Contacts of the strand formed by residues 22 - 27 (chain A) in PDB entry 3LDH
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 22 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A SER* 5.2 0.4 + - - -
20A TYR* 1.3 85.0 - - - +
23A LYS* 1.3 61.8 + - - +
45A LEU 4.2 6.7 - - - +
46A ALA* 3.3 8.4 - - - -
47A ASP* 2.3 68.8 + - - +
48A GLU 3.2 4.9 + - - -
92A LYS* 5.9 1.7 - - - +
262A MET* 3.6 27.7 - - + +
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Residues in contact with LYS 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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19A SER* 5.9 2.5 - - - +
20A TYR 3.5 7.9 + - - +
22A ASN* 1.3 75.0 - - - +
24A ILE* 1.3 63.9 + - - +
25A THR* 4.3 1.8 - - - -
46A ALA* 4.0 2.5 - - - -
48A GLU* 3.2 50.5 + - + +
50A ALA* 4.2 9.5 - - - +
79A VAL* 5.0 3.2 - - - +
87A VAL 3.7 6.7 + - - -
88A SER* 3.2 54.1 + - - +
90A GLY 4.3 8.7 - - - +
91A SER* 3.8 19.2 - - - -
92A LYS* 3.7 10.2 + - - +
93A LEU* 3.3 26.5 + - - +
262A MET* 5.2 4.2 - - - +
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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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23A LYS* 1.3 73.7 - - - +
25A THR* 1.3 61.6 + - - +
26A VAL* 4.5 9.0 - - + -
40A VAL* 3.0 42.8 - - + -
41A LEU* 5.8 0.7 - - + -
45A LEU* 4.1 11.4 - - + -
46A ALA* 3.3 30.0 - - + +
48A GLU 3.0 7.9 + - - +
49A VAL* 3.0 26.3 - - + -
50A ALA* 2.3 37.6 + - - +
93A LEU* 3.7 27.6 - - + +
262A MET* 5.3 3.1 - - + -
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Residues in contact with THR 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 LYS* 4.5 0.7 - - - -
24A ILE* 1.3 76.6 - - - +
26A VAL* 1.3 72.1 + - - +
27A VAL* 5.1 5.2 - - + -
50A ALA* 3.2 17.7 - - + +
52A VAL* 4.9 9.6 - - + -
88A SER* 2.6 32.9 + - - +
91A SER* 3.5 7.6 - - - -
93A LEU 3.2 8.0 + - - +
94A VAL* 3.8 24.0 - - + -
95A VAL* 3.3 30.0 + - - +
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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 ILE* 4.5 13.7 - - + -
25A THR* 1.3 74.4 - - - +
27A VAL* 1.3 74.4 + - - +
28A GLY 4.6 0.7 - - - +
33A GLY* 4.2 25.1 - - - +
36A ASP* 5.6 3.8 - - + -
37A ALA* 5.4 13.9 - - + +
40A VAL* 6.4 0.9 - - + -
41A LEU* 6.2 1.3 - - + -
49A VAL* 5.4 2.5 - - + -
50A ALA 2.2 23.5 + - - +
51A LEU* 3.2 31.4 - - + +
52A VAL* 3.0 28.4 + - - +
95A VAL* 3.9 13.9 - - + +
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Residues in contact with VAL 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 THR* 5.1 8.1 - - + -
26A VAL* 1.3 79.9 - - - +
28A GLY* 1.3 55.4 + - - +
52A VAL* 4.1 16.8 - - + +
85A TYR* 5.1 0.7 - - + -
94A VAL* 5.3 3.8 - - + -
95A VAL 3.1 19.4 + - - +
96A ILE* 3.8 29.9 - - + -
97A THR* 2.4 32.9 + - - -
123A ILE* 4.7 7.9 - - + -
127A ILE* 4.7 16.8 - - + -
332A NAD 3.1 33.4 - - + +
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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