Contacts of the helix formed by residues 77 - 91 (chain B) in PDB entry 3OP5
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 ASN 77 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73B GLU* 3.9 31.7 + - + +
74B PRO* 2.9 23.3 + - + +
75B SER 3.4 3.7 - - - +
76B ASP* 1.4 79.5 + - - +
78B GLY* 1.3 63.6 + - - +
79B PRO* 3.3 16.3 - - - +
80B LEU* 3.0 32.3 + - + +
81B PHE* 3.5 18.9 + - - +
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Residues in contact with GLY 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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76B ASP 3.4 6.1 + - - -
77B ASN* 1.3 68.1 - - - +
79B PRO* 1.4 73.6 - - - +
81B PHE* 3.1 17.6 + - - +
82B THR* 3.1 17.6 + - - -
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Residues in contact with PRO 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 ASN* 3.3 18.4 - - - +
78B GLY* 1.4 87.4 - - - +
80B LEU* 1.4 55.2 + - - +
82B THR* 3.3 1.0 + - - +
83B GLU* 2.9 31.7 + - - +
199B GLY* 3.3 32.1 - - - +
200B LEU* 5.1 12.6 - - + -
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Residues in contact with LEU 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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71B LYS* 3.8 39.9 - - + +
73B GLU* 3.7 26.7 - - + +
74B PRO 5.2 0.9 - - - +
77B ASN* 3.0 24.1 + - + +
78B GLY 3.3 0.4 - - - -
79B PRO* 1.4 74.9 - - - +
81B PHE* 1.4 52.9 + - - +
83B GLU* 4.3 3.8 - - - +
84B LEU* 2.8 36.5 + - - +
127B ARG* 3.4 50.3 - - + +
128B PHE* 5.1 0.9 - - - -
129B MET* 3.6 23.6 - - + +
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Residues in contact with PHE 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 11.9 + - - +
78B GLY* 3.1 12.0 + - - +
80B LEU* 1.4 75.1 - - - +
82B THR* 1.4 65.2 + - - +
84B LEU* 3.8 5.2 - - + +
85B LYS* 3.0 50.8 + - + +
127B ARG* 6.5 0.2 - - - -
366B GOL 4.1 16.6 - - - -
279D ARG* 4.8 6.3 - - - -
304D GLU* 5.2 4.7 - - - -
307D LYS* 3.6 62.1 - - + +
308D LEU* 3.6 30.3 - - + -
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Residues in contact with THR 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 GLY 3.1 14.2 + - - -
79B PRO 3.3 2.4 + - - -
81B PHE* 1.4 76.2 - - - +
83B GLU* 1.4 56.8 + - - +
85B LYS* 3.4 3.5 + - - +
86B PHE* 3.1 26.9 + - - +
173B TYR* 4.7 4.5 + - + -
198B TYR 3.6 9.4 - - - +
199B GLY 3.4 24.4 + - - +
200B LEU* 4.6 0.7 - - - -
201B ALA* 3.6 22.7 - - + +
366B GOL 4.3 21.8 + - - +
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Residues in contact with GLU 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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71B LYS* 3.3 34.5 - - - +
79B PRO 2.9 17.6 + - - +
80B LEU* 3.8 9.2 - - - +
82B THR* 1.4 73.5 - - - +
84B LEU* 1.4 63.3 + - - +
86B PHE* 3.3 3.3 + - - +
87B TYR* 3.1 54.1 + - + -
129B MET* 4.4 5.2 - - + +
131B MET* 5.4 0.2 - - - -
197B ASP* 3.5 13.7 + - - +
198B TYR* 2.9 36.6 + - + -
199B GLY* 3.8 8.8 - - - +
365B REB 4.6 6.9 + - - -
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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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80B LEU 2.8 22.4 + - - +
81B PHE* 3.8 6.3 - - - +
83B GLU* 1.4 71.8 - - - +
85B LYS* 1.3 57.9 + - - +
87B TYR* 3.4 2.2 + - - -
88B GLN* 2.9 40.8 + - + +
113B TYR* 3.5 33.0 - - + +
116B SER* 3.3 27.6 - - - +
127B ARG* 3.8 23.1 - - + -
