Contacts of the strand formed by residues 61 - 66 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52K LEU* 4.1 22.4 - - + +
56K ALA* 4.3 6.4 - - + +
57K LYS 3.5 19.5 - - - -
59K GLU* 3.0 29.3 + - + -
60K PHE* 1.3 70.3 - - - +
62K ILE* 1.3 61.5 + - - +
79K ALA 3.7 1.0 - - - +
80K THR* 3.3 2.9 - - - -
81K LEU* 2.8 33.7 + - - +
83K PRO* 4.3 5.4 - - + -
104K LEU* 4.4 6.7 - - + -
106K ALA 3.0 7.4 - - - +
107K GLY* 3.9 2.5 - - - -
108K SER* 3.6 10.5 + - - -
109K GLY* 3.1 39.4 + - - -
111K LEU* 3.9 19.1 - - + +
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Residues in contact with ILE 62 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52J LEU 4.0 3.8 - - - +
53J GLY* 4.0 11.2 - - - -
54J ASP* 3.6 40.4 - - + +
112J TYR* 4.7 7.0 - - + +
61K HIS* 1.3 77.7 - - - +
63K VAL* 1.3 64.9 + - - +
64K GLU* 4.1 0.4 - - + -
77K PRO* 3.8 27.8 - - + -
79K ALA 3.2 8.3 - - - +
80K THR* 4.0 16.6 - - + +
104K LEU* 3.4 10.5 - - - +
105K LYS* 3.2 41.3 + - + -
106K ALA* 2.9 23.5 + - + +
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Residues in contact with VAL 63 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23K LEU* 4.0 12.6 - - + -
50K VAL* 4.4 13.5 - - + -
62K ILE* 1.3 74.5 - - - +
64K GLU* 1.3 65.7 + - - +
77K PRO* 3.6 1.2 - - - +
78K ILE* 2.8 37.5 + - + +
79K ALA* 2.9 35.5 + - + +
102K PHE* 4.7 4.5 - - + -
103K ARG 3.5 7.4 - - - +
111K LEU* 4.3 15.0 - - + -
113K ILE* 3.5 31.4 - - + -
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Residues in contact with GLU 64 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63K VAL* 1.3 75.5 - - - +
65K ILE* 1.3 63.1 + - - +
66K VAL 4.1 0.3 + - - -
75K SER* 3.1 29.7 - - - +
76K VAL 3.1 19.7 - - - +
77K PRO* 3.7 9.5 - - + +
78K ILE* 4.3 1.1 - - - +
101K THR 3.9 0.2 - - - +
102K PHE* 3.5 5.7 - - - +
103K ARG* 2.8 78.5 + - + +
105K LYS* 3.6 42.9 + - + +
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Residues in contact with ILE 65 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18J ILE* 3.1 47.1 - - + -
64K GLU* 1.3 74.3 - - - +
66K VAL* 1.3 73.8 + - - +
67K ASP* 4.3 2.8 + - - +
74K LYS 4.2 1.9 - - - +
75K SER* 3.5 2.2 - - - -
76K VAL* 2.7 41.3 + - - +
78K ILE* 3.6 28.2 - - + +
94K ILE* 4.8 3.6 - - + -
96K LEU* 4.2 19.7 - - + -
100K VAL* 4.0 19.5 - - + -
101K THR 3.5 7.2 - - - +
102K PHE* 3.7 22.4 - - + -
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Residues in contact with VAL 66 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64K GLU* 4.8 0.7 - - + +
65K ILE* 1.3 78.3 - - - +
67K ASP* 1.3 57.3 + - + +
73K GLU* 3.8 31.2 - - + -
75K SER* 3.7 21.3 - - - +
100K VAL* 5.1 1.7 - - - +
101K THR* 3.2 43.2 + - + +
103K ARG* 4.1 36.8 - - + +
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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