Contacts of the helix formed by residues 101 - 118 (chain A) in PDB entry 5MDH
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 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A LYS* 3.0 21.7 + - + +
99A ASP 3.2 1.4 - - - -
100A LEU* 1.3 75.0 - - - +
102A LYS* 1.3 60.6 + - + +
105A VAL* 2.7 40.7 + - + +
131A PRO* 3.4 36.1 - - + +
134A THR* 3.9 7.2 - - + -
322A GLU* 3.7 35.0 - - + +
325A THR* 4.4 15.0 - - + -
326A ALA* 3.5 36.1 - - + +
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Residues in contact with LYS 102 (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 ASP* 5.1 3.4 + - - +
100A LEU 3.5 1.0 - - - +
101A LEU* 1.3 82.8 - - + +
103A ALA* 1.3 62.3 + - - +
105A VAL* 4.5 1.3 - - - -
106A LYS* 4.0 9.4 + - - +
325A THR* 3.5 30.9 - - + +
329A PHE* 3.3 66.2 - - + +
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Residues in contact with ALA 103 (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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89A MET* 3.4 33.0 - - + -
99A ASP* 5.0 3.2 + - - +
100A LEU* 3.2 11.6 + - - +
102A LYS* 1.3 78.6 - - - +
104A ASN* 1.3 66.7 + - - +
106A LYS* 4.3 5.9 + - - +
107A ILE* 4.1 12.5 + - - +
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Residues in contact with ASN 104 (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* 2.8 26.2 + - - +
89A MET* 3.0 45.3 + - - +
100A LEU* 2.5 26.6 + - - +
101A LEU 4.1 0.2 - - - +
103A ALA* 1.3 77.7 - - - +
105A VAL* 1.3 64.3 + - - +
106A LYS 3.1 2.0 - - - -
107A ILE* 2.9 21.0 + - - +
108A PHE* 3.3 15.5 + - + -
130A ASN 3.0 22.9 + - - +
135A ASN* 3.9 9.0 - - - +
334A NAD 4.4 0.2 + - - -
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Residues in contact with VAL 105 (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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101A LEU* 2.7 29.4 + - + +
102A LYS 4.2 1.1 - - - +
104A ASN* 1.3 71.3 - - - +
106A LYS* 1.3 66.4 + - - +
108A PHE* 3.2 3.0 + - - +
109A LYS* 3.1 21.0 + - - +
134A THR* 4.6 4.3 - - + +
135A ASN* 3.5 17.4 - - - +
138A THR* 3.1 35.2 - - + +
326A ALA* 3.8 17.9 - - + -
329A PHE* 4.1 13.2 - - + -
330A LEU* 3.4 28.0 - - + -
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Residues in contact with LYS 106 (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 LYS 4.0 12.4 + - - +
103A ALA 4.5 4.9 - - - +
104A ASN 3.1 0.8 - - - -
105A VAL* 1.3 83.2 - - - +
107A ILE* 1.3 62.0 + - + +
109A LYS* 3.3 36.2 + - - +
110A CYS* 3.4 28.2 + - - -
329A PHE* 4.6 8.1 - - + -
330A LEU* 4.1 18.5 + - + +
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Residues in contact with ILE 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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87A GLY 4.5 11.2 - - - +
88A SER* 5.7 1.1 - - - -
103A ALA 4.1 12.3 - - - +
104A ASN* 2.9 25.8 + - - +
106A LYS* 1.3 75.5 - - + +
108A PHE* 1.3 61.0 + - + +
110A CYS* 3.4 8.0 + - - +
111A GLN* 3.0 53.7 + - + +
334A NAD 3.5 33.4 - - + +
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Residues in contact with PHE 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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85A LEU* 3.5 45.8 - - + -
87A GLY 3.7 24.2 - - - -
88A SER* 3.9 10.1 - - - -
104A ASN* 3.3 14.4 - - + +
105A VAL 3.2 6.9 + - - +
107A ILE* 1.3 77.8 - - + +
109A LYS* 1.3 60.4 + - - +
111A GLN* 3.8 10.8 - - - +
112A GLY 2.9 22.2 + - - -
127A VAL* 3.9 15.3 - - + -
129A GLY* 4.3 9.4 - - - -
135A ASN* 3.2 55.6 - - + +
138A THR* 4.4 1.8 - - + -
139A ALA* 3.2 18.6 - - + +
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Residues in contact with LYS 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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105A VAL 3.1 11.7 + - - +
106A LYS* 3.6 34.4 - - - +
107A ILE 3.3 0.2 - - - -
108A PHE* 1.3 75.6 - - - +
110A CYS* 1.3 65.1 + - - +
112A GLY 3.1 2.9 + - - -
113A ALA* 3.0 20.6 + - + +
138A THR* 3.8 17.2 - - + +
142A SER* 3.5 24.8 - - - +
