Contacts of the strand formed by residues 21 - 26 (chain A) in PDB entry 5HNK
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 21 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A ARG* 1.3 78.2 - - - +
22A LEU* 1.3 62.3 + - - +
58A TYR 3.0 31.1 + - - +
59A SER* 3.1 18.1 + - - +
60A ALA* 3.2 4.3 - - + -
61A ARG 3.1 22.6 + - - +
62A THR 3.6 3.1 + - - -
144A TYR* 3.4 13.1 - - - -
145A ASP* 3.6 5.7 - - - +
146A HIS* 2.9 44.6 + - - +
148A TRP* 4.4 10.6 - - + +
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Residues in contact with LEU 22 (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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21A ASN* 1.3 77.2 - - - +
23A MET* 1.3 61.0 + - - +
24A ILE* 4.1 10.1 - - + -
60A ALA* 4.5 0.7 - - - -
62A THR* 3.5 37.5 - - + +
64A ILE* 4.2 15.0 - - + -
136A ILE* 4.1 15.9 - - + +
137A VAL* 5.6 0.4 - - - -
140A ILE* 4.1 17.9 - - + +
141A GLY* 5.2 0.7 - - - -
144A TYR* 3.6 33.1 - - + +
146A HIS 3.2 4.3 + - - +
147A VAL* 3.4 26.0 - - + +
148A TRP* 2.8 33.4 + - - +
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Residues in contact with MET 23 (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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22A LEU* 1.3 74.1 - - - +
24A ILE* 1.3 61.8 + - - +
25A VAL* 3.8 13.2 - - + -
51A ILE* 3.6 23.3 - - + +
54A LEU* 3.7 19.5 - - + +
55A ALA* 3.6 20.4 - - - +
58A TYR* 4.6 4.9 - - + -
60A ALA* 3.8 15.9 - - + +
62A THR 2.9 9.5 + - - +
63A THR* 3.3 34.7 - - + +
64A ILE 3.0 26.5 + - - +
148A TRP* 3.3 18.4 - - + +
150A ILE* 3.7 21.8 - - + -
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Residues in contact with ILE 24 (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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22A LEU* 4.1 14.8 - - + -
23A MET* 1.3 76.0 - - - +
25A VAL* 1.3 58.1 + - - +
26A ASP 4.0 0.2 + - - -
64A ILE* 3.5 10.3 - - + +
66A LEU* 3.7 30.7 - - + -
133A ALA* 3.9 15.0 - - + +
136A ILE* 3.7 31.2 - - + -
137A VAL* 4.0 17.0 - - + -
147A VAL* 4.2 7.6 - - + -
148A TRP 2.9 6.5 + - - +
149A LEU* 3.4 25.2 - - + +
150A ILE* 2.8 31.8 + - - +
156A TRP* 4.4 5.9 - - + -
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Residues in contact with VAL 25 (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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23A MET* 3.8 28.5 - - + -
24A ILE* 1.3 74.8 - - - +
26A ASP* 1.3 71.5 + - - +
27A GLY* 3.1 10.1 + - - +
30A LEU* 4.1 23.1 - - + -
51A ILE* 4.2 16.6 - - + -
54A LEU* 6.0 0.9 - - + -
63A THR* 4.2 4.5 - - + -
64A ILE 3.0 14.0 + - - +
65A VAL* 4.2 12.1 - - + -
66A LEU* 2.9 32.6 + - - +
150A ILE* 3.9 17.7 - - + +
156A TRP* 4.6 2.7 - - - -
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Residues in contact with ASP 26 (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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24A ILE 4.0 1.2 + - - -
25A VAL* 1.3 68.7 - - - +
27A GLY* 1.3 58.9 + - - +
28A THR 4.1 0.9 + - - -
29A ASN* 3.3 21.2 + - + +
30A LEU* 2.9 27.2 + - - +
66A LEU* 4.3 2.0 - - - -
67A GLY* 6.0 0.2 - - - -
68A ASP* 4.1 13.0 - - - +
129A ALA* 4.2 7.0 - - - +
130A ASP* 5.6 0.2 - - - -
150A ILE 2.9 22.0 + - - +
151A SER* 2.9 22.5 + - - +
153A LYS* 3.3 21.3 - - - -
156A TRP* 3.4 33.5 - - + -
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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