Contacts of the strand formed by residues 111 - 117 (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 LEU 111 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22C GLU* 3.5 2.6 - - - -
23C LEU* 2.9 48.7 + - + +
50C VAL* 3.8 25.6 - - + -
51C CYS 3.5 4.3 - - - +
52C LEU* 3.8 20.4 - - + -
61C HIS* 4.1 10.1 - - + -
63C VAL* 3.7 21.5 - - + +
81C LEU* 4.7 2.9 - - + -
104C LEU* 3.7 28.7 - - + -
109C GLY* 3.6 3.3 - - - -
110C PRO* 1.3 74.7 - - - +
112C TYR* 1.3 69.5 + - - +
113C ILE* 3.9 13.0 - - + -
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Residues in contact with TYR 112 (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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21C CYS 3.3 7.4 - - - +
22C GLU* 3.6 40.5 + - + -
49C THR 4.5 0.2 - - - -
50C VAL* 3.2 6.8 - - - +
51C CYS* 2.9 50.3 + - - +
52C LEU 4.3 0.9 - - - -
53C GLY* 3.7 25.6 - - - -
110C PRO* 3.8 18.4 - - + +
111C LEU* 1.3 74.7 - - - +
113C ILE* 1.3 62.9 + - - +
62D ILE* 4.6 5.8 - - + +
77D PRO* 3.6 44.0 - - + +
80D THR* 5.3 0.2 - - - -
105D LYS* 3.1 26.3 + - - -
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Residues in contact with ILE 113 (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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19C TRP* 4.0 7.6 - - + -
20C GLY* 3.1 4.0 - - - -
21C CYS* 3.0 45.6 + - - +
23C LEU* 4.5 5.4 - - + -
47C LEU* 3.9 31.4 - - + -
49C THR 3.5 9.4 - - - +
50C VAL* 4.4 11.7 - - + +
63C VAL* 4.3 14.6 - - + -
78C ILE* 5.9 1.3 - - + -
102C PHE* 3.7 36.8 - - + -
111C LEU* 3.9 12.8 - - + -
112C TYR* 1.3 77.1 - - - +
114C SER* 1.3 64.4 + - - +
76D VAL* 4.8 0.5 - - - +
77D PRO 5.2 0.4 - - - +
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Residues in contact with SER 114 (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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18C ILE* 5.4 1.9 - - - +
19C TRP* 3.3 9.0 - - - -
47C LEU* 3.6 5.2 - - - +
48C ARG* 2.8 26.4 + - - +
49C THR* 2.8 42.2 + - - +
113C ILE* 1.3 79.6 - - - +
115C GLY* 1.3 59.9 + - - +
76D VAL* 3.6 24.0 - - - -
77D PRO 3.8 6.7 - - - -
78D ILE* 4.3 8.0 - - - +
94D ILE* 5.4 0.2 - - - +
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Residues in contact with GLY 115 (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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18C ILE* 3.7 4.6 - - - +
19C TRP* 2.7 46.6 + - - +
45C LEU* 4.4 0.4 - - - -
46C ALA 3.1 13.7 - - - -
47C LEU* 4.2 0.9 - - - -
48C ARG* 3.7 8.5 - - - +
114C SER* 1.3 77.7 + - - +
116C GLN* 1.3 70.2 + - - +
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Residues in contact with GLN 116 (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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16C ASP 4.6 3.4 - - - +
17C LEU* 3.5 28.2 - - - +
18C ILE* 4.2 12.3 - - + -
19C TRP 4.7 0.7 - - - +
45C LEU* 3.6 7.7 - - - +
46C ALA* 2.8 34.1 + - - +
48C ARG* 2.8 43.0 + - + +
115C GLY* 1.3 80.5 - - - +
117C HIS* 1.3 70.0 + - - +
93D GLY 3.4 6.9 - - - +
94D ILE* 3.6 9.7 - - - +
95D GLU* 2.9 25.4 + - - +
96D LEU* 3.7 14.3 - - - +
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Residues in contact with HIS 117 (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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16C ASP* 2.5 44.6 + - - +
17C LEU* 3.4 32.1 + - + +
18C ILE 5.0 0.7 - - - -
19C TRP* 3.8 31.4 - + + +
32C PHE* 4.2 29.2 - + - -
43C HIS* 4.5 18.2 - + + -
44C GLN 3.6 7.6 - - - +
45C LEU* 4.7 3.4 - - + -
116C GLN* 1.3 74.3 - - - +
118C VAL* 1.3 59.0 - - - +
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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