330A LEU* 4.1 33.4 + - + -
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Residues in contact with CYS 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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73A GLU* 3.7 18.7 - - - +
106A LYS* 3.4 37.1 + - - -
107A ILE* 3.8 8.1 - - - +
109A LYS* 1.3 81.5 - - - +
111A GLN* 1.3 56.5 + - + +
113A ALA* 3.3 10.1 - - - +
114A ALA* 2.9 26.7 + - - +
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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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9A THR* 4.1 16.4 + - - +
40A LEU* 4.2 6.6 - - + +
73A GLU* 4.3 7.1 + - - +
77A PHE* 3.5 26.1 - - + -
85A LEU* 3.6 24.6 - - + +
87A GLY 4.9 2.3 + - - +
107A ILE* 3.0 40.4 + - + +
108A PHE* 4.1 19.3 - - - +
110A CYS* 1.3 73.2 - - + +
112A GLY* 1.3 61.6 + - - +
114A ALA* 3.0 7.5 + - - +
115A LEU* 2.8 35.5 + - - +
334A NAD 3.8 18.2 + - - -
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Residues in contact with GLY 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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108A PHE 2.9 15.2 + - - -
109A LYS 3.6 3.6 - - - -
111A GLN* 1.3 76.3 - - - +
113A ALA* 1.3 58.8 + - - +
115A LEU* 3.4 9.4 + - - +
116A ASP 3.1 19.2 + - - -
139A ALA* 3.4 28.1 - - - +
142A SER* 3.3 12.9 - - - +
143A ALA* 3.5 6.1 - - - +
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Residues in contact with ALA 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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109A LYS* 3.0 13.7 + - + +
110A CYS* 3.3 13.2 - - - +
112A GLY* 1.3 76.0 - - - +
114A ALA* 1.3 58.3 + - - +
116A ASP* 3.7 2.8 - - - +
117A LYS* 3.2 28.9 + - - +
142A SER* 3.5 16.6 + - - +
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Residues in contact with ALA 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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73A GLU* 4.2 15.7 - - + +
77A PHE* 3.7 31.8 - - + +
110A CYS 2.9 13.9 + - - +
111A GLN* 3.0 9.4 + - - +
113A ALA* 1.3 74.1 - - - +
115A LEU* 1.3 58.7 + - - +
117A LYS* 3.3 0.4 + - - -
118A TYR* 2.8 48.2 + - + +
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Residues in contact with LEU 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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77A PHE* 3.5 23.5 - - + -
80A LEU* 4.3 2.0 - - + -
83A ALA* 3.8 21.1 - - + -
85A LEU* 4.3 10.3 - - + -
111A GLN 2.8 21.9 + - - +
112A GLY* 3.6 11.0 - - - +
114A ALA* 1.3 70.8 - - - +
116A ASP* 1.3 63.0 + - - +
119A ALA* 2.7 48.5 + - + +
123A VAL* 4.3 4.3 - - + -
125A VAL* 3.7 37.2 - - + -
146A ILE* 3.9 15.2 - - + +
151A PHE* 4.0 12.8 - - + -
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Residues in contact with ASP 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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112A GLY 3.1 15.2 + - - +
113A ALA* 3.7 6.5 - - - +
115A LEU* 1.3 75.4 - - - +
117A LYS* 1.3 58.3 + - - +
121A LYS* 3.3 21.8 + - - -
142A SER 3.6 8.9 - - - +
143A ALA* 3.3 14.5 - - - +
144A PRO* 3.8 10.9 - - - +
145A SER* 2.7 41.2 + - - -
146A ILE* 3.9 12.3 - - - +
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Residues in contact with LYS 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 ALA 3.2 16.4 + - - +
114A ALA* 3.7 3.4 - - - +
115A LEU 3.2 0.6 - - - -
116A ASP* 1.3 82.7 - - - +
118A TYR* 1.3 107.3 + - + +
119A ALA 5.1 1.2 - - - +
121A LYS* 5.3 2.0 + - - -
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Residues in contact with TYR 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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73A GLU* 4.1 16.2 - - + -
74A GLU* 4.0 44.6 + - + +
77A PHE* 3.4 17.3 - - + +
78A LYS* 3.6 12.8 - - + +
79A ASP* 3.0 20.6 + - - +
114A ALA* 2.8 41.0 + - + +
117A LYS* 1.3 117.8 + - + +
119A ALA* 1.3 62.0 + - - +
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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