Contacts of the helix formed by residues 106 - 124 (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 GLY 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A GLN* 3.9 3.5 + - - -
103A GLN* 2.4 32.4 + - - +
105A GLU* 1.3 81.1 + - - +
107A GLU* 1.3 67.0 + - - +
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Residues in contact with GLU 107 (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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102A GLN* 3.8 13.1 + - - +
103A GLN* 5.1 2.8 + - - +
105A GLU 4.3 2.0 - - - +
106A GLY* 1.3 77.6 - - - +
108A SER* 1.3 79.3 + - - +
109A ARG* 3.4 2.5 + - + +
112A LEU* 6.0 0.2 - - - +
197A ASP* 3.0 28.7 - - - +
239A ASN* 5.9 2.5 - - - +
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Residues in contact with SER 108 (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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102A GLN* 4.5 0.4 - - - -
107A GLU* 1.3 90.1 + - - +
109A ARG* 1.3 58.6 + - - +
110A LEU* 2.9 5.4 - - - +
111A ASN* 2.7 55.0 + - - +
112A LEU* 3.2 9.3 + - - +
115A ARG* 4.7 2.8 + - - -
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Residues in contact with ARG 109 (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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102A GLN* 1.9 50.3 + - - +
107A GLU* 3.4 1.0 + - + +
108A SER* 1.3 77.3 - - - +
110A LEU* 1.3 57.5 + - + +
112A LEU* 2.3 48.2 - - + +
140A GLU* 2.3 32.1 + - + +
141A LEU* 3.7 16.0 - - + +
195A HIS* 3.4 30.5 + - - -
196A GLY* 4.3 11.4 - - - -
197A ASP* 5.2 4.7 + - - +
235A LEU 5.3 2.4 + - - -
238A SER* 2.3 38.6 + - - -
333A PYR 4.3 11.1 + - - -
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Residues in contact with LEU 110 (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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108A SER* 2.9 2.8 - - - -
109A ARG* 1.3 76.8 - - + +
111A ASN* 1.3 67.0 + - - +
112A LEU 2.9 2.0 - - - -
113A VAL* 2.7 28.2 + - - +
141A LEU* 4.0 14.4 - - + -
144A ASP* 6.0 1.1 - - + -
321A THR 5.9 1.1 - - - +
322A LEU* 4.8 14.1 - - + -
325A ILE* 2.5 50.0 - - + -
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Residues in contact with ASN 111 (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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108A SER* 2.7 43.2 + - - +
110A LEU* 1.3 73.0 - - - +
112A LEU* 1.3 51.7 - - - +
113A VAL* 2.1 22.6 + - - +
114A GLN* 2.9 18.8 + - - +
115A ARG* 4.2 14.6 + - - +
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Residues in contact with LEU 112 (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 ALA* 4.0 9.6 - - + +
101A ARG 4.7 6.1 - - - +
102A GLN* 3.3 8.1 - - + +
108A SER 3.2 6.0 + - - +
109A ARG* 2.3 41.1 - - + +
111A ASN* 1.3 73.7 - - - +
113A VAL* 1.3 50.4 + - - -
114A GLN 3.5 0.2 - - - -
115A ARG* 3.1 50.2 - - - +
116A ASN* 2.7 44.1 + - - +
140A GLU* 2.7 40.2 - - + -
141A LEU* 3.6 9.6 - - + -
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Residues in contact with VAL 113 (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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110A LEU 2.7 22.8 + - - +
111A ASN* 2.1 21.1 + - - +
112A LEU* 1.3 67.6 - - - +
114A GLN* 1.3 84.3 + - + +
116A ASN* 3.4 7.6 + - - +
117A VAL* 3.4 22.3 + - + +
141A LEU* 4.4 7.1 - - + +
144A ASP* 3.5 22.7 - - - +
325A ILE* 3.3 37.5 - - + +
326A GLN* 5.8 1.1 - - - -
330A LYS* 6.3 2.0 - - - -
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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 2.9 10.8 + - - +
