Contacts of the helix formed by residues 107 - 120 (chain A) in PDB entry 6LDH
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 LEU 107 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A SER* 2.9 8.4 + - - +
106A ARG* 1.4 81.8 - - - +
108A ASN* 1.3 67.9 - - - +
110A VAL* 3.4 1.2 + - - +
111A GLN* 3.0 27.4 + - + +
323A ILE* 3.7 39.7 - - + +
325A LYS* 2.9 45.3 - - + +
326A ASP* 3.9 10.8 - - - +
329A PHE* 5.2 16.8 - - + +
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Residues in contact with ASN 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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104A GLU* 4.0 14.7 - - + +
105A SER* 2.7 29.8 + - - +
107A LEU* 1.3 80.2 - - - +
109A LEU* 1.3 60.1 - - - +
111A GLN* 3.5 4.1 + - - +
112A ARG* 3.2 30.5 + - - +
329A PHE* 3.3 51.6 + - - +
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Residues in contact with LEU 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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98A ALA* 4.1 8.3 - - + +
99A ARG 4.4 2.0 - - - +
100A GLN* 3.1 45.5 - - + +
104A GLU* 3.8 14.5 - - + +
105A SER 2.7 19.2 + - - +
106A ARG* 4.2 7.9 - - + +
108A ASN* 1.3 69.9 - - - +
110A VAL* 1.3 67.6 - - + +
112A ARG* 3.4 32.6 + - - +
113A ASN* 3.0 29.3 + - - +
138A ASN 5.6 0.4 - - - +
139A PRO* 4.6 14.4 - - + -
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Residues in contact with VAL 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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106A ARG* 2.6 35.2 + - + +
107A LEU 3.7 3.4 - - - +
109A LEU* 1.3 78.6 - - + +
111A GLN* 1.3 58.6 + - - +
113A ASN* 3.3 9.5 + - - +
114A VAL* 3.0 31.9 + - + +
139A PRO* 3.6 29.2 - - + -
142A VAL* 3.2 35.7 - - + -
143A LEU* 4.7 6.1 - - + +
146A VAL* 5.3 0.2 - - + -
323A ILE* 3.4 17.9 - - + -
326A ASP* 4.1 9.9 - - - +
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Residues in contact with GLN 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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107A LEU* 3.0 18.3 + - + +
108A ASN 3.8 6.1 - - - +
109A LEU 3.3 0.4 - - - -
110A VAL* 1.3 77.7 - - - +
112A ARG* 1.3 60.4 + - - +
114A VAL* 3.1 28.5 + - - +
115A ASN* 2.8 41.0 + - - +
325A LYS 4.6 0.9 - - - +
326A ASP* 3.4 12.2 + - - +
327A LEU* 2.6 32.4 + - - +
328A LYS* 3.3 26.4 + - + +
329A PHE* 3.3 32.6 - - - +
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Residues in contact with ARG 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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98A ALA* 2.8 32.9 - - + +
99A ARG 4.1 1.6 - - - +
100A GLN* 3.3 19.4 - - - +
101A GLN* 4.0 13.5 - - - +
104A GLU* 2.5 41.7 + - - +
108A ASN 3.2 15.1 + - - +
109A LEU* 3.6 10.8 - - - +
110A VAL 3.3 0.8 - - - -
111A GLN* 1.3 76.6 - - - +
113A ASN* 1.3 60.2 + - - +
115A ASN* 3.4 17.7 + - - +
116A ILE* 3.0 25.4 + - + +
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Residues in contact with ASN 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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97A GLY* 3.1 12.2 - - - -
98A ALA* 2.8 33.7 + - - +
109A LEU* 3.0 38.6 + - - +
110A VAL 3.3 7.8 + - - +
111A GLN 3.2 0.2 - - - -
112A ARG* 1.3 75.5 - - - +
114A VAL* 1.3 59.0 + - - +
116A ILE* 3.2 5.3 + - - +
117A PHE* 2.8 41.4 + - + +
138A ASN 4.4 4.8 + - - -
139A PRO* 4.5 2.4 - - - +
143A LEU* 3.8 35.4 - - + +
