Contacts of the helix formed by residues 131 - 142 (chain B) in PDB entry 3M2K
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 ASP 131 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73B LYS* 3.9 3.3 - - - -
106B ASN* 3.9 1.2 - - - -
107B PRO* 3.0 19.0 - - + +
108B ILE* 2.8 36.7 + - - +
109B THR* 2.9 33.7 + - - +
125B ALA* 3.3 20.4 + - - +
126B SER* 3.9 2.5 - - - +
129B TYR 3.2 0.6 - - - -
130B SER* 1.3 74.4 - - - +
132B ASN* 1.3 68.4 + - - +
133B ALA 3.1 5.0 + - - -
134B ALA* 3.2 23.4 + - + +
135B GLN 3.2 15.8 + - - -
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Residues in contact with ASN 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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1B CEF 2.7 34.7 + - - +
73B LYS* 2.8 27.0 + - - +
103B VAL* 3.7 18.6 - - + -
104B ASN* 3.2 19.8 + - - +
105B TYR* 2.8 19.8 + - - +
130B SER 2.9 10.3 + - - +
131B ASP* 1.3 71.3 - - - +
133B ALA* 1.3 66.8 + - - +
135B GLN* 3.3 2.9 + - - +
136B ASN* 3.1 22.8 + - - +
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Residues in contact with ALA 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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97B TYR* 6.3 0.2 - - + -
101B ASP* 4.0 19.3 - - + +
102B LEU* 4.2 4.7 - - + +
103B VAL* 4.1 4.0 - - - +
106B ASN* 3.6 14.9 + - - +
109B THR* 3.3 29.6 - - + +
131B ASP* 3.1 3.0 + - - -
132B ASN* 1.3 75.9 - - - +
134B ALA* 1.3 54.7 + - - +
136B ASN* 2.9 33.2 + - - +
137B LEU* 3.1 18.6 + - + +
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Residues in contact with ALA 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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109B THR* 3.7 5.1 + - - +
122B LEU* 3.5 36.8 - - + +
125B ALA* 4.1 4.0 - - + -
126B SER* 3.9 5.6 - - - +
131B ASP* 3.2 33.7 + - + +
133B ALA* 1.3 71.5 - - - +
135B GLN* 1.3 68.7 + - - +
137B LEU* 3.4 3.1 + - - +
138B ILE* 3.0 28.0 + - - +
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Residues in contact with GLN 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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72B ILE* 4.1 11.9 - - + +
73B LYS* 3.3 50.8 - - + +
76B THR* 2.5 44.6 + - - +
77B VAL* 5.5 0.3 - - - +
126B SER* 3.5 8.1 + - - +
131B ASP 3.2 7.3 + - - -
132B ASN* 3.9 4.9 - - - +
134B ALA* 1.3 75.1 - - - +
136B ASN* 1.3 63.7 + - - +
138B ILE* 3.0 8.6 + - - +
139B LEU* 2.8 39.8 + - + +
148B LEU* 5.3 1.2 - - - +
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Residues in contact with ASN 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ASP* 4.9 7.6 + - - +
103B VAL* 4.2 26.1 - - - +
132B ASN* 3.1 12.7 + - - +
133B ALA* 2.9 15.2 + - + +
135B GLN* 1.3 82.0 - - - +
137B LEU* 1.3 58.5 + - + +
139B LEU* 3.3 10.3 - - - +
140B LYS* 3.2 28.8 + - - +
165B PHE* 3.7 53.7 - - + +
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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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95B ILE* 4.1 21.3 - - + -
97B TYR* 4.0 34.8 - - + -
101B ASP* 4.2 21.3 - - + +
109B THR* 5.2 1.1 - - - +
119B LEU* 5.3 0.3 - - - +
122B LEU* 4.2 25.3 - - + +
133B ALA* 3.1 25.2 + - + +
134B ALA 3.8 6.3 - - - +
136B ASN* 1.3 76.7 - - + +
138B ILE* 1.3 68.3 + - - +
140B LYS* 3.6 15.5 + - + +
141B GLN* 3.2 24.6 + - - +
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Residues in contact with ILE 138 (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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76B THR* 4.0 20.2 - - + +
77B VAL* 4.4 10.3 - - + -
80B LEU* 3.9 35.4 - - + -
119B LEU* 4.8 4.9 - - + +
122B LEU* 3.8 39.5 - - + +
123B ALA* 4.0 11.2 - - - +
126B SER* 4.6 6.7 - - - +
134B ALA 3.0 15.6 + - - +
135B GLN* 3.0 8.1 + - - +
137B LEU* 1.3 77.5 - - - +
139B LEU* 1.3 68.4 + - - +
141B GLN* 2.8 17.4 + - - +
142B ILE* 3.2 11.2 + - + +
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Residues in contact with LEU 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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76B THR* 3.9 21.1 - - + +
135B GLN* 2.8 27.2 + - + +
136B ASN* 3.3 14.8 - - - +
138B ILE* 1.3 72.8 - - - +
140B LYS* 1.3 60.2 + - - +
142B ILE* 3.0 17.6 + - + +
144B GLY* 2.7 36.8 + - - +
145B PRO* 4.1 21.8 - - + -
148B LEU* 4.7 10.3 - - + -
164B ARG 4.5 5.4 - - - +
165B PHE* 3.8 27.8 - - + -
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Residues in contact with LYS 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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101B ASP* 5.4 7.2 - - - -
136B ASN 3.2 14.8 + - - +
137B LEU* 3.6 20.2 - - + +
138B ILE 3.1 0.4 + - - -
139B LEU* 1.3 79.1 - - - +
141B GLN* 1.3 61.1 + - + +
143B GLY* 3.1 16.7 + - - -
144B GLY* 4.6 4.5 - - - +
165B PHE* 3.9 26.9 - - + -
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Residues in contact with GLN 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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80B LEU* 4.5 7.6 - - + -
83B GLN* 4.5 0.9 + - - -
86B LYS* 3.7 37.2 + - - +
93B GLN* 4.1 13.0 + - - +
95B ILE* 3.2 31.3 - - + +
119B LEU* 3.6 25.1 - - + -
137B LEU 3.2 13.0 + - - +
138B ILE* 2.8 12.6 + - - +
140B LYS* 1.3 74.4 - - - +
142B ILE* 1.3 60.0 + - - +
143B GLY 3.4 0.4 - - - -
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Residues in contact with ILE 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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76B THR* 3.9 25.8 - - + +
79B VAL* 3.8 25.1 - - + -
80B LEU* 4.0 20.0 - - + -
83B GLN* 2.8 28.3 + - - +
138B ILE* 3.4 14.4 - - + +
139B LEU* 3.0 14.8 + - + +
140B LYS 3.0 0.8 - - - -
141B GLN* 1.3 81.7 - - - +
143B GLY* 1.3 56.7 + - - +
144B GLY 3.2 7.4 - - - +
147B SER* 3.0 19.8 + - - -
148B LEU* 4.5 10.8 - - + +
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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