Contacts of the strand formed by residues 21 - 27 (chain A) in PDB entry 8LDH
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 TYR* 1.3 84.6 + - - +
22A LYS* 1.3 61.4 - - - +
23A ILE* 4.0 1.7 - - - +
44A LEU 4.0 6.3 - - - +
45A ALA* 3.0 28.1 - - - +
46A ASP* 3.0 25.2 + - - +
90A LYS* 2.8 37.4 - - - +
261A MET* 3.6 19.7 + - + +
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Residues in contact with LYS 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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19A SER* 4.9 8.1 - - - +
20A TYR 3.4 1.1 - - - -
21A ASN* 1.3 76.9 - - - +
23A ILE* 1.3 62.4 + - - +
46A ASP* 3.8 0.6 + - - -
47A GLU* 3.0 51.6 + - + +
49A ALA* 4.1 13.7 - - - -
85A VAL 2.6 30.3 + - - -
86A SER* 3.4 7.7 - - - +
87A ALA* 3.2 20.1 + - - +
88A GLY 3.3 32.1 - - - +
89A SER* 3.8 8.1 - - - +
90A LYS* 2.7 38.7 + - - +
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Residues in contact with ILE 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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21A ASN 4.0 2.2 - - - +
22A LYS* 1.3 81.4 - - - +
24A THR* 1.3 74.2 + - - +
25A VAL* 4.8 2.0 - - + -
39A ILE* 3.9 35.0 - - + -
44A LEU* 4.4 3.8 - - + -
45A ALA* 3.8 24.0 - - + -
47A GLU 2.9 6.3 + - - +
48A VAL* 3.1 13.7 - - + +
49A ALA 2.9 21.8 + - - -
89A SER* 4.5 0.2 - - - -
91A LEU* 3.3 40.2 - - + +
93A VAL* 4.6 2.7 - - + -
257A ALA* 4.6 3.8 - - + -
261A MET* 4.2 26.2 - - + -
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Residues in contact with THR 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 LYS* 4.5 0.7 - - - -
23A ILE* 1.3 76.9 + - - +
25A VAL* 1.3 68.0 + - - +
26A VAL* 5.1 5.6 - - + -
49A ALA* 3.0 23.3 - - + +
51A VAL* 3.8 17.9 - - + -
86A SER* 3.3 32.7 - - - -
89A SER* 2.3 30.7 + - - -
91A LEU 3.0 5.9 + - - +
92A VAL* 3.4 15.1 - - + +
93A VAL 3.0 24.9 + - - +
124A ILE* 5.9 0.9 - - + -
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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 ILE* 4.8 2.2 - - + -
24A THR* 1.3 77.7 - - - +
26A VAL* 1.4 60.9 + - - +
27A GLY 4.0 4.1 + - - +
28A VAL* 5.3 0.3 - - - +
32A GLY* 4.0 22.4 - - - +
35A CYS* 4.6 4.3 - - + -
36A ALA* 4.3 12.1 - - + -
39A ILE* 4.3 21.5 - - + -
48A VAL* 4.6 8.3 - - + -
49A ALA 2.7 9.9 + - - +
50A LEU* 3.4 24.0 - - + +
51A VAL* 2.8 33.1 + - - +
93A VAL* 3.6 14.1 - - + +
95A THR* 4.1 17.3 - - + -
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Residues in contact with VAL 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 THR* 5.1 2.7 - - + -
25A VAL* 1.4 75.1 - - - +
27A GLY* 1.3 55.9 + - - +
51A VAL* 3.2 21.5 - - + +
52A ASP* 5.5 1.3 - - - +
83A TYR* 4.4 5.6 - - - +
92A VAL* 4.3 9.6 - - + -
93A VAL 2.8 17.0 + - - +
94A ILE* 4.2 9.0 - - + -
95A THR* 2.7 36.2 + - - +
96A ALA* 3.9 21.3 - - + -
120A ILE* 4.0 22.4 - - + -
124A ILE* 4.1 26.2 - - + -
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Residues in contact with GLY 27 (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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25A VAL* 4.0 4.1 + - - +
26A VAL* 1.3 75.8 - - - +
28A VAL* 1.3 67.2 + - - +
29A GLY 3.3 5.6 - - - -
32A GLY* 3.2 23.6 - - - -
51A VAL 2.7 13.1 + - - -
52A ASP* 3.7 14.6 - - - -
95A THR* 3.6 10.3 - - - -
96A ALA* 4.8 4.9 - - - -
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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