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Residues in contact with VAL 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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110A VAL* 3.0 25.4 + - + +
111A GLN* 3.1 25.1 + - - +
113A ASN* 1.3 77.3 - - - +
115A ASN* 1.3 56.2 + - - +
117A PHE* 3.8 1.3 - - - +
118A LYS* 2.9 40.2 + - + +
143A LEU* 5.4 0.4 - - + -
146A VAL* 4.0 29.6 - - + +
150A LEU* 4.1 4.4 - - + +
326A ASP* 3.7 28.7 - - + +
327A LEU* 4.1 24.2 - - + +
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Residues in contact with ASN 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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111A GLN* 2.8 36.6 + - - +
112A ARG* 3.4 13.3 + - - +
113A ASN 3.2 0.2 - - - -
114A VAL* 1.3 75.5 - - - +
116A ILE* 1.3 61.7 + - - +
118A LYS* 4.1 13.5 - - - +
119A PHE* 3.0 32.2 - - + -
327A LEU* 5.9 0.9 - - - +
328A LYS* 3.4 33.9 - - - +
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Residues in contact with ILE 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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96A ALA* 5.5 4.5 - - + -
97A GLY* 4.6 5.2 - - - +
98A ALA* 4.1 28.9 - - + +
112A ARG* 3.0 22.0 - - + +
113A ASN* 3.2 11.6 + - - +
115A ASN* 1.3 77.2 - - - +
117A PHE* 1.4 68.3 + - + +
118A LYS 3.2 0.4 - - - -
119A PHE* 3.0 20.9 + - - +
120A ILE* 3.1 32.9 + - + +
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Residues in contact with PHE 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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94A ILE* 4.3 12.1 - - + -
96A ALA 3.1 29.8 - - - -
97A GLY* 4.8 0.4 - - - -
113A ASN* 2.8 24.9 + - - +
114A VAL* 4.0 2.7 - - - +
116A ILE* 1.4 81.2 - - + +
118A LYS* 1.3 57.1 - - - +
119A PHE 2.9 5.6 - - - -
120A ILE* 3.0 26.1 + - + +
121A ILE* 3.3 36.8 + - + +
122A PRO* 3.4 4.3 - - - +
135A VAL* 4.6 7.4 - - + -
137A SER* 4.0 8.5 - - - -
143A LEU* 3.9 47.6 - - + -
146A VAL* 4.3 15.5 - - + -
147A ALA* 4.7 1.6 - - + -
150A LEU* 3.7 14.7 - - + +
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Residues in contact with LYS 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 VAL* 2.9 31.0 + - + +
115A ASN* 4.1 14.4 - - - +
116A ILE 3.2 0.2 - - - -
117A PHE* 1.3 75.9 - - - +
119A PHE* 1.3 78.9 + - + +
122A PRO* 3.1 21.9 - - - +
150A LEU* 3.6 26.4 - - + +
327A LEU* 4.3 25.7 - - + +
328A LYS* 5.4 7.9 - - - +
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Residues in contact with PHE 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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83A TYR* 4.5 6.2 - - - -
115A ASN* 3.0 29.6 - - + -
116A ILE* 3.0 9.6 + - - +
117A PHE 2.9 0.6 - - - -
118A LYS* 1.3 101.9 - - + +
120A ILE* 1.3 64.9 + - + +
122A PRO* 4.5 0.5 - - - +
123A ASN* 4.2 17.2 - - - +
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Residues in contact with ILE 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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26A VAL* 4.0 17.9 - - + -
53A VAL* 6.4 1.3 - - + -
83A TYR* 2.7 39.3 - - + +
94A ILE* 4.7 7.9 - - + -
96A ALA* 3.8 29.4 - - + -
116A ILE* 3.2 28.0 - - + +
117A PHE* 3.0 17.6 + - + +
119A PHE* 1.3 81.0 - - + +
121A ILE* 1.3 70.2 + - + +
122A PRO* 3.4 0.2 - - - -
123A ASN* 3.2 14.4 + - - +
124A ILE* 3.2 20.1 + - + +
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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