +
94H ILE 3.2 6.3 - - - +
95H GLU* 3.8 23.3 - - + +
115H GLY* 3.1 2.2 - - - -
116H GLN* 2.9 40.6 + - + +
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Residues in contact with LEU 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H TRP* 4.2 1.3 - - + -
45H LEU* 4.0 18.4 - - + +
46H ALA* 1.3 76.3 - - - +
48H ARG* 1.3 68.3 + - - +
78H ILE* 3.6 30.3 - - + -
91H MET* 3.9 28.0 - - + +
92H VAL* 5.5 0.2 - - - -
93H GLY 5.6 0.7 + - - -
94H ILE* 3.0 38.8 + - + +
96H LEU* 4.5 5.6 - - + -
102H PHE* 3.8 27.8 - - + -
113H ILE* 3.7 27.1 - - + -
114H SER 3.6 3.8 - - - +
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Residues in contact with ARG 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16H ASP* 3.9 11.1 + - - -
46H ALA* 3.8 32.1 - - - +
47H LEU* 1.3 82.7 + - - +
49H THR* 1.3 68.8 + - + +
90H THR* 3.7 4.7 - - - +
91H MET* 3.0 29.2 + - - +
92H VAL* 6.4 0.2 - - - +
93H GLY 5.9 3.4 - - - +
95H GLU* 5.7 1.0 + - - -
114H SER* 2.7 21.3 + - - +
115H GLY* 4.1 11.0 - - - +
116H GLN* 3.0 28.4 + - + +
92I VAL 3.5 20.4 + - - +
93I GLY* 2.8 31.7 + - - -
94I ILE* 3.7 22.9 - - + -
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Residues in contact with THR 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47H LEU 4.0 0.2 - - - -
48H ARG* 1.3 93.3 - - + +
50H VAL* 1.3 73.7 + - - +
51H CYS* 4.9 1.2 + - - -
88H MET* 4.4 9.0 - - + -
89H ALA 3.3 13.5 - - - +
90H THR* 4.6 2.9 - - + +
91H MET* 4.1 3.2 - - - +
112H TYR 4.6 0.2 - - - -
113H ILE* 3.5 2.8 - - - +
114H SER* 2.8 44.6 + - - +
77I PRO 4.3 0.9 + - - -
78I ILE* 3.1 37.9 + - + +
91I MET* 4.4 17.3 - - + -
92I VAL 6.3 0.2 - - - +
94I ILE* 4.6 3.1 - - + -
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Residues in contact with VAL 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47H LEU* 5.8 0.2 - - + -
49H THR* 1.3 80.6 - - - +
51H CYS* 1.3 62.3 + - - +
63H VAL* 4.3 10.1 - - + -
78H ILE* 5.2 4.5 - - + -
79H ALA* 4.2 21.1 - - + -
81H LEU* 3.9 17.0 - - + -
88H MET* 3.0 5.4 - - - +
89H ALA* 2.8 35.5 + - + +
91H MET* 4.2 22.7 - - + -
111H LEU* 4.2 17.3 - - + -
112H TYR 3.4 9.6 - - - +
113H ILE* 4.4 15.5 - - + -
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Residues in contact with CYS 51 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49H THR* 4.9 1.3 - - - -
50H VAL* 1.3 76.4 - - - +
52H LEU* 1.3 61.1 + - - +
81H LEU* 4.2 1.3 - - - -
87H PRO 3.6 5.6 - - - -
88H MET* 3.6 13.9 - - + +
111H LEU* 3.6 2.1 - - - +
112H TYR* 2.7 56.4 + - - +
62I ILE* 5.4 0.2 - - - -
77I PRO* 4.2 10.5 - - - -
78I ILE* 4.2 6.3 - - - -
79I ALA* 4.0 20.2 - - - +
80I THR* 3.6 22.9 - - - +
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Residues in contact with LEU 52 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51H CYS* 1.3 73.9 - - - +
53H GLY* 1.3 69.8 + - - +
56H ALA* 4.3 2.5 - - + -
61H HIS* 3.8 33.4 - - + +
81H LEU* 4.1 9.2 - - + -
82H LYS* 3.8 13.5 - - - +
83H PRO* 3.5 46.2 - - + -
87H PRO* 3.1 21.8 + - + +
110H PRO 3.6 5.4 - - - +
111H LEU* 3.9 25.6 - - + -
112H TYR* 4.3 3.8 - - - -
62I ILE* 3.7 1.6 - - - +
80I THR* 2.7 28.9 + - + +
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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