Contacts of the helix formed by residues 101 - 118 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98B LYS 4.6 3.6 - - - +
100B LEU* 1.3 77.5 - - - +
102B LYS* 1.3 68.6 + - - +
104B ASN* 3.9 1.0 - - - +
105B VAL* 2.8 40.4 + - + +
131B PRO* 3.4 18.3 - - + +
134B THR* 3.5 30.5 - - + +
135B ASN* 4.5 0.8 + - - +
322B GLU* 3.6 28.3 - - + +
325B THR* 3.7 13.9 - - + -
326B ALA* 3.1 46.4 - - + +
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Residues in contact with LYS 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B ASP* 2.8 44.9 + - - +
100B LEU 4.3 0.8 - - - +
101B LEU* 1.3 88.3 - - + +
103B ALA* 1.3 60.1 + - + +
104B ASN 3.4 0.6 + - - -
105B VAL* 3.9 7.0 + - - +
106B LYS* 4.9 2.8 + - - +
325B THR* 4.1 23.6 - - + +
329B PHE* 3.5 52.6 - - + -
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Residues in contact with ALA 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B MET* 2.9 31.5 - - + +
99B ASP* 5.9 1.6 - - - +
100B LEU* 3.0 18.3 + - + +
102B LYS* 1.3 80.0 - - + +
104B ASN* 1.3 59.7 + - - +
105B VAL 3.7 0.2 - - - -
106B LYS* 5.2 2.6 - - - +
107B ILE* 4.3 4.8 - - - +
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Residues in contact with ASN 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B SER* 3.2 11.1 - - - -
89B MET* 2.4 39.1 + - - +
100B LEU* 2.9 45.1 + - - +
103B ALA* 1.3 74.2 - - - +
105B VAL* 1.8 57.5 - - - +
106B LYS 3.4 2.2 - - - -
107B ILE* 3.2 25.2 - - - +
108B PHE* 3.2 11.3 - - - -
130B ASN 2.9 22.3 + - - +
131B PRO* 4.2 0.2 - - + -
135B ASN* 3.7 18.8 - - - +
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Residues in contact with VAL 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B LEU* 2.8 19.2 + - + +
102B LYS* 3.9 2.6 - - - -
103B ALA 3.7 0.8 - - - -
104B ASN 1.8 55.3 - - - +
106B LYS* 1.3 66.7 + - - +
108B PHE* 3.2 3.0 + - - -
109B LYS* 3.0 19.2 + - - +
134B THR* 4.1 6.7 - - + +
135B ASN* 3.7 17.3 - - - +
138B THR* 2.9 38.8 - - - +
326B ALA* 4.0 26.5 - - + +
329B PHE* 4.6 7.6 - - + -
330B LEU* 3.3 33.0 - - + -
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Residues in contact with LYS 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B LYS 4.9 3.3 + - - +
103B ALA 5.8 1.6 - - - -
104B ASN 5.8 0.7 - - - +
105B VAL* 1.3 82.6 - - - +
107B ILE* 1.3 62.9 + - + +
109B LYS* 3.1 38.6 + - - +
110B CYS* 3.1 46.4 + - - -
329B PHE* 4.8 12.1 - - + -
330B LEU* 4.1 21.7 + - + +
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Residues in contact with ILE 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B GLY 4.5 6.1 - - - +
88B SER* 4.9 0.9 - - - -
89B MET* 4.1 17.3 - - - -
103B ALA 4.3 2.7 - - - +
104B ASN* 3.2 29.6 - - - +
106B LYS* 1.3 78.2 - - + +
108B PHE* 1.3 70.0 + - + +
110B CYS* 3.5 7.3 + - - +
111B GLN* 2.9 47.4 + - - +
334B NAD 3.3 47.6 - - + +
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Residues in contact with PHE 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B LEU* 3.4 53.6 - - + -
87B GLY 3.6 25.8 - - - -
88B SER* 4.3 5.8 - - - -
104B ASN 3.2 21.5 - - - -
105B VAL 3.2 7.4 + - - +
107B ILE* 1.3 83.1 - - + +
109B LYS* 1.3 60.1 + - - +
111B GLN* 3.8 9.6 - - - -
112B GLY 2.9 22.3 + - - -
127B VAL* 3.8 13.5 - - + -
129B GLY* 4.6 4.3 - - - -
135B ASN* 3.1 55.6 - - + +
138B THR* 4.1 4.3 - - - -
139B ALA* 3.3 17.5 - - + +
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Residues in contact with LYS 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B VAL 3.0 11.9 + - - +
106B LYS* 3.1 40.4 - - - +
108B PHE* 1.3 73.4 - - - +
110B CYS* 1.3 66.2 + - - +
112B GLY 3.4 1.4 + - - -
113B ALA* 3.2 20.5 + - + +
138B THR* 3.7 12.5 - - + +
142B SER* 3.2 31.4 + - - +
330B LEU* 4.2 32.8 - - + -
