Contacts of the helix formed by residues 71 - 83 (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 THR 71 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B PHE* 2.8 29.4 + - - +
70B SER* 1.3 76.9 - - - +
72B ILE* 1.3 65.8 + - - +
73B LYS 3.1 0.9 + - - -
74B ALA* 3.3 17.5 + - - +
75B LEU* 4.3 3.3 + - - +
186B LEU* 4.4 7.6 - - - +
234B LYS* 3.6 28.3 - - - +
235B THR 3.6 9.0 + - - -
236B GLY 4.1 0.4 - - - +
245B ASN* 4.0 23.3 - - + +
246B ASP 4.4 0.9 - - - +
247B ILE* 4.0 30.2 - - + +
264B LEU* 5.1 1.3 - - + -
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Residues in contact with ILE 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B PHE* 3.5 35.7 - - + -
69B ALA 3.5 12.5 + - - +
70B SER* 2.8 4.6 - - - +
71B THR* 1.3 85.1 + - - +
73B LYS* 1.4 60.0 + - + +
74B ALA 3.1 0.2 - - - -
75B LEU* 3.0 42.1 + - + +
76B THR* 3.0 12.5 + - - +
135B GLN* 4.1 14.8 - - + +
148B LEU* 4.2 24.9 - - + -
152B LEU* 4.4 0.9 - - + -
160B THR* 4.1 21.5 - - + -
162B PRO* 5.2 2.2 - - + -
186B LEU* 5.6 2.2 - - + -
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Residues in contact with LYS 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B CEF 3.9 1.0 - - - -
70B SER* 2.9 38.0 + - - +
72B ILE* 1.4 73.1 - - + +
74B ALA* 1.3 63.4 + - - +
76B THR* 3.7 3.6 - - - -
77B VAL* 3.2 19.6 + - - +
126B SER* 3.3 29.4 - - - +
127B LEU* 3.7 12.1 - - + +
130B SER* 3.2 31.1 + - - -
131B ASP 3.9 2.7 - - - -
132B ASN* 2.8 27.7 + - - -
135B GLN* 3.3 48.4 - - + +
234B LYS* 4.0 5.2 - - - -
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Residues in contact with ALA 74 (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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70B SER 4.4 0.6 + - - -
71B THR 3.3 12.0 + - - +
72B ILE 3.1 0.6 - - - -
73B LYS* 1.3 81.2 - - - +
75B LEU* 1.3 58.8 + - + +
77B VAL* 3.5 2.8 + - - -
78B GLY* 3.1 20.6 + - - -
127B LEU* 4.0 11.4 - - + +
190B LEU* 4.0 25.7 - - + +
193B PHE* 5.5 0.7 - - - +
207B LEU* 3.9 12.9 - - + +
211B MET* 4.2 15.5 - - - -
234B LYS* 4.3 14.1 - - + +
247B ILE* 4.5 3.4 - - + -
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Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B THR 4.7 6.1 - - - +
72B ILE* 3.0 30.3 + - + +
74B ALA* 1.3 79.4 - - + +
76B THR* 1.3 59.0 + - - +
78B GLY* 2.9 16.5 + - - +
79B VAL* 3.2 15.6 + - - +
148B LEU* 4.5 3.8 - - + -
152B LEU* 4.1 24.0 - - + -
160B THR* 4.7 3.4 - - - +
186B LEU* 4.3 20.4 - - + +
189B SER* 3.4 36.3 - - - +
190B LEU* 3.5 24.7 - - + +
193B PHE* 4.3 13.8 - - + -
247B ILE* 5.5 2.9 - - + -
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Residues in contact with THR 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ILE* 3.0 11.9 + - - +
73B LYS 3.7 2.5 - - - -
74B ALA 3.2 0.4 - - - -
75B LEU* 1.3 76.5 - - - +
77B VAL* 1.3 57.3 + - - +
79B VAL* 3.3 3.8 + - - +
80B LEU* 2.9 24.5 + - - +
135B GLN* 2.5 43.4 + - - +
138B ILE* 4.0 11.9 - - + -
139B LEU* 3.9 12.3 - - + -
142B ILE* 3.9 22.1 - - + +
148B LEU* 3.8 18.9 - - + +
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Residues in contact with VAL 77 (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 LYS 3.2 13.3 + - - +
74B ALA 4.0 6.3 - - - +
