Contacts of the strand formed by residues 19 - 23 (chain H) in PDB entry 2A3W
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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11H PHE* 4.2 3.6 - - - -
17H THR 2.7 24.9 + - - -
18H ASP* 1.3 75.4 - - - +
20H VAL* 1.3 65.9 + - - +
21H ASN* 3.2 30.5 + - - -
132H VAL* 3.8 8.7 - - + -
133H LEU 3.3 15.0 - - - +
135H GLN* 3.7 11.2 - - + -
141H GLY 5.1 2.0 + - - -
144H PHE* 3.5 31.6 - + - -
193H ARG* 2.9 63.8 + - + +
196H VAL* 3.8 3.5 - - - +
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Residues in contact with VAL 20 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H PHE* 3.7 29.8 - - + -
11H PHE* 3.7 11.9 - - + -
19H HIS* 1.3 77.8 - - - +
21H ASN* 1.3 75.2 + - - +
22H LEU* 3.7 16.6 + - + +
132H VAL* 3.4 5.0 - - - -
133H LEU* 2.9 40.8 + - + +
190H TYR* 3.8 6.3 - - + -
191H GLU 3.2 12.1 - - - +
192H ILE* 4.2 5.6 - - + -
196H VAL* 3.7 28.9 - - + -
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Residues in contact with ASN 21 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H HIS* 3.2 31.2 + - - -
20H VAL* 1.3 71.8 - - - +
22H LEU* 1.3 60.9 + - - +
23H ILE* 4.0 4.7 + - + +
130H LYS* 5.6 7.0 - - + +
131H ILE 3.4 4.7 - - - +
132H VAL* 3.6 13.7 - - - +
141H GLY* 5.2 3.1 - - - +
190H TYR* 3.1 10.0 - - - +
191H GLU* 2.8 65.2 + - + +
193H ARG* 4.1 11.9 - - - +
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Residues in contact with LEU 22 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20H VAL* 3.7 28.0 - - + +
21H ASN* 1.3 74.5 - - - +
23H ILE* 1.3 62.3 + - - +
24H THR* 3.9 1.7 + - - +
50H PHE* 4.2 4.3 - - + -
129H PRO 5.4 1.2 - - - +
131H ILE* 2.8 52.6 + - + +
133H LEU* 3.8 39.3 - - + -
157H LEU* 4.3 9.6 - - + -
183H LEU* 4.0 27.8 - - + -
188H LEU* 4.2 25.6 - - + -
189H ASN 3.9 1.8 - - - -
190H TYR* 4.2 1.1 - - + -
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Residues in contact with ILE 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H ASN* 4.7 5.6 - - + +
22H LEU* 1.3 76.4 - - - +
24H THR* 1.3 68.7 + - - +
25H PRO* 4.3 3.5 - - - +
183H LEU* 4.1 8.6 - - - +
189H ASN* 2.8 67.2 + - - +
190H TYR 4.8 0.2 - - - -
191H GLU* 3.7 35.7 - - + +
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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