Contacts of the helix formed by residues 69 - 86 (chain A) in PDB entry 2IMT
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 SER 69 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A GLU* 2.6 32.2 + - - -
66A GLN* 2.9 34.0 + - - +
68A SER* 1.3 83.1 + - - +
70A THR* 1.3 59.9 + - - +
71A MET 3.7 1.5 + - - -
72A GLY 3.0 8.3 + - - -
73A GLN* 2.8 28.6 + - - +
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Residues in contact with THR 70 (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 SER 3.9 0.4 + - - -
69A SER* 1.3 73.1 - - - +
71A MET* 1.3 73.6 + - + +
73A GLN* 3.1 15.0 + - - +
74A VAL* 2.8 33.7 + - + +
178A VAL* 3.5 32.5 - - + -
181A LEU* 5.0 6.3 - - + -
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Residues in contact with MET 71 (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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30A ASP* 3.7 41.5 - - + +
33A GLU* 3.6 30.7 - - + +
34A VAL* 3.6 23.2 - - + -
37A SER* 4.1 0.3 - - - -
69A SER* 3.3 2.0 + - - -
70A THR* 1.3 92.1 - - + +
72A GLY* 1.3 64.8 + - - +
74A VAL* 3.6 4.1 - - - +
75A GLY* 3.0 20.6 + - - -
177A TRP* 3.6 34.1 - - + +
178A VAL* 4.4 9.0 - - + +
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Residues in contact with GLY 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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33A GLU* 3.9 3.9 + - - -
37A SER* 2.8 30.4 + - - -
41A TYR* 4.2 3.0 - - - -
65A LEU* 5.8 0.9 - - - -
66A GLN 3.8 13.0 - - - -
67A PRO* 4.1 7.9 - - - -
69A SER* 3.0 19.5 + - - -
71A MET* 1.3 76.7 - - - +
73A GLN* 1.3 60.3 + - - +
76A ARG* 3.1 13.3 + - - +
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Residues in contact with GLN 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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67A PRO 4.0 10.7 + - - +
68A SER* 3.2 23.7 + - - +
69A SER 2.8 14.4 + - - +
70A THR* 3.3 15.0 + - - +
72A GLY* 1.3 73.7 - - - +
74A VAL* 1.3 64.8 + - - +
76A ARG* 3.3 8.9 + - - +
77A GLN* 3.0 26.9 + - - +
181A LEU* 3.8 25.7 - - + +
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Residues in contact with VAL 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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34A VAL* 4.2 7.2 - - + -
70A THR* 2.8 27.3 + - + +
71A MET* 3.3 9.4 + - - +
73A GLN* 1.3 72.4 - - - +
75A GLY* 1.3 63.5 + - - +
77A GLN* 3.1 3.9 + - - +
78A LEU* 2.9 32.6 + - + +
177A TRP* 3.5 46.4 - - + +
178A VAL* 4.1 5.4 - - - +
180A ALA* 3.9 14.1 - - + -
181A LEU* 3.9 23.3 - - + +
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Residues in contact with GLY 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A VAL* 3.6 31.6 - - - +
37A SER* 3.7 10.1 - - - -
38A TYR* 3.6 11.0 - - - -
71A MET 3.0 12.0 + - - -
74A VAL* 1.3 75.5 - - - +
76A ARG* 1.3 56.9 + - - +
78A LEU* 3.3 3.8 + - - +
79A ALA* 2.9 28.9 + - - +
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Residues in contact with ARG 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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37A SER* 3.5 0.6 + - - -
41A TYR* 3.5 43.3 - - + -
72A GLY 3.1 18.2 + - - +
73A GLN* 3.6 8.5 - - - +
74A VAL 3.1 0.6 - - - -
75A GLY* 1.3 77.4 - - - +
77A GLN* 1.3 85.8 + - - +
79A ALA* 3.2 3.6 + - - +
80A ILE* 3.1 43.5 + - + +
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Residues in contact with GLN 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 GLN* 3.0 9.2 + - + +
74A VAL* 3.1 6.9 + - - +
76A ARG* 1.3 110.5 - - - +
78A LEU* 1.4 57.8 + - + +
80A ILE* 3.2 11.7 + - - +
81A ILE* 2.9 46.1 + - + +
180A ALA 4.8 10.5 - - - +
181A LEU* 3.3 41.6 - - + +
183A LEU 4.6 5.2 - - - +
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Residues in contact with LEU 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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34A VAL* 4.3 2.7 - - + -
