Contacts of the helix formed by residues 113 - 122 (chain A) in PDB entry 5LDH
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 VAL 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A ASN 4.0 3.6 - - - +
112A LEU* 1.3 96.8 - - - +
114A GLN* 1.3 68.2 + - - +
116A ASN* 2.7 20.6 + - - -
117A VAL* 2.5 46.8 + - + +
144A ILE* 3.1 47.3 - - + -
145A LEU* 4.7 7.9 - - + -
148A VAL* 6.0 0.7 - - + -
326A GLN* 6.2 0.9 - - + -
329A LEU* 4.5 20.2 - - + +
330A LYS* 5.1 9.2 - - + +
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Residues in contact with GLN 114 (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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111A ASN* 5.7 0.7 - - - +
112A LEU* 3.0 37.3 + - + +
113A VAL* 1.3 87.7 - - - +
115A ARG* 1.3 62.6 + - + +
117A VAL* 2.5 34.0 - - - +
329A LEU* 2.9 42.4 - - + +
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Residues in contact with ARG 115 (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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100A VAL* 5.7 12.1 - - + +
112A LEU* 4.5 17.9 - - + -
114A GLN* 1.3 83.6 - - + +
116A ASN* 1.3 63.3 + - - +
117A VAL* 4.8 0.2 - - - -
118A ASN* 3.5 20.1 - - - +
119A VAL* 3.6 10.7 + - + +
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Residues in contact with ASN 116 (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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100A VAL* 3.6 29.5 - - - +
110A LEU* 6.0 1.7 - - - +
112A LEU* 4.3 15.6 - - + +
113A VAL* 2.7 29.0 + - - +
115A ARG* 1.3 79.6 - - - +
117A VAL* 1.3 67.3 + - - +
118A ASN 2.9 1.8 - - - -
119A VAL* 2.8 26.3 + - - +
120A PHE* 3.1 21.3 + - - +
139A SER* 4.6 5.9 + - - -
145A LEU* 3.7 31.3 - - + +
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Residues in contact with VAL 117 (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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113A VAL* 2.5 29.3 + - + +
114A GLN* 2.5 31.6 - - - +
116A ASN* 1.3 71.4 - - - +
118A ASN* 1.3 73.5 + - - +
120A PHE* 3.4 2.8 + - - +
121A LYS* 2.7 46.5 + - + +
148A VAL* 5.8 10.8 - - + -
152A LEU* 5.9 4.5 - - + -
330A ASP 5.8 2.9 - - - +
331A LEU* 4.4 25.8 - - + +
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Residues in contact with ASN 118 (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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115A ARG* 3.5 14.6 - - + +
116A ASN 2.8 0.4 + - - -
117A VAL* 1.3 92.5 - - + +
119A VAL* 1.3 65.8 + - - +
120A PHE 3.0 0.5 + - - -
121A LYS* 3.2 16.6 + - - -
122A PHE* 3.2 44.6 + - - +
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Residues in contact with VAL 119 (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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98A ALA* 3.5 28.7 - - + +
100A VAL* 3.4 27.8 - - + -
115A ARG* 3.6 10.3 + - + +
116A ASN* 2.8 30.3 + - - +
118A ASN* 1.3 76.5 - - - +
120A PHE* 1.3 67.4 - - + +
122A PHE* 5.6 0.9 - - - +
123A ILE* 4.1 11.6 + - - +
332A LNC 4.0 26.6 + - - +
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Residues in contact with PHE 120 (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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96A VAL* 2.6 55.0 - - + -
97A THR 4.1 4.7 - - - -
116A ASN* 3.1 23.9 + - - +
117A VAL* 4.1 3.1 - - - +
119A VAL* 1.3 85.4 - - + +
121A LYS* 1.3 54.5 + - - +
123A ILE* 2.1 37.0 - - - +
124A ILE* 2.1 33.3 - - + +
137A VAL* 3.8 31.2 - - + -
138A VAL 3.9 3.4 - - - -
139A SER* 4.0 26.5 - - - -
145A LEU* 4.1 14.6 - - + -
148A VAL* 5.8 8.5 - - + -
149A ALA* 5.9 2.7 - - + -
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Residues in contact with LYS 121 (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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117A VAL* 2.7 43.6 + - + +
118A ASN* 3.8 11.4 + - - +
120A PHE* 1.3 71.1 - - + +
122A PHE* 1.3 75.7 + - + +
123A ILE 2.9 5.4 - - - -
124A ILE* 2.6 14.3 - - + +
125A PRO* 1.9 47.4 - - + +
152A LEU* 4.6 12.3 - - + -
331A LEU* 3.1 38.6 + - + +
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Residues in contact with PHE 122 (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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85A TYR* 3.4 14.7 - - - -
118A ASN* 3.2 56.8 + - - +
119A VAL 5.7 1.3 - - - +
121A LYS* 1.3 94.4 - - + +
123A ILE* 1.3 58.0 + - - +
125A PRO* 4.3 3.6 - - - -
126A GLN* 4.1 12.7 + - - +
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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