Contacts of the helix formed by residues 142 - 154 (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 142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A LEU* 4.4 5.5 - - - +
139A PRO 3.8 2.8 + - - -
140A GLU 3.4 1.0 - - - -
141A LEU* 1.3 79.7 - - - +
143A THR* 1.3 63.9 + - - +
145A LYS* 4.5 0.7 - - - +
146A ASN* 3.4 16.4 + - - +
162A GLY* 4.3 4.1 - - - -
164A GLY* 3.6 23.6 - - - -
194A GLN 4.7 3.4 + - - -
195A HIS* 4.8 5.5 - - - +
272A SER* 4.9 0.9 - - - -
332A NAD 3.6 23.6 + - - -
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Residues in contact with THR 143 (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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141A LEU* 4.8 0.9 - - - -
142A GLY* 1.3 70.3 - - - +
144A ASP* 1.3 85.6 + - - +
146A ASN* 3.0 19.9 - - - +
147A LYS 3.6 2.3 + - - -
164A GLY* 4.3 3.9 - - - -
194A GLN* 2.4 58.5 - - + +
272A SER* 3.8 10.5 - - - -
286A PHE* 3.1 27.6 + - - +
287A LEU* 3.4 7.2 - - - -
288A SER* 3.8 8.1 - - - +
322A LEU* 3.5 16.5 - - - +
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Residues in contact with ASP 144 (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* 6.1 1.1 - - + -
113A VAL* 3.5 27.1 - - - +
141A LEU* 3.2 30.3 + - + +
143A THR* 1.3 87.7 + - - +
145A LYS* 1.3 70.6 + - - +
146A ASN 3.0 0.9 + - - -
147A LYS* 3.1 11.1 + - - +
148A GLN* 3.1 28.4 - - - +
286A PHE 4.5 2.0 - - - -
322A LEU* 4.8 14.8 - - + +
325A ILE* 5.0 10.1 - - - +
326A GLN* 4.6 13.3 + - - +
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Residues in contact with LYS 145 (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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97A THR 4.1 11.5 + - - -
98A ALA* 4.1 4.6 - - - +
116A ASN* 3.7 31.5 - - + +
117A VAL* 6.3 3.1 - - + -
120A PHE* 2.2 70.6 - - + +
137A LEU* 4.1 7.6 - - + -
139A PRO* 3.9 16.6 - - + +
140A GLU 3.4 20.0 - - - +
141A LEU* 3.1 20.5 + - + +
142A GLY 4.5 0.4 - - - +
144A ASP* 1.3 82.4 - - - +
146A ASN* 1.3 70.0 + - - +
148A GLN* 3.0 25.5 + - + +
149A ASP 3.5 2.6 + - - -
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Residues in contact with ASN 146 (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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135A LYS* 4.7 0.4 + - - +
137A LEU* 3.0 27.9 - - - +
142A GLY 3.4 10.1 + - - +
143A THR 3.0 15.2 + - - +
144A ASP 3.0 0.2 - - - -
145A LYS* 1.3 82.0 - - - +
147A LYS* 1.3 65.3 + - - +
148A GLN 3.1 0.2 + - - -
149A ASP* 3.2 4.9 + - - +
150A TRP* 3.2 17.5 + - - +
160A ILE* 3.4 20.2 - - - +
161A ILE 3.5 4.9 + - - +
162A GLY* 3.0 17.8 + - - +
272A SER* 2.0 42.6 + - - +
286A PHE* 3.5 3.2 - - + -
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Residues in contact with LYS 147 (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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143A THR 3.6 1.0 + - - -
144A ASP* 3.1 11.2 + - - +
146A ASN* 1.3 79.1 - - - +
148A GLN* 1.3 73.8 + - - +
150A TRP* 3.0 15.2 + - + -
151A LYS* 2.9 50.6 + - + +
284A ASN* 1.6 50.9 - - - +
286A PHE* 3.8 35.7 - - + +
323A TRP* 4.7 0.6 - - - -
326A GLN* 2.8 29.0 + - + +
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Residues in contact with GLN 148 (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* 4.2 23.3 - - + -
120A PHE* 4.2 11.9 - - + -
144A ASP* 3.1 34.7 - - - +
145A LYS* 3.0 21.1 + - + +
147A LYS* 1.3 77.6 - - - +
149A ASP* 1.3 52.5 + - - +
151A LYS* 4.2 0.6 - - - +
152A LEU* 2.7 43.3 + - + +
326A GLN* 3.8 25.9 - - - +
329A LEU 5.8 0.2 + - - -
331A PHE* 3.1 35.2 - - + -
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Residues in contact with ASP 149 (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* 5.7 3.5 - - - +
120A PHE* 3.3 32.8 - - + -
124A ILE* 4.0 16.7 - - + +
127A ILE* 6.1 1.4 - - - +
128A VAL* 4.9 2.0 - - - +
135A LYS* 4.1 23.7 - - - +
137A LEU* 5.1 6.5 - - + +
145A LYS 3.5 0.2 + - - -
146A ASN 3.2 6.5 + - - +
148A GLN* 1.3 78.0 - - - +
150A TRP* 1.3 54.5 + - - +
152A LEU* 2.7 8.5 - - - +
153A SER* 2.2 56.9 + - - -
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Residues in contact with TRP 150 (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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146A ASN* 3.2 11.5 + - - +
147A LYS* 3.0 20.3 + - + +
149A ASP* 1.3 75.1 - - - +
151A LYS* 1.3 79.9 + - + +
153A SER* 3.4 6.5 - - - -
154A GLY* 2.0 43.3 + - - -
155A LEU 2.9 27.7 + - - -
156A PRO* 5.7 0.2 - - + -
157A MET* 2.7 41.6 - - + +
160A ILE* 3.1 37.7 - - + -
274A MET* 3.4 28.5 - - + -
284A ASN* 5.4 2.9 - - + -
286A PHE* 3.5 27.6 - + + -
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Residues in contact with LYS 151 (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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147A LYS* 2.9 37.6 + - + +
148A GLN 4.2 0.7 - - - +
150A TRP* 1.3 92.7 - - + +
152A LEU* 1.3 67.8 + - - +
153A SER 3.7 0.5 - - - -
154A GLY* 3.5 8.3 + - - -
326A GLN* 5.6 3.0 + - - -
329A LEU* 5.4 3.8 - - - +
331A PHE* 4.3 32.6 - - + -
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Residues in contact with LEU 152 (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* 4.6 15.0 - - + +
124A ILE* 3.1 43.5 - - + -
125A PRO* 5.2 1.1 - - + -
148A GLN* 2.7 20.6 + - + +
149A ASP* 2.7 14.6 + - - +
151A LYS* 1.3 81.5 - - + +
153A SER* 1.3 58.0 + - - +
331A PHE* 3.1 36.1 - - + -
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Residues in contact with SER 153 (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* 4.5 5.4 - - - -
128A VAL* 3.2 39.3 - - - +
135A LYS* 5.2 2.4 - - - -
149A ASP* 2.2 48.8 + - - -
150A TRP* 3.1 6.1 + - - -
151A LYS 3.7 0.2 - - - -
152A LEU* 1.3 72.1 - - - +
154A GLY* 1.3 65.5 + - - +
155A LEU* 3.7 16.4 + - - +
160A ILE* 5.5 0.9 - - - +
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Residues in contact with GLY 154 (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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150A TRP* 2.0 30.5 + - - -
151A LYS* 3.5 8.3 + - - -
153A SER* 1.3 71.0 + - - +
155A LEU* 1.3 69.3 + - - +
156A PRO* 3.6 3.3 - - - +
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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