113A VAL* 1.3 86.3 + - + +
115A ARG* 1.3 60.6 + - - +
116A ASN 2.8 6.6 + - - -
117A VAL* 3.6 7.6 + - - +
118A ASN* 3.2 23.2 + - - +
330A LYS* 2.9 55.3 + - - +
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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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99A GLY 5.4 0.4 - - - -
100A ALA* 4.1 27.5 - - - +
101A ARG 4.0 14.5 + - - -
103A GLN* 6.2 1.2 - - - +
108A SER* 4.7 2.8 + - - -
111A ASN* 4.3 12.7 - - - +
112A LEU* 3.1 51.5 - - - +
114A GLN* 1.3 76.1 - - - +
116A ASN* 1.3 61.0 + - - +
118A ASN* 4.0 17.9 - - - +
119A ILE* 4.2 7.4 - - - +
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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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98A ALA* 4.8 2.6 - - - +
99A GLY 3.9 6.3 + - - -
100A ALA* 3.3 30.3 - - - +
112A LEU* 2.7 24.1 + - - +
113A VAL* 3.7 5.2 - - - +
114A GLN 2.8 4.4 + - - -
115A ARG* 1.3 77.2 + - - +
117A VAL* 1.3 65.7 + - - +
118A ASN 3.0 3.7 + - - -
119A ILE* 3.3 13.5 + - - +
120A PHE* 3.1 23.1 + - - +
140A GLU* 4.3 4.0 + - - +
141A LEU* 3.4 19.9 - - - +
145A LYS* 3.7 29.5 - - + +
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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* 3.4 17.6 + - + +
114A GLN* 3.6 5.1 + - - +
116A ASN* 1.3 76.7 - - + +
118A ASN* 1.3 75.3 + - - +
120A PHE* 4.2 11.4 - - + -
121A LYS* 2.8 41.1 + - + +
145A LYS* 6.3 3.4 - - + -
148A GLN* 4.2 26.0 - - + -
329A LEU 5.3 3.6 - - - +
330A LYS* 3.6 24.7 - - + +
331A PHE* 5.2 7.2 - - + -
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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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114A GLN* 3.2 33.3 + - - +
115A ARG* 4.0 16.0 - - - +
116A ASN 3.0 1.0 - - - -
117A VAL* 1.3 86.6 - - - +
119A ILE* 1.3 65.4 + - + +
121A LYS* 3.9 4.3 + - - +
122A PHE* 3.8 19.9 - - - -
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Residues in contact with ILE 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* 3.4 32.5 - - + -
99A GLY 4.3 8.3 - - - +
115A ARG 4.2 8.5 - - - +
116A ASN* 3.7 17.9 - - - +
118A ASN* 1.3 76.2 - - + +
120A PHE* 1.3 71.3 + - + +
121A LYS 3.2 0.7 + - - -
122A PHE* 3.4 9.7 + - - +
123A ILE* 3.0 25.5 + - + +
332A NAD 3.3 34.2 + - - +
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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 ILE* 4.2 11.4 - - + -
116A ASN 3.1 11.6 + - - +
117A VAL* 4.2 9.6 - - + -
119A ILE* 1.3 80.4 - - - +
121A LYS* 1.3 58.6 + - - +
123A ILE* 2.5 29.1 + - + +
124A ILE* 2.6 47.3 - - + +
137A LEU* 3.1 26.5 - - + -
145A LYS* 2.2 63.9 - - + +
148A GLN* 4.2 9.0 - - + -
149A ASP* 3.3 37.2 - - + -
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Residues in contact with LYS 121 (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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117A VAL* 2.8 36.3 + - + +
118A ASN 3.9 2.7 - - - +
120A PHE* 1.3 75.1 - - - +
122A PHE* 1.3 76.8 + - + +
124A ILE* 2.4 48.3 + - + +
125A PRO* 3.2 1.1 - - - +
152A LEU* 5.0 13.9 - - + -
331A PHE* 3.1 38.0 + - + -
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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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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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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