Contacts of the helix formed by residues 80 - 88 (chain X) in PDB entry 1NJI
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 ASP 80 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67X ALA* 5.7 0.4 - - - -
78X ASP* 3.3 19.0 + - + +
79X VAL* 1.3 73.7 - - - +
81X ASP* 1.3 66.2 + - - +
82X GLU* 3.2 14.3 + - - +
83X TRP* 2.7 34.2 + - - +
84X VAL* 2.9 25.8 + - - +
93X ILE* 4.0 6.7 - - - -
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Residues in contact with ASP 81 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80X ASP* 1.3 74.7 - - - +
82X GLU* 1.3 58.2 + - - +
84X VAL* 3.1 7.6 + - - +
85X ALA* 2.8 30.1 + - - +
91X ASP 3.9 3.6 - - - +
92X ASP* 2.9 19.0 - - + +
93X ILE* 2.9 39.7 + - - +
94X SER 4.6 0.2 + - - -
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Residues in contact with GLU 82 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80X ASP* 3.2 12.5 + - - +
81X ASP* 1.3 77.5 - - - +
83X TRP* 1.3 59.1 + - - +
85X ALA* 3.2 6.0 + - - +
86X GLU* 2.8 62.7 + - + +
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Residues in contact with TRP 83 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72X PRO* 3.9 23.5 - - + +
77X ALA* 3.8 22.1 - - + +
78X ASP 3.4 22.7 - - - +
79X VAL* 3.9 14.6 - - + -
80X ASP* 2.7 26.1 + - - +
82X GLU* 1.3 72.7 - - - +
84X VAL* 1.3 72.6 + - + +
86X GLU* 3.2 2.4 + - - -
87X HIS* 2.9 76.0 + + + +
88X THR* 3.9 12.6 - - - -
110X GLN 3.9 9.9 - - - -
111X GLY* 4.0 6.5 - - - -
112X LEU* 3.3 30.7 - - + -
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Residues in contact with VAL 84 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79X VAL* 3.7 18.8 - - + -
80X ASP 2.9 16.1 + - - +
81X ASP 3.3 6.1 - - - +
83X TRP* 1.3 82.7 - - - +
85X ALA* 1.3 55.9 + - - +
88X THR* 2.7 47.4 + - - +
90X TYR* 3.6 6.2 - - + +
92X ASP* 3.4 31.2 - - - +
93X ILE* 3.6 23.8 - - + +
96X LEU* 4.2 20.2 - - + -
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Residues in contact with ALA 85 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81X ASP 2.8 15.3 + - - +
82X GLU* 3.6 7.0 - - - +
84X VAL* 1.3 76.8 - - - +
86X GLU* 1.3 59.9 + - + +
87X HIS 3.2 4.4 + - - -
88X THR 3.7 11.4 - - - +
90X TYR 3.5 12.4 - - - +
91X ASP* 3.3 24.2 + - - +
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Residues in contact with GLU 86 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82X GLU* 2.8 55.0 + - + +
83X TRP* 4.1 2.7 - - - +
85X ALA* 1.3 73.2 - - + +
87X HIS* 1.3 73.1 + - + +
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Residues in contact with HIS 87 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83X TRP* 2.9 76.2 + + + +
85X ALA 3.2 0.2 - - - -
86X GLU* 1.3 89.4 + - + +
88X THR* 1.3 62.1 + - - +
110X GLN* 4.6 7.6 + - - +
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Residues in contact with THR 88 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83X TRP* 3.9 16.1 - - - -
84X VAL* 2.7 28.6 + - + +
85X ALA 3.7 7.8 - - - +
87X HIS* 1.3 78.2 + - - +
89X ASP* 1.3 78.8 + - - +
90X TYR* 3.2 31.7 - - + +
96X LEU* 4.5 6.3 - - + +
110X GLN* 2.9 42.2 + - + +
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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