Contacts of the helix formed by residues 56 - 66 (chain B) in PDB entry 2E7Y
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 GLY 56 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A GLU* 3.7 17.9 - - - +
26B ALA 2.7 22.1 + - - -
27B GLY 3.6 11.9 - - - -
28B GLU* 3.5 4.2 - - - +
30B VAL* 3.9 8.0 - - - +
31B SER* 4.8 0.3 + - - -
55B ALA* 1.3 71.5 - - - +
57B LEU* 1.3 62.4 + - - +
58B TRP 3.3 1.6 - - - -
59B GLY* 3.3 5.3 + - - -
60B VAL* 3.2 23.7 + - - +
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Residues in contact with LEU 57 (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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26B ALA* 3.5 20.7 + - + -
44B VAL* 4.8 14.1 - - + -
46B LEU* 4.6 10.1 - - + -
54B ILE* 3.0 17.8 + - + +
56B GLY* 1.3 74.7 - - - +
58B TRP* 1.3 66.4 + - - +
60B VAL* 3.2 21.3 + - + +
61B VAL* 3.2 23.8 + - + +
75B LEU* 5.5 0.7 - - + -
77B VAL* 4.3 31.9 - - + -
89B TYR* 3.9 11.4 - - + -
90B THR* 3.9 28.0 - - + -
93B ILE* 4.5 6.3 - - + -
104B PHE* 4.9 4.7 - - + -
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Residues in contact with TRP 58 (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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49A GLY 4.8 2.5 - - - -
51A VAL* 3.3 41.3 - - + +
54A ILE* 3.9 26.0 - - + -
55A ALA* 4.3 9.2 - - + -
85A ALA* 5.6 3.1 - - + -
89A TYR* 3.8 32.5 - + + -
55B ALA 4.5 2.0 - - - +
57B LEU* 1.3 78.5 - - - +
59B GLY* 1.3 64.0 + - - +
61B VAL* 3.3 1.9 - - - +
62B ASN* 3.0 21.3 + - + +
89B TYR* 3.2 23.3 + + - +
92B PHE* 3.9 22.4 - + - -
93B ILE* 3.7 22.6 - - + +
97B ASN* 3.7 36.0 + - - +
100B LEU* 3.8 22.8 - - + +
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Residues in contact with GLY 59 (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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11A PHE 6.2 0.2 - - - -
28A GLU* 4.9 6.5 + - - -
51A VAL* 4.4 10.6 - - - +
55A ALA* 5.8 1.2 - - - +
31B SER* 3.6 15.7 - - - -
55B ALA 4.9 0.6 + - - -
56B GLY* 3.3 8.6 + - - -
57B LEU 3.2 0.4 - - - -
58B TRP* 1.3 80.3 - - - +
60B VAL* 1.3 60.7 + - - +
62B ASN* 3.4 6.4 + - - +
63B ILE* 3.0 30.6 + - - +
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Residues in contact with VAL 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LEU* 4.5 7.2 - - + -
26B ALA* 5.2 0.2 - - + -
30B VAL* 3.7 22.0 - - + -
31B SER* 3.9 13.2 - - - +
38B VAL* 4.3 4.3 - - + +
41B PHE* 3.7 37.7 - - + -
44B VAL* 5.4 0.4 - - + -
56B GLY 3.2 14.8 + - - +
57B LEU* 3.2 16.4 + - + +
59B GLY* 1.3 76.9 - - - +
61B VAL* 1.3 59.4 + - + +
63B ILE* 3.6 2.2 + - - +
64B ARG* 3.0 37.5 + - + +
75B LEU* 4.2 17.0 - - + -
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Residues in contact with VAL 61 (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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57B LEU* 3.2 18.1 + - + +
58B TRP* 3.3 15.3 - - - +
60B VAL* 1.3 75.8 - - + +
62B ASN* 1.3 68.4 + - - +
64B ARG* 3.8 7.9 - - - +
65B ASN* 2.9 26.7 + - - +
75B LEU* 4.4 16.2 - - + -
93B ILE* 4.3 4.9 - - + -
100B LEU* 3.7 14.5 - - + +
103B SER* 4.0 14.6 + - - +
104B PHE* 3.7 47.1 - - + -
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Residues in contact with ASN 62 (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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10A LEU* 4.2 6.9 + - - +
51A VAL* 3.4 33.6 - - + +
58B TRP* 3.0 19.2 + - + +
59B GLY* 3.7 3.9 + - - +
61B VAL* 1.3 80.6 - - - +
63B ILE* 1.3 78.9 + - - +
65B ASN* 3.3 2.6 + - - +
66B ASN* 3.2 23.8 + - - +
99B ASP* 5.2 2.6 - - - +
100B LEU* 3.9 25.3 - - + +
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Residues in contact with ILE 63 (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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10A LEU* 3.6 27.8 - - + +
11A PHE* 3.6 47.3 - - + -
31B SER* 4.2 5.4 - - - +
35B GLY 4.7 1.1 - - - +
38B VAL* 3.6 22.4 - - + -
39B TYR* 3.4 17.3 - - + +
59B GLY* 3.0 21.0 + - - +
60B VAL 4.0 2.5 - - - +
62B ASN* 1.3 81.2 - - - +
64B ARG* 1.3 62.7 + - - +
66B ASN* 2.4 42.6 - - - +
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Residues in contact with ARG 64 (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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38B VAL* 2.7 26.4 + - + +
39B TYR* 3.0 42.0 + - + +
41B PHE* 2.2 48.2 + - - +
60B VAL* 3.0 29.4 + - + +
61B VAL* 3.8 7.6 - - - +
62B ASN 3.3 0.2 - - - -
63B ILE* 1.3 77.7 - - - +
65B ASN* 1.3 64.2 + - - +
66B ASN 3.8 4.9 - - - +
72B GLU* 6.1 2.4 - - - +
73B LYS 4.8 6.3 + - - -
75B LEU* 3.7 41.5 - - - +
103B SER* 5.6 2.2 + - - -
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Residues in contact with ASN 65 (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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61B VAL 2.9 19.5 + - - +
62B ASN 3.8 1.1 - - - +
64B ARG* 1.3 79.6 - - - +
66B ASN* 1.3 62.8 + - - +
99B ASP* 2.8 30.0 + - - +
100B LEU* 3.5 17.2 - - + +
103B SER* 4.2 18.0 - - - +
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Residues in contact with ASN 66 (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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10A LEU* 4.0 24.2 - - - +
39B TYR* 3.3 19.3 + - - -
62B ASN* 3.2 11.3 + - - +
63B ILE* 2.4 42.9 + - - +
64B ARG 3.8 5.2 - - - +
65B ASN* 1.3 83.6 - - - +
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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