Contacts of the helix formed by residues 71 - 83 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A PHE* 2.8 27.2 + - - +
70A SER* 1.3 74.2 - - - +
72A ILE* 1.3 59.1 + - - +
73A LYS 3.0 3.2 + - - -
74A ALA* 3.3 19.1 + - - +
75A LEU* 4.1 4.0 + - - +
186A LEU* 3.7 10.4 - - - +
234A LYS* 3.6 27.6 - - - +
235A THR 3.6 0.2 + - - -
236A GLY 3.6 17.3 - - - +
245A ASN* 3.8 21.9 + - + +
247A ILE* 3.8 28.3 - - + +
264A LEU* 5.1 0.7 - - + -
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Residues in contact with ILE 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A PHE* 3.7 47.3 - - + -
69A ALA 3.5 14.8 + - - +
70A SER* 3.0 3.7 - - - -
71A THR* 1.3 77.4 + - - +
73A LYS* 1.3 58.8 + - + +
74A ALA 3.2 0.7 - - - -
75A LEU* 3.6 16.6 - - + +
76A THR* 2.6 43.4 + - - +
135A GLN* 3.5 15.5 - - - +
148A LEU* 4.0 22.2 - - + -
152A LEU* 4.8 1.1 - - + -
160A THR* 4.4 12.3 - - + -
162A PRO* 4.6 2.7 - - + -
186A LEU* 6.3 0.9 - - + -
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Residues in contact with LYS 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A CEF 3.4 0.4 - - - -
70A SER* 2.7 35.2 + - - +
71A THR 3.0 0.6 - - - -
72A ILE* 1.3 81.5 - - + +
74A ALA* 1.3 63.8 + - - +
76A THR* 3.8 1.2 - - - -
77A VAL* 3.2 20.1 + - - +
126A SER* 3.3 32.5 - - - +
127A LEU* 3.6 13.1 - - + +
130A SER* 2.7 28.4 + - - +
131A ASP 3.5 17.0 - - - -
132A ASN* 2.7 24.0 + - - +
135A GLN* 3.5 38.7 - - - +
234A LYS* 3.9 8.7 - - - -
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Residues in contact with ALA 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A THR 3.3 13.6 + - - +
73A LYS* 1.3 79.8 - - - +
75A LEU* 1.3 65.8 + - + +
77A VAL* 3.5 4.7 + - - +
78A GLY* 3.3 15.9 + - - -
127A LEU* 3.8 12.4 - - + +
190A LEU* 5.3 4.0 - - + -
193A PHE* 5.5 0.9 - - - +
207A LEU* 4.7 7.8 - - - +
211A MET* 4.3 21.3 - - + -
234A LYS* 4.1 20.3 - - + +
247A ILE* 4.8 6.5 - - + -
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Residues in contact with LEU 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A THR 4.6 7.4 - - - +
72A ILE* 3.2 17.2 + - + +
74A ALA* 1.3 78.8 - - + +
76A THR* 1.3 66.7 + - - +
77A VAL 3.1 0.2 - - - -
78A GLY* 3.0 11.0 + - - +
79A VAL* 3.2 17.9 + - - +
148A LEU* 4.7 2.2 - - + -
152A LEU* 4.3 28.9 - - + -
160A THR* 4.8 5.2 - - + +
186A LEU* 4.1 26.2 - - + +
189A SER* 3.9 15.7 - - - +
190A LEU* 3.7 37.2 - - + +
193A PHE* 4.2 14.0 - - + -
247A ILE* 5.6 3.4 - - + -
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Residues in contact with THR 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A ILE* 2.6 28.5 + - - +
73A LYS 3.8 3.1 - - - -
74A ALA 3.2 0.2 - - - -
75A LEU* 1.3 78.3 - - - +
77A VAL* 1.3 57.2 + - - +
79A VAL* 3.6 5.5 - - - +
80A LEU* 3.2 22.6 + - - +
135A GLN* 2.9 37.5 + - - +
138A ILE* 3.8 9.9 - - + -
139A LEU* 4.3 9.1 - - + +
142A ILE* 3.6 27.0 - - + +
148A LEU* 4.0 15.5 - - + +
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Residues in contact with VAL 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A LYS 3.2 17.1 + - - +
