Contacts of the helix formed by residues 122 - 131 (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 PHE 122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A ASN 3.8 16.6 - - - -
119A ILE* 3.4 9.0 + - - +
121A LYS* 1.3 92.2 - - + +
123A ILE* 1.3 60.6 + - - +
125A PRO* 2.3 38.9 - - + +
126A ASN* 3.5 11.0 - - - +
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Residues in contact with ILE 123 (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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27A VAL* 4.7 12.6 - - + -
85A TYR* 4.5 15.0 - - + +
96A ILE* 4.3 15.3 - - + -
119A ILE* 3.0 24.7 - - + +
120A PHE* 2.5 51.1 - - + +
122A PHE* 1.3 78.2 - - - +
124A ILE* 1.3 61.7 + - + +
126A ASN* 3.1 10.5 + - - +
127A ILE* 2.2 68.1 + - + +
332A NAD 4.2 16.4 - - + +
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Residues in contact with ILE 124 (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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120A PHE* 2.6 57.2 - - + +
121A LYS* 2.4 29.2 + - - +
123A ILE* 1.3 72.9 - - + +
125A PRO* 1.3 68.7 - - + +
127A ILE* 3.6 4.7 + - + +
128A VAL* 3.2 26.2 + - + +
149A ASP* 4.0 22.0 - - + +
152A LEU* 3.1 42.0 - - + -
153A SER* 4.4 11.0 - - - +
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Residues in contact with PRO 125 (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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121A LYS* 3.2 2.5 - - + +
122A PHE* 2.3 43.7 - - + +
124A ILE* 1.3 89.6 - - + +
126A ASN* 1.3 68.3 + - - +
128A VAL* 4.1 4.4 - - + +
129A LYS* 2.9 48.5 + - + +
152A LEU* 5.2 1.3 - - + -
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Residues in contact with ASN 126 (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* 3.2 51.3 + - + +
122A PHE* 3.5 15.2 - - - +
123A ILE* 3.1 8.9 + - - +
125A PRO* 1.3 86.5 - - - +
127A ILE* 1.3 64.8 + - - +
128A VAL 3.1 1.6 + - - -
129A LYS* 3.4 14.7 + - - +
130A HIS* 3.3 29.3 + - - +
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Residues in contact with ILE 127 (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* 6.2 0.2 - - + -
27A VAL* 4.7 11.9 - - + -
85A TYR* 4.4 17.5 - - + -
94A VAL* 3.9 24.9 - - + -
96A ILE* 5.5 9.4 - - + -
123A ILE* 2.2 68.0 + - + +
124A ILE* 3.8 6.3 - - + +
126A ASN* 1.3 80.5 - - - +
128A VAL* 1.3 52.9 + - + +
130A HIS* 5.1 1.0 - - - +
131A SER* 2.0 46.1 + - - +
133A CYS* 4.9 1.3 - - - -
135A LYS* 5.0 11.0 - - + -
149A ASP* 6.1 1.3 - - - +
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Residues in contact with VAL 128 (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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124A ILE* 3.2 19.4 + - + +
125A PRO* 4.1 5.6 - - + +
127A ILE* 1.3 76.4 - - + +
129A LYS* 1.3 77.5 + - + +
130A HIS 3.2 2.8 + - - -
131A SER* 3.3 20.1 + - - +
132A PRO* 3.6 5.5 - - - +
135A LYS* 4.3 14.6 - - - +
149A ASP* 4.9 3.4 - - - +
153A SER* 3.2 37.7 - - - +
155A LEU* 4.0 16.3 - - + +
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Residues in contact with LYS 129 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A PRO* 2.9 46.1 + - + +
126A ASN* 4.0 15.2 - - - +
128A VAL* 1.3 89.4 - - + +
130A HIS* 1.3 77.3 + - + +
132A PRO* 4.1 9.5 - - - +
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Residues in contact with HIS 130 (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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84A ASP 3.7 5.6 - - - -
85A TYR* 1.7 43.0 + - + +
86A SER* 3.4 17.0 + - - -
88A SER* 5.6 2.7 - - - -
89A ALA* 3.3 20.3 - - + +
90A GLY 2.6 31.8 + - - -
126A ASN* 3.3 21.9 + - - +
127A ILE* 5.1 1.3 - - - +
128A VAL 3.2 0.4 - - - -
129A LYS* 1.3 93.0 + - + +
131A SER* 1.3 51.3 + - - +
132A PRO* 2.7 14.8 - - - +
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Residues in contact with SER 131 (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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88A SER* 5.6 3.1 - - - -
90A GLY 4.3 4.3 - - - +
91A SER* 3.7 14.4 - - - +
94A VAL* 4.2 2.9 - - - -
127A ILE* 2.0 33.9 + - - +
128A VAL* 3.3 7.3 + - - +
130A HIS* 1.3 77.3 - - - +
132A PRO* 1.3 66.0 - - - +
133A CYS* 2.1 72.0 + - - +
135A LYS* 4.5 2.1 + - - -
155A LEU* 4.9 1.0 - - - +
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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