Contacts of the strand formed by residues 14 - 19 (chain A) in PDB entry 2HQ6
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 LYS 14 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A GLY* 1.3 76.2 - - - +
15A VAL* 1.3 68.9 + - - +
25A ASP* 2.7 43.6 + - - +
26A ILE 3.3 5.8 - - - +
27A GLU* 3.3 27.5 + - + +
28A LEU* 4.2 1.4 - - - +
134A THR* 3.9 2.4 - - - +
166A VAL* 3.7 1.4 - - - +
167A LEU* 2.9 53.5 + - + -
168A PHE* 3.0 27.9 + - + +
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Residues in contact with VAL 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LYS* 1.3 81.5 - - - +
16A LEU* 1.3 61.9 + - - +
17A LEU* 3.9 10.5 - - + -
24A ILE 3.8 0.9 - - - +
25A ASP* 3.6 2.6 - - - +
26A ILE* 2.8 39.3 + - + +
28A LEU* 4.1 17.2 - - + +
40A PHE* 3.7 32.5 - - + -
41A ILE* 4.2 12.3 - - + -
44A CYS* 4.7 1.8 - - + -
164A CYS* 3.4 31.4 - - - -
165A GLU 3.3 7.9 - - - +
166A VAL* 4.3 9.6 - - + -
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Residues in contact with LEU 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A VAL* 1.3 72.1 - - - +
17A LEU* 1.3 66.7 + - - +
18A LYS* 3.9 27.5 + - + +
23A ASP* 4.0 24.5 - - + +
24A ILE 3.5 20.9 - - - +
25A ASP* 4.1 15.3 - - + +
137A THR* 5.8 0.4 - - + -
163A SER 3.9 0.2 - - - +
164A CYS* 3.5 2.1 - - - -
165A GLU* 2.8 55.6 + - + +
167A LEU* 3.8 25.5 - - + +
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Residues in contact with LEU 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A VAL* 3.9 6.7 - - + -
16A LEU* 1.3 73.2 - - - +
18A LYS* 1.3 62.2 + - - +
19A THR* 3.6 15.0 + - + -
22A GLY 3.9 0.2 - - - +
23A ASP* 3.4 4.5 - - - +
24A ILE* 2.8 41.3 + - + +
26A ILE* 3.8 26.2 - - + -
40A PHE* 4.6 6.1 - - + -
49A TYR* 5.7 1.1 - - + -
54A PHE* 4.7 2.0 - - + -
113A PHE* 4.2 9.0 - - + -
115A PHE* 4.0 18.8 - - + -
161A ILE* 4.2 28.5 - - + -
163A SER 3.6 2.9 - - - +
164A CYS* 3.3 37.9 - - + -
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Residues in contact with LYS 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LEU* 4.0 19.3 - - + +
17A LEU* 1.3 72.3 - - - +
19A THR* 1.3 61.9 + - - +
23A ASP* 3.7 23.6 - - - +
161A ILE* 3.7 0.7 - - - -
162A LYS* 2.8 48.5 + - - +
163A SER* 2.8 34.5 + - - +
165A GLU* 3.3 25.0 + - - +
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Residues in contact with THR 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LEU* 3.8 18.6 - - + -
18A LYS* 1.3 78.4 - - - +
20A THR* 1.3 60.5 + - - +
21A ALA* 2.9 20.3 + - - +
22A GLY* 2.8 37.9 + - - +
24A ILE* 3.7 25.2 - - + +
54A PHE* 4.3 14.4 - - + -
144A LEU* 3.7 8.6 - - - +
160A LYS 3.2 13.0 - - - +
161A ILE* 4.4 3.8 - - - -
162A LYS* 5.0 1.8 - - - -
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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