129B MET* 3.7 20.8 - - + +
308D LEU* 3.7 30.1 - - + -
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Residues in contact with LYS 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 PHE* 3.0 47.0 + - + +
82B THR 3.7 4.9 - - - +
83B GLU 3.3 0.2 - - - -
84B LEU* 1.3 76.1 - - - +
86B PHE* 1.4 61.4 + - - +
88B GLN* 3.2 19.1 + - - +
89B ARG* 3.1 53.9 + - - +
173B TYR* 3.8 2.7 - - - +
366B GOL 3.9 10.8 - - - +
307D LYS 5.2 1.3 - - - -
308D LEU* 2.7 47.5 + - + +
309D LEU 5.3 0.7 - - - -
310D ASP* 3.3 32.3 + - - -
313D GLU* 4.2 2.4 + - - -
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Residues in contact with PHE 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 THR 3.1 13.8 + - - +
83B GLU 3.3 6.5 + - - +
85B LYS* 1.4 76.3 - - - +
87B TYR* 1.3 74.9 + + - +
89B ARG* 3.3 0.9 + - - +
90B ALA* 2.8 53.5 + - + +
91B ALA* 4.5 4.3 - - + -
110B VAL* 4.3 9.9 - - + -
168B ILE* 3.7 26.9 - - + -
173B TYR* 3.6 49.5 + + + -
198B TYR* 3.5 62.8 - + + +
201B ALA* 5.0 0.2 - - + -
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Residues in contact with TYR 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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83B GLU* 3.1 46.3 + - + +
84B LEU* 3.8 4.3 - - - +
86B PHE* 1.3 85.4 - + - +
88B GLN* 1.3 61.3 + - - +
91B ALA* 3.0 49.8 + - + -
92B LYS 3.7 0.2 + - - -
111B PRO* 3.2 48.0 - - + +
113B TYR* 3.6 33.0 - + + +
129B MET* 4.0 10.5 - - - -
131B MET* 3.7 20.0 - - + -
196B VAL* 4.7 0.5 - - - -
198B TYR* 3.4 22.7 - + - -
365B REB 3.5 12.6 + - - -
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Residues in contact with GLN 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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32B MET* 4.6 15.4 - - - +
84B LEU* 2.9 36.7 + - + +
85B LYS* 3.2 33.9 + - - +
87B TYR* 1.3 74.4 - - - +
89B ARG* 1.3 52.4 + - + +
92B LYS* 2.8 36.7 + - - +
113B TYR* 3.3 40.4 + - + -
308D LEU* 3.7 14.9 - - - +
313D GLU* 4.9 8.8 + - - +
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Residues in contact with ARG 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 LYS* 3.1 34.6 + - - +
86B PHE 3.8 2.2 - - - +
88B GLN* 1.3 80.5 - - - +
90B ALA* 1.3 60.0 + - + +
92B LYS* 3.1 10.4 + - - +
95B GLN* 2.9 20.4 + - - -
171B HIS* 4.9 2.0 - - - +
172B GLU* 5.8 0.9 - - - -
173B TYR* 2.7 42.5 + - + -
203B ARG* 3.6 28.7 - - - +
366B GOL 3.1 44.8 + - - -
241D ARG* 5.9 1.4 - - - +
310D ASP* 3.1 42.6 + - - +
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Residues in contact with ALA 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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86B PHE* 2.8 40.6 + - + +
89B ARG* 1.3 75.6 - - + +
91B ALA* 1.3 53.4 + - - +
95B GLN* 3.3 12.1 - - - +
167B TYR* 2.5 37.7 + - + -
168B ILE* 5.7 0.2 - - - -
171B HIS* 3.7 31.0 - - + +
173B TYR* 4.7 0.7 - - + -
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Residues in contact with ALA 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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86B PHE* 3.8 2.2 + - + -
87B TYR* 3.0 45.6 + - + +
90B ALA* 1.3 78.8 - - - +
92B LYS* 1.3 63.2 + - - +
96B ILE* 3.8 15.0 - - + +
110B VAL* 4.0 9.9 - - + -
111B PRO 3.5 11.9 - - - +
112B LYS* 3.9 0.2 - - - -
113B TYR* 3.0 22.4 + - - +
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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