Contacts of the helix formed by residues 75 - 91 (chain B) in PDB entry 1E8O
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 GLU 75 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B GLU* 4.6 10.1 - - - +
6B SER* 2.5 34.7 + - - +
70B VAL 4.1 9.5 - - - +
71B VAL* 4.3 4.2 - - + -
72B SER* 3.2 21.9 + - - +
73B SER 3.0 0.2 - - - -
74B LYS* 1.3 86.9 - - + +
76B VAL* 1.3 64.7 + - - +
77B ASN 3.1 4.5 + - - -
78B LYS* 3.6 10.3 + - + +
79B PHE* 3.2 24.1 + - + +
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Residues in contact with VAL 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A MET* 4.4 16.2 - - + +
74A VAL* 3.8 17.7 - - + -
71B VAL* 3.9 15.5 - - + -
72B SER 2.8 21.3 + - - +
73B SER* 3.2 23.9 + - - +
75B GLU* 1.3 71.9 - - - +
77B ASN* 1.3 53.2 + - - +
80B GLN* 2.7 39.2 + - + +
136E A 3.4 46.0 - - + +
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Residues in contact with ASN 77 (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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73B SER 5.0 1.2 + - - -
74B LYS 6.0 0.4 - - - +
75B GLU 3.1 1.6 + - - -
76B VAL* 1.3 79.2 - - - +
78B LYS* 1.3 72.6 + - + +
79B PHE 3.0 0.7 + - - -
80B GLN* 3.3 5.7 + - - +
81B MET* 3.5 35.6 + - - +
113E G 4.9 1.9 - - - +
135E U 3.0 56.4 + - - +
136E A 3.7 38.8 + - + +
1149E SO4 5.3 0.8 + - - -
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Residues in contact with LYS 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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74B LYS 5.7 4.7 + - - -
75B GLU* 3.6 10.9 + - + +
77B ASN* 1.3 81.4 - - + +
79B PHE* 1.3 60.9 + - - +
81B MET* 4.0 7.0 + - - +
82B ALA* 3.3 22.2 + - - +
1149E SO4 5.1 10.5 - - - +
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Residues in contact with PHE 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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70A MET* 3.6 21.3 - - + -
6B SER* 4.2 18.6 - - - -
9B PHE* 4.0 15.9 - + - -
10B LEU* 3.6 32.3 - - + -
58B LEU* 3.5 31.9 - - + -
69B THR* 4.7 1.3 - - + -
71B VAL* 3.5 33.9 - - + -
75B GLU* 3.2 20.9 + - + +
76B VAL 3.8 2.2 - - - +
77B ASN 3.0 1.6 + - - -
78B LYS* 1.3 77.3 - - - +
80B GLN* 1.3 54.6 + - - +
82B ALA* 3.2 3.5 + - - +
83B TYR* 2.6 56.5 + + + +
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Residues in contact with GLN 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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67A SER* 3.1 24.5 + - - +
70A MET* 5.3 7.2 - - - -
76B VAL* 2.7 25.1 + - + +
77B ASN* 4.4 1.6 - - - +
79B PHE* 1.3 74.4 - - - +
81B MET* 1.3 66.1 + - + +
83B TYR* 3.6 6.1 - - - +
84B SER* 2.5 44.9 + - - -
113E G 2.7 60.2 + - + +
136E A 3.2 22.4 - - + +
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Residues in contact with MET 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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77B ASN* 3.5 33.9 + - - +
78B LYS* 4.3 5.4 - - - +
79B PHE 3.4 0.6 - - - -
80B GLN* 1.3 89.6 - - + +
82B ALA* 1.3 58.3 + - - +
84B SER* 3.2 7.0 + - - -
85B ASN* 2.9 37.7 + - - +
113E G 6.0 1.8 - - - +
135E U 5.7 6.5 - - + +
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Residues in contact with ALA 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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10B LEU* 3.4 25.2 - - + +
78B LYS 3.3 17.2 + - - +
79B PHE 3.2 1.4 + - - +
81B MET* 1.3 77.5 - - - +
83B TYR* 1.3 63.4 + - - +
85B ASN* 3.1 8.5 + - - +
86B LEU* 2.9 23.0 + - - +
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Residues in contact with TYR 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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63A GLU* 5.3 1.6 - - - -
66A HIS* 2.8 43.6 + + + -
67A SER* 5.1 8.3 - - - -
70A MET* 4.6 14.8 - - + -
9B PHE* 5.1 0.2 - + - -