38A TYR* 3.8 15.7 - - + -
74A VAL* 2.9 30.0 + - + +
75A GLY* 3.7 4.9 - - - +
76A ARG 3.2 0.2 - - - -
77A GLN* 1.4 74.4 - - + +
79A ALA* 1.3 56.9 + - - +
81A ILE* 3.6 14.6 - - + +
82A GLY* 2.9 29.1 + - - -
125A TRP* 5.1 3.6 - - + -
128A VAL* 5.3 0.9 - - + -
129A VAL* 3.9 25.1 - - + +
132A LEU* 3.9 16.4 - - + -
177A TRP* 3.8 29.6 - - + -
180A ALA* 4.0 21.5 - - + +
183A LEU* 4.3 8.3 - - + -
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Residues in contact with ALA 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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38A TYR* 3.5 19.8 - - + +
41A TYR* 3.9 6.1 - - + -
42A ARG* 3.7 33.3 - - - +
45A GLN* 3.0 22.2 - - - +
75A GLY 2.9 14.2 + - - +
76A ARG 3.2 8.9 + - - +
78A LEU* 1.3 75.5 - - - +
80A ILE* 1.3 60.3 + - - +
82A GLY* 4.0 0.9 - - - -
83A ASP 3.2 14.6 + - - -
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Residues in contact with ILE 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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45A GLN* 3.2 23.6 - - - +
76A ARG* 3.1 53.4 + - + +
77A GLN* 3.6 17.7 - - - +
79A ALA* 1.3 75.3 - - - +
81A ILE* 1.3 67.1 - - + +
83A ASP* 3.3 13.4 + - - +
84A ASP* 3.1 17.0 - - - +
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Residues in contact with ILE 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 GLN* 2.9 28.9 + - + +
78A LEU* 3.6 21.1 - - + +
80A ILE* 1.3 81.8 - - + +
82A GLY* 1.3 67.4 + - - +
84A ASP* 3.2 16.5 + - - +
85A ILE* 3.2 29.2 + - + +
129A VAL* 4.5 9.9 - - + -
183A LEU* 4.0 48.7 - - + +
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Residues in contact with GLY 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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38A TYR* 5.3 4.0 - - - -
42A ARG* 6.5 1.1 - - - -
78A LEU 2.9 19.4 + - - -
79A ALA* 4.0 2.2 - - - -
81A ILE* 1.3 74.6 - - - +
83A ASP* 1.3 66.7 + - - +
84A ASP 3.0 1.0 + - - -
85A ILE* 4.0 2.9 - - - -
86A ASN* 3.0 31.7 + - - +
87A ARG 4.2 0.2 + - - -
129A VAL* 3.8 20.6 - - - -
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Residues in contact with ASP 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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42A ARG* 6.4 0.2 - - - +
45A GLN* 3.8 25.0 - - - +
49A ALA* 5.5 6.8 - - - +
79A ALA 3.2 6.6 + - - -
80A ILE* 3.3 14.1 - - - +
81A ILE 3.2 0.6 - - - -
82A GLY* 1.3 77.6 - - - +
84A ASP* 1.3 64.2 + - - +
87A ARG* 3.1 41.9 + - - +
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Residues in contact with ASP 84 (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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80A ILE* 3.1 23.6 - - - +
81A ILE* 3.6 9.5 - - - +
82A GLY 3.0 0.4 - - - -
83A ASP* 1.3 90.5 - - - +
85A ILE* 1.3 70.1 + - + +
86A ASN 3.5 0.6 + - - -
87A ARG* 3.9 28.4 + - - +
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Residues in contact with ILE 85 (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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81A ILE* 3.2 28.2 + - + +
82A GLY* 4.0 9.2 - - - -
84A ASP* 1.3 79.7 - - + +
86A ASN* 1.3 64.3 + - + +
87A ARG 3.2 5.3 + - - -
88A ARG* 4.7 16.6 + - - -
89A TYR* 5.0 2.7 - - + -
126A GLY* 4.7 15.3 - - - +
129A VAL* 4.1 22.0 - - + -
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Residues in contact with ASN 86 (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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38A TYR* 4.3 1.6 + - - +
42A ARG* 3.8 23.4 - - - +
82A GLY* 3.0 27.1 + - - +
85A ILE* 1.3 81.5 - - + +
87A ARG* 1.3 65.7 + - - +
88A ARG 3.1 3.0 + - - -
89A TYR* 3.2 15.0 + - - +
90A ASP* 2.9 35.5 + - - +
93A PHE* 4.7 2.4 - - - -
126A GLY 4.9 0.7 - - - +
129A VAL* 4.3 7.3 - - + +
130A ALA* 3.2 34.4 + - - +
133A GLY* 4.1 10.1 - - - -
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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