Contacts of the helix formed by residues 131 - 143 (chain B) in PDB entry 4MDH
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 PRO 131 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91B ARG* 3.5 24.8 - - + +
101B LEU* 4.1 21.5 - - + +
102B LYS* 5.5 8.1 - - + -
104B ASN* 4.6 3.4 - - + +
105B VAL* 5.3 4.0 - - + -
129B GLY 3.7 1.3 - - - -
130B ASN* 1.3 79.6 - - + +
132B ALA* 1.4 65.5 + - - +
133B ASN 3.4 2.0 - - - +
134B THR* 3.3 11.1 + - + +
135B ASN* 3.1 33.3 + - - +
185B ASN* 5.5 2.5 - - - +
322B GLU* 4.1 24.7 - - - +
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Residues in contact with ALA 132 (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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91B ARG* 5.1 0.2 - - - +
127B VAL* 3.4 24.3 - - - +
128B VAL 4.1 4.7 - - - +
129B GLY 3.4 12.8 - - - +
130B ASN* 3.0 22.2 + - - +
131B PRO* 1.4 69.4 - - - +
133B ASN* 1.3 66.9 + - - +
136B CYS* 3.1 26.9 + - - +
153B CYS* 3.6 10.8 - - + +
154B LEU 4.5 1.8 - - - +
186B HIS* 4.6 7.5 - - + +
335B NAD 4.1 9.2 - - - +
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Residues in contact with ASN 133 (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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131B PRO 3.3 0.8 + - - -
132B ALA* 1.3 78.3 - - - +
134B THR* 1.3 59.8 + - - +
136B CYS* 3.7 0.7 - - - +
137B LEU* 3.0 22.7 + - - +
153B CYS* 3.6 23.1 - - - -
155B THR* 4.9 0.9 - - - +
184B GLY 3.1 21.6 + - - -
185B ASN* 3.2 23.4 + - - +
186B HIS* 2.6 32.0 + - - +
284B LEU* 2.7 40.1 + - - +
285B TYR* 4.1 1.0 - - - +
286B SER* 4.3 2.8 - - - +
319B LEU* 3.8 7.4 - - + -
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Residues in contact with THR 134 (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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102B LYS* 5.5 3.1 - - - -
105B VAL* 4.5 10.3 - - + -
131B PRO* 3.3 12.4 + - + -
133B ASN* 1.3 81.0 - - - +
135B ASN* 1.4 51.6 + - - +
137B LEU* 3.8 7.0 - - - +
138B THR* 2.7 36.7 + - - +
319B LEU* 4.5 8.5 + - - +
322B GLU* 2.7 56.8 + - + +
323B LYS* 4.4 4.5 + - - +
326B ALA* 3.9 16.2 - - + -
327B PHE* 6.4 0.4 - - + -
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Residues in contact with ASN 135 (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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104B ASN* 3.3 17.0 + - - +
105B VAL* 3.4 20.4 - - - +
108B PHE* 2.9 44.1 - - + +
127B VAL* 4.1 5.2 - - + -
129B GLY 2.9 19.0 + - - -
130B ASN 3.6 17.4 + - - -
131B PRO* 3.1 18.0 + - - +
132B ALA 4.1 3.4 - - - +
134B THR* 1.4 72.7 - - - +
136B CYS* 1.3 57.0 + - - +
138B THR* 3.6 5.5 - - - -
139B ALA* 2.7 35.3 + - - +
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Residues in contact with CYS 136 (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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127B VAL* 3.6 23.0 - - + +
132B ALA 3.1 18.1 + - - +
133B ASN 3.7 3.8 - - - +
135B ASN* 1.3 78.3 - - - +
137B LEU* 1.3 66.7 + - - +
139B ALA* 3.0 2.9 + - - +
140B SER* 2.9 21.3 + - - -
151B PHE* 4.0 10.8 - - - -
152B SER 3.6 31.9 - - - -
153B CYS* 4.0 1.3 - - + -
284B LEU* 3.7 28.3 - - + -
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Residues in contact with LEU 137 (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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133B ASN 3.0 16.7 + - - +
