Contacts of the strand formed by residues 111 - 118 (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 LEU 111 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21K CYS 3.5 1.0 - - - +
22K GLU* 3.3 4.0 - - - -
23K LEU* 2.8 51.4 + - + +
50K VAL* 3.6 30.3 - - + -
51K CYS 3.7 3.8 - - - +
52K LEU* 4.1 14.6 - - + -
61K HIS* 3.9 21.3 - - + +
62K ILE 5.1 0.2 - - - -
63K VAL* 4.3 11.9 - - + -
79K ALA 5.9 0.2 - - - +
81K LEU* 4.5 3.6 - - + -
104K LEU* 3.4 28.3 - - + -
109K GLY* 4.5 2.7 - - - -
110K PRO* 1.3 75.6 - - - +
112K TYR* 1.3 65.7 + - - +
113K ILE* 3.9 15.5 - - + -
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Residues in contact with TYR 112 (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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62G ILE* 4.8 8.1 - - + +
77G PRO* 3.7 51.4 - - + +
105G LYS* 3.8 18.9 + - - +
21K CYS 3.3 5.6 - - - +
22K GLU* 3.3 32.1 + - + -
50K VAL* 3.2 10.4 - - - +
51K CYS* 2.9 50.8 + - - +
52K LEU 4.1 2.7 - - - -
53K GLY* 3.6 28.7 - - - -
110K PRO* 4.0 16.4 - - + +
111K LEU* 1.3 75.5 - - - +
113K ILE* 1.3 63.1 + - - +
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Residues in contact with ILE 113 (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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76G VAL* 4.5 1.4 - - - +
77G PRO* 5.0 0.4 - - - +
19K TRP* 4.1 8.3 - - + -
20K GLY* 3.1 22.8 - - - -
21K CYS* 2.9 23.9 + - - +
23K LEU* 4.2 7.0 - - + -
47K LEU* 4.0 27.6 - - + -
49K THR 3.5 6.1 - - - +
50K VAL* 4.4 9.0 - - + +
63K VAL* 3.5 30.3 - - + -
102K PHE* 3.6 31.0 - - + -
111K LEU* 3.9 9.6 - - + -
112K TYR* 1.3 82.3 - - - +
114K SER* 1.3 73.1 + - - +
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Residues in contact with SER 114 (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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76G VAL* 3.7 22.0 - - - -
77G PRO 3.8 7.2 - - - -
78G ILE* 4.2 8.9 - - - +
18K ILE* 4.5 2.4 - - - +
19K TRP* 3.5 8.5 - - - -
20K GLY* 4.2 0.4 - - - -
47K LEU* 3.5 5.5 - - - +
48K ARG* 2.8 32.2 + - - +
49K THR* 2.7 41.7 + - - +
113K ILE* 1.3 81.3 - - - +
115K GLY* 1.3 55.6 + - - +
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Residues in contact with GLY 115 (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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18K ILE* 2.9 12.4 - - - +
19K TRP* 2.8 42.6 + - - -
45K LEU* 4.4 5.4 - - - -
46K ALA 3.1 13.9 - - - -
47K LEU* 4.2 1.1 - - - -
48K ARG* 3.9 5.8 - - - -
114K SER* 1.3 77.5 + - - +
116K GLN* 1.3 65.3 + - - -
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Residues in contact with GLN 116 (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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93G GLY 3.3 7.6 - - - +
94G ILE* 3.6 12.3 - - - -
95G GLU* 3.0 29.3 + - - +
96G LEU* 4.0 14.5 - - - +
17K LEU* 3.5 24.9 - - + +
18K ILE* 4.2 12.9 - - + +
19K TRP* 4.6 0.4 - - - +
44K GLN 3.7 0.3 - - - +
45K LEU* 3.7 6.9 - - - +
46K ALA* 2.9 33.3 + - - +
48K ARG* 2.9 41.6 + - + +
115K GLY* 1.3 80.7 - - - +
117K HIS* 1.3 68.6 + - - +
118K VAL* 3.8 1.0 + - + +
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Residues in contact with HIS 117 (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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17K LEU* 3.3 55.2 + - + +
18K ILE 5.3 0.7 - - - -
19K TRP* 4.1 17.6 - + + +
32K PHE* 3.2 41.6 - + - -
34K VAL* 4.8 8.5 - - + +
43K HIS* 4.6 20.4 - + + -
44K GLN 3.4 9.9 - - - +
45K LEU* 4.4 4.9 - - + -
116K GLN* 1.3 77.3 - - - +
118K VAL* 1.3 61.0 + - - +
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Residues in contact with VAL 118 (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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43K HIS* 3.5 13.0 - - - +
44K GLN* 3.0 56.2 + - + +
46K ALA* 4.0 17.0 - - + -
48K ARG* 5.1 10.8 - - - +
95K GLU* 3.6 25.8 - - - +
116K GLN 4.2 3.4 - - - +
117K HIS* 1.3 76.3 - - - +
119K ALA* 1.3 70.5 + - + +
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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