Contacts of the helix formed by residues 77 - 88 (chain B) in PDB entry 2X7N
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 77 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54B ALA* 4.7 5.4 - - - -
55B GLY* 4.9 3.6 - - - +
75B GLN 4.0 7.6 - - - +
76B THR* 1.3 71.4 - - - +
78B ASP* 1.3 59.9 + - - +
79B GLN* 3.5 10.6 + - - +
80B GLU* 2.8 43.7 + - - +
81B LEU* 3.0 25.6 + - - +
1D MET* 2.8 11.6 - - - +
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Residues in contact with ASP 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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77B THR* 1.3 65.9 - - - +
79B GLN* 1.3 54.9 + - - +
81B LEU* 3.7 7.8 - - - +
82B GLN* 2.9 32.2 + - - +
96B ARG* 3.0 11.9 + - - +
1D MET* 0.7 155.6 + - + +
30D ARG* 5.2 7.1 + - - -
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Residues in contact with GLN 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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77B THR* 3.1 9.9 + - - +
78B ASP* 1.3 75.1 - - - +
80B GLU* 1.3 62.0 + - + +
82B GLN* 3.4 10.5 + - - +
83B HIS* 2.9 29.0 + - + +
1D MET* 3.1 10.4 - - + +
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Residues in contact with GLU 80 (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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51B THR* 4.6 4.3 + - - +
52B THR* 2.8 46.8 + - - +
54B ALA 2.8 15.9 + - - -
55B GLY* 3.0 22.1 + - - -
76B THR* 3.5 9.1 - - + +
77B THR* 2.8 45.7 + - - +
79B GLN* 1.3 77.7 - - + +
81B LEU* 1.3 57.8 + - - +
83B HIS* 3.3 7.1 + - - +
84B LEU* 2.9 36.5 + - + +
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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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72B VAL* 4.5 13.5 - - + -
76B THR* 4.2 6.4 - - + +
77B THR 3.0 16.0 + - - +
78B ASP* 3.7 9.9 - - - +
80B GLU* 1.3 75.1 - - - +
82B GLN* 1.3 60.3 + - - +
84B LEU* 3.1 8.4 + - + +
85B ARG* 2.9 31.5 + - + +
94B ILE* 3.5 38.8 - - + +
96B ARG* 4.0 32.8 - - + +
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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 ASP 2.9 19.6 + - - +
79B GLN* 3.8 10.4 - - - +
81B LEU* 1.3 76.6 - - - +
83B HIS* 1.3 60.0 + - - +
85B ARG* 3.9 6.8 - - - +
86B ASN* 2.7 48.8 + - - +
1D MET* 5.9 2.6 - - - +
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Residues in contact with HIS 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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28B VAL* 6.2 0.4 - - + -
49B VAL* 4.1 7.9 - - + +
50B HIS* 2.9 32.1 + - + -
51B THR* 4.6 9.3 + - - -
79B GLN* 2.9 19.8 + - + +
80B GLU* 3.6 6.7 - - - +
81B LEU 3.2 0.2 - - - -
82B GLN* 1.3 78.9 - - - +
84B LEU* 1.3 61.0 + - - +
86B ASN* 3.6 8.1 + - + +
87B SER* 2.9 44.8 + - - -
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Residues in contact with LEU 84 (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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25B LEU* 4.1 21.8 - - + -
49B VAL* 4.2 10.5 - - + -
51B THR* 4.2 15.3 - - - +
53B ILE* 4.1 25.4 - - + -
70B LEU* 4.3 15.9 - - + -
72B VAL* 4.5 7.6 - - + -
76B THR* 5.0 1.8 - - + -
80B GLU 2.9 24.0 + - - +
81B LEU* 3.1 9.4 + - + +
83B HIS* 1.3 75.6 - - - +
85B ARG* 1.3 66.5 + - - +
87B SER* 3.1 1.3 + - - -
88B LEU* 2.9 48.9 + - + +
94B ILE* 3.7 16.6 - - + -
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Residues in contact with ARG 85 (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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81B LEU* 2.9 18.1 + - + +
82B GLN* 3.9 7.6 - - - +
84B LEU* 1.3 75.3 - - - +
86B ASN* 1.3 67.0 + - - +
88B LEU* 3.3 16.6 - - - +
90B ASP* 6.0 0.3 - - - -
94B ILE* 3.4 17.2 - - + +
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Residues in contact with ASN 86 (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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82B GLN* 2.7 43.4 + - - +
83B HIS* 3.9 8.2 - - + +
85B ARG* 1.3 83.5 - - - +
87B SER* 1.3 62.1 + - - +
88B LEU 4.3 2.3 - - - +
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Residues in contact with SER 87 (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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47B PRO* 4.0 17.5 - - - +
49B VAL* 3.5 28.7 - - - +
83B HIS* 2.9 36.9 + - - -
84B LEU 3.1 2.5 + - - -
86B ASN* 1.3 78.0 - - - +
88B LEU* 1.3 63.4 + - - +
89B PRO 3.9 0.2 - - - -
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Residues in contact with LEU 88 (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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23B TYR* 4.3 24.2 - - + -
25B LEU* 4.0 11.0 - - + -
47B PRO* 5.2 0.2 - - - -
49B VAL* 3.3 28.5 - - + -
70B LEU* 4.2 24.2 - - + -
84B LEU* 2.9 30.5 + - + +
85B ARG 3.3 15.3 - - - +
86B ASN 4.3 2.3 - - - +
87B SER* 1.3 74.1 - - - +
89B PRO* 1.3 77.5 - - + +
90B ASP* 3.7 0.7 + - - -
92B VAL* 3.6 24.9 - - + -
94B ILE* 4.3 15.0 - - + -
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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