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Residues in contact with CYS 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLU* 3.8 21.3 - - - +
106B LYS* 3.1 42.6 + - - -
107B ILE* 3.6 9.2 - - - +
109B LYS* 1.3 81.4 - - - +
111B GLN* 1.3 63.0 + - - +
113B ALA* 3.1 11.6 - - - +
114B ALA* 3.0 21.3 + - - +
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Residues in contact with GLN 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B THR* 4.2 12.8 + - - +
40B LEU* 4.5 4.4 - - + +
73B GLU* 4.0 14.0 + - - +
77B PHE* 3.6 25.7 - - + -
85B LEU* 3.7 29.2 - - + +
87B GLY 5.1 1.6 + - - -
107B ILE* 2.9 32.1 + - - +
108B PHE* 3.8 16.9 - - - +
109B LYS 3.4 0.2 - - - -
110B CYS* 1.3 77.2 - - - +
112B GLY* 1.3 61.3 + - - +
114B ALA* 3.3 4.5 + - - +
115B LEU* 3.1 27.5 + - - +
334B NAD 3.5 30.9 + - - -
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Residues in contact with GLY 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B PHE 2.9 16.0 + - - -
109B LYS 3.4 1.5 + - - -
110B CYS 3.3 0.2 - - - -
111B GLN* 1.3 74.0 - - - +
113B ALA* 1.3 57.2 + - - +
115B LEU* 2.9 13.4 + - - +
116B ASP* 2.8 29.8 + - - +
139B ALA* 3.5 26.6 - - - +
142B SER 3.6 7.6 - - - -
143B ALA* 3.4 4.9 - - - +
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Residues in contact with ALA 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B LYS 3.2 12.3 + - - +
110B CYS* 3.1 17.2 + - - +
112B GLY* 1.3 74.6 - - - +
114B ALA* 1.3 58.9 + - - +
116B ASP* 3.1 18.6 - - - +
117B LYS* 3.2 11.3 + - - +
142B SER* 3.3 16.9 + - - +
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Residues in contact with ALA 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B GLU* 4.2 17.9 - - + +
77B PHE* 3.7 29.2 - - + -
110B CYS 3.0 12.1 + - - +
111B GLN 3.3 4.9 + - - +
113B ALA* 1.3 72.4 - - - +
115B LEU* 1.3 61.7 + - - +
117B LYS 3.2 0.7 + - - -
118B TYR* 2.7 55.4 + - + +
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Residues in contact with LEU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B PHE* 3.3 28.2 - - + -
80B LEU* 4.4 0.9 - - + -
83B ALA* 4.0 19.1 - - + -
85B LEU* 4.6 7.4 - - + -
111B GLN 3.1 21.1 + - - +
112B GLY* 2.9 15.0 + - - +
114B ALA* 1.3 75.2 - - - +
116B ASP* 1.3 64.7 + - - +
119B ALA* 2.8 49.4 + - + +
123B VAL* 4.0 12.3 - - + -
125B VAL* 4.1 28.0 - - + -
143B ALA* 5.0 0.7 - - + -
146B ILE* 3.6 15.9 - - + +
151B PHE* 4.6 5.6 - - + -
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Residues in contact with ASP 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B GLY 2.8 11.7 + - - +
113B ALA* 3.1 15.2 - - - +
115B LEU* 1.3 77.5 - - - +
117B LYS* 1.3 61.8 + - - +
119B ALA 4.8 3.3 - - - +
142B SER 4.1 3.1 - - - +
143B ALA* 3.9 15.5 - - - -
144B PRO* 3.9 13.6 - - - +
145B SER* 2.4 37.1 + - - -
146B ILE* 3.7 12.8 - - - +
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Residues in contact with LYS 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B ALA 3.2 12.5 + - - +
114B ALA 4.0 1.6 - - - +
116B ASP* 1.3 80.8 - - + +
118B TYR* 1.3 105.7 + - + +
119B ALA 5.1 0.2 - - - -
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Residues in contact with TYR 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B GLU* 4.2 2.9 - - + -
74B GLU* 3.8 45.9 - - + +
77B PHE* 3.3 19.7 - - + +
78B LYS* 3.8 8.8 - - + +
79B ASP* 3.1 22.2 + - - +
114B ALA* 2.7 48.1 + - + +
117B LYS* 1.3 119.3 + - + +
119B ALA* 1.3 65.1 + - - +
120B LYS 3.7 0.3 + - - -
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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
------------------------------------------------------------
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