75B LEU 3.4 0.2 - - - -
76B THR* 1.3 73.8 - - - +
78B GLY* 1.3 65.7 + - - +
79B VAL 3.0 0.9 - - - -
80B LEU* 4.0 10.5 - - + -
81B LEU* 2.7 51.8 + - + +
123B ALA* 4.4 15.0 - - + -
126B SER* 5.3 3.4 - - - +
127B LEU* 4.1 26.5 - - + -
135B GLN* 5.5 0.4 - - - +
138B ILE* 4.4 15.7 - - + -
207B LEU* 4.4 3.4 - - + -
210B TRP* 4.0 18.8 - - + -
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Residues in contact with GLY 78 (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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74B ALA 3.1 10.2 + - - -
75B LEU 2.9 13.3 + - - -
77B VAL* 1.3 73.0 - - - +
79B VAL* 1.3 57.5 - - - +
81B LEU* 4.2 0.9 - - - -
82B GLN* 2.9 14.9 + - - +
193B PHE* 3.5 30.1 - - - -
199B LEU* 2.8 27.3 - - - +
207B LEU* 4.6 6.0 - - - +
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Residues in contact with VAL 79 (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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75B LEU 3.2 6.4 + - - +
76B THR 3.6 7.0 - - - +
77B VAL 3.0 0.4 - - - -
78B GLY* 1.3 74.1 - - - +
80B LEU* 1.3 67.5 - - - +
82B GLN* 2.9 21.7 + - - +
83B GLN* 3.2 25.8 + - - +
142B ILE* 3.8 19.7 - - + -
148B LEU* 3.3 27.8 - - + -
151B GLU* 4.2 31.2 - - + +
152B LEU* 4.4 4.5 - - + -
193B PHE* 3.9 17.7 - - + -
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Residues in contact with LEU 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B THR 2.9 16.5 + - - +
77B VAL* 3.9 15.0 - - + +
79B VAL* 1.3 77.4 - - - +
81B LEU* 1.3 67.2 + - + +
83B GLN* 3.1 26.4 + - - +
86B LYS* 3.6 14.0 - - + +
91B LEU* 4.2 22.7 - - + -
119B LEU* 4.4 30.5 - - + +
123B ALA* 5.0 3.6 - - + -
138B ILE* 3.9 38.4 - - + -
141B GLN* 4.5 9.9 - - + -
142B ILE* 4.0 13.0 - - + +
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Residues in contact with LEU 81 (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 VAL* 2.7 44.2 + - + +
78B GLY* 3.4 7.0 - - - +
80B LEU* 1.3 79.9 - - + +
82B GLN* 1.3 60.4 + - - +
86B LYS 3.2 20.1 - - - +
88B ILE* 6.3 0.2 - - + -
91B LEU* 4.6 25.6 - - + -
199B LEU* 3.7 11.4 - - + -
203B LYS* 3.4 47.8 - - + +
206B LEU* 4.7 6.3 - - + -
207B LEU* 3.9 22.7 - - + +
210B TRP* 4.7 7.2 - - + -
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Residues in contact with GLN 82 (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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78B GLY 2.9 13.5 + - - +
79B VAL* 2.9 15.1 + - - +
81B LEU* 1.3 74.6 - - - +
83B GLN* 1.3 61.4 + - + +
86B LYS 4.1 2.2 + - - -
151B GLU* 4.0 21.0 + - - +
154B LYS* 6.1 0.4 - - - +
155B ILE* 4.6 16.0 - - - +
193B PHE* 4.5 7.6 - - - -
198B LYS* 3.2 18.9 - - - +
199B LEU* 2.7 28.8 - - + +
203B LYS* 4.7 3.7 + - - -
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Residues in contact with GLN 83 (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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79B VAL* 3.2 25.9 + - - +
80B LEU* 3.1 4.5 + - - +
81B LEU 3.2 0.2 - - - -
82B GLN* 1.3 87.0 + - + +
86B LYS* 1.6 86.2 + - + +
141B GLN 4.5 1.4 + - - -
142B ILE* 2.8 48.8 + - - +
151B GLU* 4.3 13.7 - - - +
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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