134B THR* 4.0 7.4 - - + +
136B CYS* 1.3 75.6 - - - +
138B THR* 1.3 65.4 + - - +
140B SER* 2.9 16.5 + - - -
141B LYS* 3.2 17.6 + - + +
148B LYS* 4.3 13.7 - - - +
271B ILE* 3.8 25.8 - - + -
282B ASP* 3.3 29.6 - - - +
283B LEU* 4.2 8.7 - - + -
284B LEU* 4.1 17.6 - - + +
323B LYS* 3.9 20.9 - - + -
327B PHE* 4.6 12.8 - - + -
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Residues in contact with THR 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B VAL* 2.9 40.7 - - + +
108B PHE 4.6 0.2 - - - -
109B LYS* 4.1 9.2 - - + +
134B THR* 2.7 18.6 + - - +
135B ASN 3.7 3.6 - - - +
137B LEU* 1.3 80.0 - - - +
139B ALA* 1.3 63.6 + - - +
140B SER 3.2 0.7 + - - -
141B LYS* 3.3 12.8 + - - +
142B SER* 3.5 12.7 + - - +
326B ALA* 4.0 3.5 - - - +
327B PHE* 3.8 14.7 - - + -
330B LEU* 3.0 35.7 - - + +
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Residues in contact with ALA 139 (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* 4.9 8.3 - - + -
108B PHE* 3.6 33.4 - - + +
112B GLY* 3.5 18.3 - - - +
115B LEU* 5.6 0.9 - - + -
125B VAL* 5.7 0.2 - - + -
127B VAL* 5.0 1.3 - - + -
135B ASN 2.7 23.9 + - - +
136B CYS* 3.0 7.8 + - - +
138B THR* 1.3 74.4 - - - +
140B SER* 1.4 59.7 + - - +
142B SER 3.6 0.5 + - - -
143B ALA* 3.4 18.0 + - - +
151B PHE* 4.0 11.7 - - + -
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Residues in contact with SER 140 (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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136B CYS 2.9 10.0 + - - -
137B LEU* 2.9 16.5 + - - -
139B ALA* 1.4 74.4 - - - +
141B LYS* 1.3 60.7 + - - -
142B SER 3.3 0.9 - - - -
143B ALA 3.5 15.6 + - - +
144B PRO* 4.2 2.6 - - - +
146B ILE 4.8 1.2 + - - +
148B LYS* 4.1 35.3 + - - +
151B PHE* 3.3 38.5 - - - -
284B LEU* 5.4 2.5 - - - -
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Residues in contact with LYS 141 (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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137B LEU* 3.2 20.3 + - + +
138B THR* 3.3 6.0 + - - +
140B SER* 1.3 75.5 - - - +
142B SER* 1.3 61.2 + - - +
143B ALA 3.3 1.1 + - - -
144B PRO* 3.8 13.7 - - - +
148B LYS* 4.8 11.0 - - - +
282B ASP* 4.7 14.7 + - - -
323B LYS* 4.8 2.2 - - - +
327B PHE* 2.8 61.5 - - + +
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Residues in contact with SER 142 (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* 3.4 43.7 - - - +
112B GLY 3.6 3.4 - - - +
113B ALA* 3.7 11.5 + - - +
116B ASP* 3.6 15.1 - - - +
138B THR* 3.5 7.7 + - - +
139B ALA 3.9 7.4 - - - -
140B SER 3.3 0.2 - - - -
141B LYS* 1.3 77.1 - - - +
143B ALA* 1.3 56.2 + - - +
144B PRO* 2.9 15.3 - - - +
330B LEU* 5.6 0.2 - - - +
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Residues in contact with ALA 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B GLY* 3.3 20.2 - - - +
115B LEU* 4.8 0.7 - - + -
116B ASP* 3.8 3.6 - - - -
139B ALA 3.4 9.2 + - - +
140B SER 3.5 6.6 + - - +
141B LYS 3.3 1.4 - - - -
142B SER* 1.3 78.4 - - - +
144B PRO* 1.3 53.6 - - - +
145B SER 2.8 4.9 - - - -
146B ILE* 2.6 45.8 + - + +
151B PHE* 3.4 30.5 - - + -
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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