Contacts of the helix formed by residues 77 - 88 (chain B) in PDB entry 1N33
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 ALA 77 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B GLY* 5.3 1.8 - - - -
74B LYS* 2.7 19.1 + - + +
75B LYS 3.0 1.6 + - - -
76B GLN* 1.3 78.5 - - - +
78B GLN* 1.3 65.1 + - - +
79B ASP 3.4 2.9 - - - +
80B ILE* 3.7 16.0 + - - +
81B VAL* 2.9 33.1 + - - +
165B VAL* 4.5 12.1 - - + -
211B ILE* 3.4 29.2 - - + -
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Residues in contact with GLN 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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72B GLY 4.4 5.2 - - - -
73B THR 4.3 5.8 + - - +
74B LYS 2.8 12.0 + - - +
75B LYS* 3.4 34.6 + - - +
77B ALA* 1.3 78.6 - - - +
79B ASP* 1.3 69.4 + - - +
81B VAL* 3.5 7.8 - - - +
82B ARG 3.5 0.3 + - - -
94B ASN* 2.4 69.1 + - - +
95B GLN* 2.8 28.9 + - - +
96B ARG* 3.1 20.0 - - - +
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Residues in contact with ASP 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LYS 4.8 4.5 + - - +
77B ALA 4.8 0.2 - - - +
78B GLN* 1.3 83.3 - - - +
80B ILE* 1.3 57.6 - - + +
81B VAL 2.8 15.4 + - - -
82B ARG* 3.1 18.9 + - + +
83B MET* 2.8 26.2 + - - +
94B ASN* 4.1 7.0 + - - +
238B LEU* 4.3 23.7 - - + +
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Residues in contact with ILE 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ALA* 4.0 18.4 - - - +
78B GLN 3.5 0.2 - - - -
79B ASP* 1.3 76.5 - - + +
81B VAL* 1.3 59.8 + - - +
83B MET* 3.6 7.4 - - - +
84B GLU* 3.4 30.8 + - + +
208B ILE* 3.4 35.0 - - + +
211B ILE* 4.6 8.5 - - + +
212B GLN* 3.4 50.9 - - + +
215B LEU* 4.4 7.3 - - + +
235B SER* 4.7 5.8 - - - +
238B LEU* 3.6 20.6 - - + +
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Residues in contact with VAL 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B PHE* 4.1 33.4 - - + +
71B VAL 4.7 0.9 - - - -
72B GLY* 3.7 28.3 - - - +
77B ALA* 2.9 22.7 - - + +
78B GLN 3.5 8.5 - - - +
79B ASP 2.8 1.8 + - - -
80B ILE* 1.3 77.4 - - + +
82B ARG* 1.3 56.3 + - - +
83B MET 2.6 15.2 + - - -
84B GLU* 3.1 5.2 + - - +
85B ALA* 3.1 20.3 + - - +
92B TYR* 4.1 13.7 - - + -
93B VAL 4.8 2.5 - - - +
94B ASN* 4.2 6.1 - - - +
165B VAL* 4.6 8.3 - - + -
211B ILE* 6.1 2.0 - - + -
215B LEU* 5.6 9.0 - - + -
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Residues in contact with ARG 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 GLN 3.5 1.8 + - - -
79B ASP* 3.1 22.9 + - + +
81B VAL* 1.3 78.4 - - - +
83B MET* 1.3 79.1 + - + +
85B ALA* 3.4 0.8 - - - +
86B GLU* 2.6 37.8 + - - +
92B TYR* 3.1 44.6 + - + -
94B ASN* 3.5 24.5 - - + +
150B SER* 4.7 6.7 + - - -
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Residues in contact with MET 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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79B ASP* 2.8 17.2 + - - +
80B ILE* 3.6 11.2 - - - +
81B VAL 2.6 0.8 + - - -
82B ARG* 1.3 94.7 - - - +
84B GLU* 1.3 58.7 + - + +
85B ALA 2.6 15.7 + - - -
86B GLU* 3.9 0.9 - - - +
87B ARG* 2.9 20.1 + - + +
234B PRO* 4.8 21.1 - - + +
235B SER* 3.3 31.6 - - - +
238B LEU* 4.2 19.3 - - + -
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Residues in contact with GLU 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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70B PHE* 4.7 9.4 - - - -
80B ILE* 3.4 18.3 - - + +
81B VAL 3.1 4.6 + - - +
83B MET* 1.3 77.6 - - - +
85B ALA* 1.3 60.4 + - - +
87B ARG* 3.0 25.0 + - - +
88B ALA* 3.8 1.7 - - - +
90B MET* 5.1 0.2 - - - +
212B GLN* 3.8 1.4 + - - +
215B LEU* 3.4 22.0 - - + -
216B SER* 3.0 26.2 + - - -
219B VAL* 3.1 36.5 - - + +
233B SER* 2.7 29.6 + - - -
235B SER* 2.9 16.9 + - - -
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Residues in contact with ALA 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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70B PHE* 5.6 4.0 - - + -
81B VAL* 3.1 7.0 + - + +
82B ARG 3.4 3.4 - - - +
83B MET 2.6 7.9 + - - -
84B GLU* 1.3 72.4 - - - +
86B GLU* 1.3 58.5 + - + +
87B ARG 2.7 2.9 - - - -
88B ALA* 2.7 37.2 + - - +
90B MET* 3.2 13.8 - - - +
91B PRO 3.8 12.8 - - - +
92B TYR* 3.1 37.2 - - + -
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Residues in contact with GLU 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 ARG* 2.6 36.1 + - - +
83B MET 3.9 1.7 - - - +
85B ALA* 1.3 71.3 - - + +
87B ARG* 1.3 55.2 + - - +
88B ALA 2.7 20.2 + - - +
89B GLY 4.5 1.8 - - - -
90B MET 4.3 3.4 - - - +
91B PRO* 6.3 0.2 - - + -
92B TYR* 4.1 20.1 + - + -
150B SER 5.2 1.6 - - - +
151B GLY* 6.3 0.4 - - - -
154B LEU* 4.7 19.1 - - + -
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Residues in contact with ARG 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B MET* 2.9 22.9 + - + +
84B GLU* 3.0 30.3 + - - +
86B GLU* 1.3 77.0 - - - +
88B ALA* 1.3 56.9 + - - +
216B SER 5.0 0.8 + - - -
219B VAL* 3.4 21.1 - - - +
220B ASP* 4.0 16.4 + - - -
223B ILE* 4.3 14.9 - - - +
230B VAL* 3.9 20.4 - - - +
231B GLU 3.4 12.7 + - - -
232B PRO* 4.5 0.8 + - - +
233B SER* 3.0 40.9 + - - +
234B PRO* 4.1 18.0 - - + +
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Residues in contact with ALA 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B GLU 3.8 1.3 - - - +
85B ALA 2.7 16.5 + - - +
86B GLU* 2.7 12.4 + - - +
87B ARG* 1.3 80.1 - - - +
89B GLY* 1.3 68.6 + - - +
90B MET* 3.9 17.0 - - + -
219B VAL* 3.4 25.1 - - + +
222B ILE* 4.2 11.2 - - + -
223B ILE* 4.8 10.1 - - + -
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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