Contacts of the helix formed by residues 114 - 128 (chain B) in PDB entry 1MDU
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 114 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77B ILE* 4.0 16.6 - - + -
112B LEU 3.7 7.9 - - - +
113B ASN* 1.3 95.5 - - - +
115B LYS* 1.3 67.7 + - - +
116B ALA* 4.3 7.2 - - + +
117B ASN* 2.8 33.6 + - - +
118B ARG* 3.3 9.1 + - - +
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Residues in contact with LYS 115 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113B ASN 3.4 2.9 + - - +
114B PRO* 1.3 71.8 - - - +
116B ALA* 1.3 61.6 + - - +
118B ARG* 3.3 11.7 + - - +
119B GLU* 3.0 33.5 + - - +
373B HIS* 3.5 33.6 - - + +
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Residues in contact with ALA 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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114B PRO* 3.0 5.7 + - + +
115B LYS* 1.3 79.8 - - - +
117B ASN* 1.3 61.9 + - - +
119B GLU* 3.3 12.0 + - - +
120B LYS* 2.9 30.6 + - - +
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Residues in contact with ASN 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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77B ILE* 3.5 16.0 - - - +
78B ILE* 3.2 29.9 + - + +
81B TRP* 3.5 24.9 - - + +
113B ASN* 3.5 20.7 + - - +
114B PRO* 2.8 34.0 + - - +
116B ALA* 1.3 71.9 - - - +
118B ARG* 1.3 59.5 + - - +
120B LYS 3.1 1.0 + - - -
121B MET* 2.8 37.8 + - - +
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Residues in contact with ARG 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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109B GLU* 2.6 42.7 + - - +
113B ASN* 3.5 16.8 - - - +
114B PRO 3.3 12.8 - - - +
115B LYS* 3.5 14.1 - - - +
117B ASN* 1.3 73.6 - - - +
119B GLU* 1.3 62.2 + - - +
121B MET* 3.3 12.1 + - - +
122B THR* 2.9 28.4 + - - -
136B VAL* 4.0 30.1 + - + +
372B VAL* 2.9 28.5 + - + +
373B HIS* 2.8 31.5 + - + +
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Residues in contact with GLU 119 (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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115B LYS* 3.0 24.7 + - - +
116B ALA* 3.6 8.7 + - - +
118B ARG* 1.3 76.5 - - - +
120B LYS* 1.3 58.5 + - - +
122B THR* 3.3 4.4 + - - -
123B GLN* 3.0 28.6 + - - +
369B PRO* 3.7 26.2 - - + +
370B SER* 4.1 14.7 + - - -
372B VAL* 4.2 4.3 - - - -
373B HIS* 3.1 32.8 + - + +
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Residues in contact with LYS 120 (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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81B TRP* 3.6 55.8 - - + +
116B ALA 2.9 17.8 + - - +
117B ASN 3.7 3.1 - - - +
119B GLU* 1.3 76.9 - - - +
121B MET* 1.3 62.5 + - - +
123B GLN* 3.4 18.5 + - - +
124B ILE* 3.1 34.8 + - + +
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Residues in contact with MET 121 (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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14B ASN* 5.2 2.0 - - - +
78B ILE* 3.8 19.3 - - + -
81B TRP* 3.5 22.2 - - + -
88B TRP* 4.1 13.8 - - + -
107B LEU* 4.2 27.8 - - + -
108B THR 3.9 21.8 - - - +
109B GLU* 4.9 3.1 - - - -
113B ASN* 4.1 19.7 - - - -
117B ASN* 2.8 23.0 + - - +
118B ARG* 3.5 8.3 - - - +
119B GLU 3.3 0.2 - - - -
120B LYS* 1.3 76.9 - - - +
122B THR* 1.3 63.6 + - - +
124B ILE* 3.9 2.6 - - - +
125B MET* 3.1 29.9 + - - +
134B MET* 5.0 0.9 - - - -
136B VAL* 4.5 15.7 - - + -
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Residues in contact with THR 122 (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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118B ARG 2.9 14.1 + - - -
119B GLU* 3.4 11.2 - - - -
121B MET* 1.3 75.2 - - - +
123B GLN* 1.3 66.0 + - - +
125B MET* 3.3 2.4 + - - +
126B PHE* 3.1 51.1 + - + -
134B MET* 3.6 19.0 - - + +
136B VAL* 4.6 0.2 - - - +
359B ILE* 5.5 4.3 - - + -
364B TYR* 4.1 14.1 - - + -
369B PRO* 4.4 7.6 - - + -
371B ILE* 5.8 1.1 - - + -
372B VAL* 3.0 28.5 - - + +
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Residues in contact with GLN 123 (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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119B GLU 3.0 14.3 + - - +
120B LYS* 3.7 21.8 + - - +
121B MET 3.3 0.2 - - - -
122B THR* 1.3 77.6 - - - +
124B ILE* 1.3 60.0 + - + +
127B GLU* 2.8 57.2 + - + +
364B TYR* 3.5 25.5 - - - +
369B PRO* 4.2 9.1 - - + +
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Residues in contact with ILE 124 (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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81B TRP* 3.9 35.0 - - + +
85B GLU* 3.8 40.8 - - + +
88B TRP* 4.1 15.3 - - + -
120B LYS* 3.1 33.1 + - + +
121B MET 3.9 3.4 - - - +
123B GLN* 1.3 77.4 - - + +
125B MET* 1.3 62.3 + - - +
127B GLU* 5.2 0.2 - - - -
128B THR* 2.8 42.4 + - - +
129B PHE* 3.1 17.9 + - + -
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Residues in contact with MET 125 (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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88B TRP* 3.4 53.6 - - + -
92B PHE* 4.2 14.4 - - + -
105B THR* 4.9 5.4 - - - -
107B LEU* 3.5 28.9 - - + -
121B MET 3.1 19.2 + - - +
122B THR 3.3 4.5 + - - +
124B ILE* 1.3 76.9 - - - +
126B PHE* 1.3 56.8 - - - +
129B PHE* 3.2 21.3 + - + +
130B ASN 2.9 23.2 + - - -
131B VAL* 3.3 31.4 + - + +
134B MET* 3.8 18.8 - - + -
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Residues in contact with PHE 126 (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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122B THR* 3.1 27.1 + - + +
125B MET* 1.3 79.3 - - - +
127B GLU* 1.3 60.6 + - - +
130B ASN* 3.0 34.0 + - - +
131B VAL* 3.4 33.0 - - + -
133B ALA* 4.0 3.6 - - - -
134B MET* 3.7 20.4 - - + -
359B ILE* 3.1 32.8 - - + -
360B THR 3.7 7.6 - - - -
361B LYS* 3.5 32.5 - - + -
364B TYR* 3.3 49.1 - + + -
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Residues in contact with GLU 127 (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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123B GLN* 2.8 40.3 + - + +
126B PHE* 1.3 74.3 - - - +
128B THR* 1.3 59.7 + - - +
130B ASN* 4.2 9.9 + - - +
361B LYS* 5.3 5.6 - - - +
364B TYR* 2.5 38.5 + - + -
365B ASP* 5.8 1.3 - - - +
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Residues in contact with THR 128 (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 GLU* 3.5 33.8 + - - +
124B ILE* 2.8 33.2 + - - +
127B GLU* 1.3 76.7 - - - +
129B PHE* 1.3 77.4 + - + +
130B ASN* 3.5 4.7 - - - +
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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