Contacts of the helix formed by residues 19 - 26 (chain B) in PDB entry 2XVA
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 19 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17B ARG 3.5 2.6 + - - -
18B THR* 1.3 72.0 - - - +
20B SER* 1.3 66.1 + - - +
21B GLU* 3.1 44.0 + - + +
22B VAL* 3.0 21.2 + - + +
23B LEU* 3.2 10.4 + - - +
43B ARG* 3.5 31.4 - - - +
44B ASN* 2.9 28.0 + - - +
102B THR* 4.0 15.8 - - + +
103B VAL* 4.5 9.5 - - + +
133B VAL* 4.1 25.7 - - + +
1199B ZN 3.6 23.7 - - - -
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Residues in contact with SER 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ARG* 3.9 22.9 - - - +
18B THR 3.2 3.2 + - - -
19B HIS* 1.3 74.1 + - - +
21B GLU* 1.3 68.6 + - - +
23B LEU* 3.2 9.4 + - - +
24B GLU* 2.9 27.7 + - - +
1199B ZN 3.3 21.4 - - - -
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Residues in contact with GLU 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B HIS* 3.1 25.9 + - + +
20B SER* 1.3 80.8 + - - +
22B VAL* 1.3 61.3 + - - +
24B GLU* 3.7 7.2 - - - +
25B ALA* 2.8 28.8 + - - +
131B LEU* 3.9 24.5 - - + +
133B VAL* 4.1 3.8 - - + -
167B LYS* 2.7 41.3 + - - +
169B ASN* 5.1 1.7 + - - -
191B THR* 3.6 28.8 + - + +
193B LEU* 5.6 0.5 - - - +
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Residues in contact with VAL 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B THR* 4.0 15.5 - - + -
19B HIS* 3.0 16.9 + - + +
21B GLU* 1.3 75.1 - - - +
23B LEU* 1.3 64.0 + - - +
25B ALA* 3.1 13.0 + - - +
26B VAL* 3.1 16.4 + - + +
44B ASN* 3.7 27.6 - - + +
47B TYR* 4.7 3.1 - - + -
48B LEU* 4.0 34.8 - - + -
98B PHE* 5.4 2.7 - - + -
100B LEU* 3.8 12.6 - - + -
102B THR* 4.2 2.7 - - + -
131B LEU* 3.8 20.4 - - + -
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Residues in contact with LEU 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B GLU* 3.8 24.5 - - + +
17B ARG* 3.6 39.3 - - - +
18B THR* 3.9 18.4 - - + +
19B HIS 3.2 8.5 + - - +
20B SER* 3.5 7.4 - - - +
22B VAL* 1.3 74.4 - - - +
24B GLU* 1.3 61.6 + - - +
26B VAL* 3.3 22.3 - - - +
27B LYS* 4.2 6.1 + - - +
47B TYR* 3.5 42.0 - - + +
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Residues in contact with GLU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B SER 2.9 16.2 + - - +
21B GLU* 3.7 8.0 - - - +
23B LEU* 1.3 76.3 - - - +
25B ALA* 1.3 62.6 + - - +
27B LYS* 3.1 45.9 + - + +
28B VAL* 4.4 2.1 + - - +
167B LYS* 2.6 40.3 + - - +
193B LEU* 5.3 3.4 - - + +
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Residues in contact with ALA 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B GLU 2.8 22.7 + - - +
22B VAL* 3.1 7.4 + - - +
24B GLU* 1.3 73.6 - - - +
26B VAL* 1.3 56.6 + - - +
27B LYS 3.0 0.2 - - - -
28B VAL* 3.0 6.8 + - - +
29B VAL* 2.9 31.4 + - + +
98B PHE* 3.9 28.7 - - + -
131B LEU* 4.6 2.2 - - + -
193B LEU* 4.0 25.7 - - + +
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Residues in contact with VAL 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0B ALA* 5.1 9.9 - - + -
22B VAL 3.1 13.4 + - - +
23B LEU* 3.3 19.3 - - - +
25B ALA* 1.3 75.6 - - + +
27B LYS* 1.3 63.0 + - + +
28B VAL 3.2 1.5 + - - -
29B VAL* 4.1 8.0 - - - +
47B TYR* 4.2 25.8 - - + +
48B LEU* 3.6 28.5 - - + -
53B TYR* 3.8 26.6 + - + +
98B PHE* 5.9 1.3 - - + -
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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