Contacts of the strand formed by residues 61 - 66 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C LEU* 3.7 32.0 - - + +
56C ALA* 3.9 12.8 - - + +
57C LYS 3.5 25.6 - - - -
59C GLU* 2.9 31.8 + - + -
60C PHE* 1.3 73.2 - - - +
62C ILE* 1.3 63.1 + - - +
63C VAL 4.3 0.2 - - - -
79C ALA 3.7 0.7 - - - +
80C THR* 3.2 5.4 - - - +
81C LEU* 2.7 36.9 + - + +
104C LEU* 4.4 6.7 - - + -
106C ALA 3.4 5.4 - - - +
107C GLY* 4.1 2.2 - - - -
108C SER 3.8 6.8 + - - -
109C GLY* 3.1 37.1 + - - -
111C LEU* 4.1 10.3 - - + +
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Residues in contact with ILE 62 (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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52B LEU 3.8 12.3 - - - +
53B GLY* 3.8 5.2 - - - -
54B ASP* 3.6 37.0 - - + +
112B TYR* 4.7 4.9 - - + -
61C HIS* 1.3 81.0 - - - +
63C VAL* 1.3 63.9 + - - +
77C PRO* 4.0 26.2 - - + -
79C ALA 3.3 11.0 - - - +
80C THR* 4.0 13.0 - - + +
104C LEU* 3.4 8.8 - - - +
105C LYS* 2.8 45.2 + - + -
106C ALA* 3.2 24.4 + - + +
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Residues in contact with VAL 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C LEU* 4.4 10.3 - - + -
50C VAL* 4.2 11.9 - - + -
62C ILE* 1.3 76.6 - - - +
64C GLU* 1.3 71.1 + - - +
77C PRO* 3.8 1.2 - - - +
78C ILE* 3.0 32.5 + - + +
79C ALA* 3.1 27.9 + - + +
102C PHE* 4.6 4.3 - - + -
103C ARG 3.2 11.4 - - - +
104C LEU* 4.8 0.2 - - - -
111C LEU* 3.7 29.2 - - + -
113C ILE* 4.3 20.0 - - + -
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Residues in contact with GLU 64 (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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63C VAL* 1.3 75.5 - - - +
65C ILE* 1.3 64.6 + - - +
66C VAL* 4.7 0.2 - - + -
75C SER* 3.2 30.1 + - - +
76C VAL 3.2 22.0 - - - +
77C PRO* 3.5 11.2 - - + +
78C ILE* 4.3 1.3 - - - +
102C PHE* 3.5 5.2 - - - -
103C ARG* 2.8 65.8 + - + +
105C LYS* 3.4 41.4 + - + +
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Residues in contact with ILE 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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18B ILE* 3.9 40.4 - - + +
64C GLU* 1.3 76.6 - - - +
66C VAL* 1.4 60.7 + - - +
67C ASP* 4.3 4.0 - - - +
74C LYS 3.9 1.0 - - - +
75C SER* 3.6 1.7 + - - -
76C VAL* 2.9 35.0 + - - +
78C ILE* 3.8 33.9 - - + -
94C ILE* 4.7 4.7 - - + -
96C LEU* 4.0 20.6 - - + -
100C VAL* 4.1 25.6 - - + -
101C THR 3.6 5.2 - - - +
102C PHE* 3.8 19.3 - - + -
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Residues in contact with VAL 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 GLU* 4.4 0.9 - - + +
65C ILE* 1.4 77.0 - - - +
67C ASP* 1.3 65.2 + - - +
74C LYS 3.5 14.6 - - - +
75C SER* 3.9 11.2 - - - +
100C VAL* 4.3 0.2 - - - -
101C THR* 3.1 45.6 + - + +
103C ARG* 3.8 48.7 - - + +
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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