Contacts of the helix formed by residues 18 - 26 (chain B) in PDB entry 2H1O
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 ASN 18 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11B GLU* 2.9 20.5 + - - +
16B GLN 3.3 2.8 + - - +
17B PRO* 1.3 69.6 - - - +
19B GLU* 1.3 61.4 + - - +
20B ARG* 2.6 39.9 + - - +
21B VAL* 2.8 26.7 + - + +
22B VAL* 3.2 13.4 + - - +
137B TRP* 3.0 38.7 + - - +
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Residues in contact with GLU 19 (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 PRO* 3.9 11.4 - - + +
18B ASN* 1.3 71.5 + - - +
20B ARG* 1.3 58.0 + - - +
21B VAL 3.3 0.2 - - - -
22B VAL* 3.8 11.5 - - + +
23B ALA* 3.0 28.8 + - - +
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Residues in contact with ARG 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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18B ASN* 2.6 22.7 + - - +
19B GLU* 1.3 74.2 - - - +
21B VAL* 1.3 54.1 + - - -
23B ALA* 3.4 22.9 + - - +
24B TRP* 3.0 28.1 + - - +
136B PRO 3.6 8.5 - - - +
137B TRP 3.9 11.7 - - - +
138B HIS 3.4 27.4 - - - +
139B LEU* 4.1 28.8 - - + +
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Residues in contact with VAL 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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8B VAL* 4.5 6.3 - - + +
11B GLU* 4.0 24.0 - - + -
12B PRO* 5.1 0.9 - - + -
18B ASN* 2.8 22.8 + - + +
20B ARG* 1.3 74.8 - - - +
22B VAL* 1.3 65.9 + - - +
24B TRP* 3.3 3.8 + - - +
25B LEU* 2.9 37.6 + - + +
136B PRO* 3.5 33.2 - - + +
137B TRP* 3.6 36.1 - - + -
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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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12B PRO* 4.3 17.0 - - + -
17B PRO* 4.5 7.4 - - + -
18B ASN 3.2 14.8 + - - +
19B GLU* 3.8 12.1 - - + +
20B ARG 3.3 0.2 - - - -
21B VAL* 1.3 73.9 - - + +
23B ALA* 1.3 68.8 + - - +
25B LEU* 3.2 3.9 + - - -
26B ASP* 2.9 37.2 + - - +
49F GLY* 3.5 21.1 - - - +
50F SER* 3.7 7.0 - - - +
53F ALA* 4.1 22.2 - - + -
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Residues in contact with ALA 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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19B GLU 3.0 18.3 + - - +
20B ARG* 3.6 25.4 - - - +
22B VAL* 1.3 78.2 - - - +
24B TRP* 1.3 61.5 + - - +
26B ASP* 3.0 18.4 + - - +
27B SER* 3.3 12.3 + - - -
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Residues in contact with TRP 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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2B ILE* 3.9 19.3 - - + -
4B LEU* 3.8 17.9 - - + -
8B VAL* 4.7 1.6 - - + -
20B ARG* 3.0 16.6 + - - +
21B VAL 3.6 6.1 - - - +
22B VAL 3.2 0.2 - - - -
23B ALA* 1.3 74.9 - - - +
25B LEU* 1.3 81.3 + - + +
27B SER* 2.8 37.1 + - - -
28B LEU* 3.7 43.1 - - + +
119B ALA* 3.8 24.5 - - + -
134B PHE* 3.1 43.2 - + + -
136B PRO* 3.7 22.9 - - + +
138B HIS 6.0 0.4 - - - +
140B GLU 5.2 4.2 + - - -
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Residues in contact with LEU 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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4B LEU* 3.9 27.1 - - + -
8B VAL* 4.2 9.6 - - + +
9B ILE* 5.1 1.3 - - - -
12B PRO* 3.5 35.9 - - + -
21B VAL* 2.9 27.2 + - + +
24B TRP* 1.3 101.0 - - + +
26B ASP* 1.3 57.9 + - - +
27B SER 3.1 4.2 + - - -
28B LEU* 3.4 19.2 + - + +
48F LEU* 3.7 25.3 + - + +
49F GLY* 3.4 21.8 - - - +
52F LEU* 4.6 9.0 - - + -
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Residues in contact with ASP 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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22B VAL* 2.9 17.9 + - - +
23B ALA* 3.3 14.5 - - - +
24B TRP 3.0 0.2 - - - -
25B LEU* 1.3 76.7 - - - +
27B SER* 1.3 56.3 + - - +
28B LEU 3.4 3.2 + - - +
46F VAL 5.6 0.4 - - - +
47F ARG* 3.0 60.2 + - - +
48F LEU 4.7 2.5 - - - +
49F GLY 3.9 0.4 - - - +
50F SER* 2.6 43.0 + - - -
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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