Contacts of the helix formed by residues 57 - 63 (chain B) in PDB entry 1D7I
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 ARG 57 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55B VAL 3.6 1.8 + - - -
56B ILE* 1.3 71.0 - - - +
58B GLY* 1.3 62.7 + - - +
60B GLU* 3.0 13.2 + - - +
61B GLU* 3.0 47.7 + - - +
79B ASP 5.1 3.5 + - - +
80B TYR* 3.6 50.4 + - + +
81B ALA 5.4 0.2 + - - -
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Residues in contact with GLY 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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2B VAL* 4.2 9.0 - - - +
56B ILE 3.0 1.0 + - - -
57B ARG* 1.3 76.6 - - - +
59B TRP* 1.3 56.2 - - - +
61B GLU* 3.9 0.7 - - - -
62B GLY* 2.9 24.9 + - - -
74B LEU* 4.5 0.7 - - - +
76B ILE* 4.0 30.9 - - - +
80B TYR* 2.9 29.0 + - - -
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Residues in contact with TRP 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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24B VAL* 3.8 14.6 - - + -
26B TYR* 3.4 45.5 - + + -
46B PHE* 3.6 25.4 - + - -
48B PHE* 3.6 20.4 - + + -
55B VAL* 3.6 19.3 - - + -
56B ILE* 2.8 30.4 + - + +
58B GLY* 1.3 69.9 - - - -
60B GLU* 1.3 68.0 + - - +
63B VAL* 2.9 42.0 + - + +
74B LEU* 4.6 5.8 - - + -
76B ILE* 3.9 13.7 - - + -
99B PHE* 3.6 39.5 - + - +
101B VAL* 4.4 8.4 - - + +
302B DSS 3.9 17.7 - - - -
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Residues in contact with GLU 60 (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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18B ARG* 3.6 13.2 + - - +
48B PHE* 5.2 0.4 - - - -
49B MET 4.4 2.3 - - - +
50B LEU* 3.7 19.9 - - - +
51B GLY* 2.7 32.8 + - - -
52B LYS 3.6 0.3 + - - -
53B GLN* 3.0 36.9 + - + -
54B GLU 4.2 2.4 + - - -
55B VAL* 3.9 24.1 - - + +
56B ILE 3.3 5.1 + - - +
57B ARG* 3.0 13.6 + - - +
59B TRP* 1.3 81.0 - - - +
61B GLU* 1.3 61.6 + - + +
64B ALA* 3.4 21.5 - - - +
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Residues in contact with GLU 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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2B VAL* 4.4 12.3 - - + +
18B ARG* 5.4 2.5 - - - +
57B ARG* 3.0 47.7 + - + +
58B GLY* 4.5 0.7 - - - +
60B GLU* 1.3 82.1 - - + +
62B GLY* 1.3 61.0 + - - +
64B ALA* 4.0 7.2 + - - +
65B GLN* 2.9 30.6 + - - +
80B TYR* 3.4 23.0 + - - -
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Residues in contact with GLY 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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2B VAL* 4.2 12.1 - - - +
4B VAL* 4.2 15.7 - - - +
58B GLY 2.9 18.6 + - - -
61B GLU* 1.3 73.7 - - - +
63B VAL* 1.3 65.5 + - - +
64B ALA 3.1 1.6 - - - -
65B GLN* 3.2 15.3 + - - +
66B MET* 3.5 14.0 - - - +
74B LEU* 4.3 11.4 - - - -
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Residues in contact with VAL 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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16B PRO* 3.6 14.2 - - + +
22B CYS* 4.3 19.1 - - + -
24B VAL* 4.8 2.7 - - + -
48B PHE* 4.0 27.6 - - + -
50B LEU* 5.0 2.0 - - + -
59B TRP* 2.9 30.7 + - + +
60B GLU 5.1 0.2 - - - +
62B GLY* 1.3 77.6 - - - +
64B ALA* 1.3 61.6 + - - +
66B MET* 3.2 24.4 + - - +
74B LEU* 4.4 15.5 - - + +
101B VAL* 4.4 17.9 - - + -
103B LEU* 4.6 11.2 - - + -
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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