10B LEU* 3.8 21.9 - - + +
13B LEU* 4.1 17.0 - - + -
28B ILE* 3.7 15.0 - - + +
58B LEU* 4.4 12.3 - - + -
79B PHE* 2.6 46.0 + + + +
80B GLN* 3.6 4.0 - - - +
82B ALA* 1.3 72.1 - - - +
84B SER* 1.3 64.8 + - - +
86B LEU* 3.2 3.4 + - + +
87B LEU* 3.0 60.7 + - + +
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Residues in contact with SER 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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63A GLU* 2.8 35.3 + - - +
80B GLN* 2.5 32.0 + - - -
81B MET* 3.3 8.5 - - - -
83B TYR* 1.3 74.5 - - - +
85B ASN* 1.3 71.1 + - - +
87B LEU* 3.5 2.5 + - - +
88B ARG* 3.1 30.2 + - - +
113E G 4.3 4.2 + - - -
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Residues in contact with ASN 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 MET* 2.9 20.5 + - - +
82B ALA* 3.6 10.2 - - - +
84B SER* 1.3 82.9 + - - +
86B LEU* 1.3 65.2 + - - +
88B ARG* 3.3 8.0 + - - +
89B ALA* 3.1 28.1 + - - +
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Residues in contact with LEU 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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10B LEU* 3.4 29.2 - - + +
13B LEU* 3.6 15.5 - - + -
14B THR* 3.1 35.4 - - - +
17B PHE* 3.8 29.2 - - + -
82B ALA 2.9 13.4 + - - +
83B TYR* 3.4 10.8 - - + +
85B ASN* 1.3 78.1 - - - +
87B LEU* 1.3 70.6 + - + +
89B ALA* 5.5 0.2 - - - -
90B ASN* 3.1 33.7 + - - +
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Residues in contact with LEU 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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29A LEU* 4.6 6.3 - - + -
59A VAL* 4.8 1.1 - - - -
63A GLU* 4.3 24.0 - - + -
66A HIS* 4.1 8.7 - - + -
17B PHE* 4.0 8.7 - - + -
28B ILE* 3.6 20.6 - - + -
83B TYR* 3.0 61.7 + - + +
84B SER 4.1 2.7 - - - +
86B LEU* 1.3 83.8 - - + +
88B ARG* 1.3 65.7 + - - +
90B ASN* 5.2 0.2 - - - -
91B MET* 3.3 57.4 + - + +
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Residues in contact with ARG 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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59A VAL* 4.6 12.4 - - + +
60A LYS* 2.9 58.8 - - + +
63A GLU* 4.3 20.0 + - + +
84B SER* 3.1 21.7 + - - +
85B ASN* 3.3 7.8 + - - +
87B LEU* 1.3 81.9 - - - +
89B ALA* 1.3 61.7 + - - +
91B MET 3.7 11.3 + - - +
92B ASP* 5.6 0.2 - - - -
112E U 4.1 9.9 + - - -
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Residues in contact with ALA 89 (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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85B ASN 3.1 13.3 + - - +
86B LEU* 4.6 1.1 - - - +
88B ARG* 1.3 79.9 - - - +
90B ASN* 1.3 66.8 + - - +
91B MET 3.7 0.3 + - - -
92B ASP* 4.4 14.4 - - - +
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Residues in contact with ASN 90 (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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31A TYR* 3.8 7.6 + - - -
33A HIS* 5.3 0.2 + - - -
14B THR* 4.5 17.7 - - - +
17B PHE* 3.4 43.4 - - + +
18B GLN* 5.1 9.4 + - - +
21B ARG* 5.7 0.5 + - - -
86B LEU* 3.1 43.0 + - - +
87B LEU 4.4 0.2 - - - +
88B ARG 3.4 0.2 - - - -
89B ALA* 1.3 83.7 - - - +
91B MET* 1.3 60.0 + - - +
92B ASP* 3.5 10.8 + - - +
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Residues in contact with MET 91 (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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29A LEU* 3.9 17.9 - - + -
31A TYR* 3.4 27.3 - - + -
38A LEU* 3.5 31.6 - - + -
56A ALA* 5.9 1.0 - - - +
59A VAL* 3.6 43.0 - - + +
62A ILE* 5.8 1.8 - - + -
17B PHE* 3.8 14.4 - - + -
87B LEU* 3.3 61.6 + - + +
88B ARG 3.7 5.6 + - - +
89B ALA 3.5 1.6 - - - -
90B ASN* 1.3 80.2 - - - +
92B ASP* 1.3 58.3 + - - +
94B LEU* 4.6 3.4 + - + +
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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