74A ALA 4.0 1.6 - - - +
75A LEU 3.1 0.4 - - - -
76A THR* 1.3 78.9 - - - +
78A GLY* 1.3 65.0 + - - +
79A VAL 3.3 0.2 - - - -
80A LEU* 3.5 10.7 - - + +
81A LEU* 3.2 29.9 + - + +
123A ALA* 4.3 14.6 - - + -
126A SER* 5.6 1.3 - - - -
127A LEU* 4.0 16.8 - - + -
135A GLN* 6.0 0.2 - - - +
138A ILE* 4.1 26.2 - - + -
207A LEU* 3.4 30.5 - - + -
210A TRP* 4.3 7.4 - - + -
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Residues in contact with GLY 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A ALA 3.3 9.3 + - - -
75A LEU 3.0 8.0 + - - -
77A VAL* 1.3 79.1 - - - +
79A VAL* 1.3 65.1 + - - +
82A GLN* 3.2 3.1 + - - -
193A PHE* 3.5 29.1 - - - -
199A LEU* 3.2 34.5 - - - +
207A LEU* 4.5 4.5 - - - -
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Residues in contact with VAL 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A LEU 3.2 13.4 + - - +
76A THR 3.6 8.1 - - - +
78A GLY* 1.3 75.3 - - - +
80A LEU* 1.4 64.8 + - - +
82A GLN* 2.9 31.2 - - - +
83A GLN* 3.0 41.3 + - - +
142A ILE* 4.4 17.7 - - + -
148A LEU* 3.6 22.2 - - + -
151A GLU* 4.1 27.4 - - + -
152A LEU* 4.7 5.8 - - + -
193A PHE* 3.8 12.6 - - + -
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Residues in contact with LEU 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A THR 3.2 15.0 + - - +
77A VAL* 3.8 18.2 - - + +
78A GLY 3.2 1.0 - - - -
79A VAL* 1.4 78.6 - - - +
81A LEU* 1.3 62.8 + - + +
83A GLN* 2.8 16.9 + - - +
86A LYS* 3.2 34.2 + - + +
91A LEU* 3.9 13.5 - - + -
119A LEU* 3.7 33.0 - - + -
123A ALA* 4.9 7.4 - - + -
138A ILE* 4.2 18.8 - - + -
141A GLN* 4.8 4.0 - - + -
142A ILE* 3.7 27.8 - - + -
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Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A VAL* 3.2 30.4 + - + +
79A VAL 3.2 0.4 - - - -
80A LEU* 1.3 77.9 - - + +
82A GLN* 1.3 68.5 + - - +
83A GLN 2.8 1.7 + - - -
86A LYS* 3.1 19.1 - - - +
88A ILE* 6.1 0.7 - - + -
91A LEU* 3.7 32.3 - - + -
199A LEU* 3.5 26.0 - - + -
203A LYS* 3.3 51.7 - - + +
206A LEU* 5.1 4.7 - - + -
207A LEU* 4.4 12.1 - - + +
210A TRP* 4.4 11.9 - - + -
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Residues in contact with GLN 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A GLY 3.2 4.4 + - - +
79A VAL* 2.9 33.6 + - - +
81A LEU* 1.3 82.0 - - - +
83A GLN* 1.3 65.2 + - + +
86A LYS 3.6 1.2 + - - +
151A GLU* 4.6 15.0 + - - +
155A ILE* 5.1 6.3 - - - +
193A PHE* 3.7 18.1 - - - -
198A LYS* 3.2 32.2 - - - +
199A LEU* 3.3 6.6 - - - +
200A PRO* 5.7 1.8 - - - -
203A LYS* 4.5 5.5 + - - -
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Residues in contact with GLN 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A VAL* 3.0 35.5 - - - +
80A LEU* 2.8 10.6 + - - +
81A LEU 2.8 2.4 - - - -
82A GLN* 1.3 85.7 - - + +
86A LYS* 1.4 73.1 + - + +
90A ASP* 4.9 1.2 - - - +
141A GLN 4.7 2.2 + - - -
142A ILE* 3.9 30.2 + - - +
147A SER* 5.6 0.2 + - - -
151A GLU* 4.2 14.9 - - - +
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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