Contacts of the strand formed by residues 61 - 67 (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 HIS 61 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52H LEU* 3.8 22.7 - - + +
56H ALA* 4.0 13.9 - - + +
57H LYS 3.6 20.2 + - - -
59H GLU* 2.9 38.6 + - + -
60H PHE* 1.3 73.6 - - - +
62H ILE* 1.4 60.6 + - - +
79H ALA 3.7 1.0 - - - +
80H THR* 3.2 4.7 - - - +
81H LEU* 2.7 43.6 + - + +
104H LEU* 4.6 2.0 - - + -
106H ALA 3.3 5.8 - - - +
107H GLY* 3.7 8.5 - - - -
108H SER 3.6 3.0 + - - -
109H GLY* 3.1 39.8 + - - -
111H LEU* 3.9 23.2 - - + +
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Residues in contact with ILE 62 (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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52G LEU 3.5 15.5 - - - +
53G GLY* 3.5 6.1 - - - -
54G ASP* 3.4 35.7 - - + +
112G TYR* 4.3 5.6 - - + +
61H HIS* 1.4 77.8 - - - +
63H VAL* 1.3 62.7 + - - +
77H PRO* 4.0 22.9 - - + -
79H ALA 3.3 8.1 - - - +
80H THR* 4.0 12.6 - - + +
104H LEU* 3.4 10.0 - - - +
105H LYS* 3.1 54.6 + - + -
106H ALA* 3.3 17.8 + - + +
111H LEU* 5.1 0.2 - - - -
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Residues in contact with VAL 63 (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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23H LEU* 4.4 5.2 - - + -
50H VAL* 4.3 15.7 - - + -
61H HIS 4.3 0.4 - - - -
62H ILE* 1.3 73.9 - - - +
64H GLU* 1.4 62.8 - - - +
77H PRO* 3.7 2.5 - - - +
78H ILE* 2.9 39.0 + - + +
79H ALA* 3.1 32.6 + - + +
102H PHE* 4.6 6.3 - - + -
103H ARG 3.4 9.9 - - - +
104H LEU* 4.7 0.4 - - + +
111H LEU* 4.0 18.8 - - + +
113H ILE* 4.1 23.3 - - + -
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Residues in contact with GLU 64 (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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63H VAL* 1.4 76.8 - - - +
65H ILE* 1.3 61.7 - - - +
66H VAL* 4.2 3.4 - - + -
75H SER* 3.0 30.9 + - - -
76H VAL 3.5 19.3 - - - +
77H PRO* 3.6 10.0 - - + +
78H ILE* 4.2 0.4 - - - +
102H PHE* 3.5 2.9 - - - -
103H ARG* 2.8 74.5 + - + +
105H LYS* 3.7 37.9 + - + +
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Residues in contact with ILE 65 (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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18G ILE* 3.9 45.7 - - + +
47H LEU* 4.7 0.2 - - + -
64H GLU* 1.3 71.8 - - - +
66H VAL* 1.3 63.1 + - - +
67H ASP* 4.4 0.4 - - - +
74H LYS 3.5 2.1 - - - +
75H SER* 3.7 0.7 - - - -
76H VAL* 2.9 35.4 + - - +
78H ILE* 4.0 27.3 - - + +
94H ILE* 4.4 4.9 - - + -
96H LEU* 3.7 21.5 - - + -
100H VAL* 4.3 20.2 - - + -
101H THR 3.5 8.3 - - - +
102H PHE* 3.8 20.4 - - + -
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Residues in contact with VAL 66 (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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64H GLU* 4.2 3.4 - - + +
65H ILE* 1.3 74.4 - - - +
67H ASP* 1.3 61.0 + - - +
73H GLU* 3.5 31.9 - - + +
74H LYS 3.4 4.7 - - - +
75H SER* 3.5 20.4 - - - +
100H VAL* 4.3 2.1 - - - -
101H THR* 2.7 47.4 + - + +
103H ARG* 3.6 36.8 - - + +
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Residues in contact with ASP 67 (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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17G LEU* 5.0 8.1 - - + +
18G ILE* 3.8 32.7 + - + +
65H ILE* 4.1 1.5 - - - +
66H VAL* 1.3 74.6 - - - +
68H GLN* 1.3 76.1 + - - +
69H GLU* 4.2 7.6 - - + +
73H GLU* 3.6 6.1 - - - -
74H LYS* 3.0 31.3 + - + +
96H LEU* 4.9 2.4 - - - +
97H ASP 5.2 1.9 - - - +
99H PRO* 4.0 13.7 - - - +
100H VAL* 3.6 23.2 - - - +
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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