Contacts of the helix formed by residues 73 - 82 (chain 1) 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 THR 73 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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671 GLY* 3.5 28.9 - - - -
701 GLN* 4.2 9.6 - - + +
721 GLU* 1.3 75.1 - - - +
741 VAL* 1.3 67.1 + - - +
751 ALA* 2.8 9.3 + - - +
761 GLY 2.9 18.5 + - - -
771 LYS* 3.2 15.0 + - - +
1876A C 5.8 2.5 - - - -
72C GLU* 2.4 32.1 + - - +
158C VAL* 4.8 0.9 - - - +
162C GLY* 3.9 23.4 - - - +
163C GLY* 5.7 0.2 - - - -
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Residues in contact with VAL 74 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701 GLN* 5.0 3.5 + - - +
721 GLU 4.4 0.2 + - - -
731 THR* 1.3 72.5 - - - +
751 ALA* 1.3 59.6 + - - +
771 LYS* 3.7 13.0 + - + +
781 ALA* 3.6 16.8 + - - +
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Residues in contact with ALA 75 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731 THR* 2.8 8.6 + - - +
741 VAL* 1.3 76.4 - - - +
761 GLY* 1.3 65.5 + - - +
771 LYS 3.0 2.0 - - - -
781 ALA* 3.1 17.3 + - - +
791 VAL* 3.4 14.0 + - - +
1876A C 5.3 5.2 - - - +
104C PRO* 5.7 0.3 - - - +
123C GLY 4.8 9.6 - - - +
125C ASN* 4.8 6.5 - - - +
158C VAL* 4.2 22.6 - - + +
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Residues in contact with GLY 76 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731 THR* 2.9 13.1 + - - -
751 ALA* 1.3 77.1 - - - +
771 LYS* 1.3 62.3 + - - +
791 VAL* 3.3 19.9 - - - +
801 MET* 3.7 10.8 + - - +
72C GLU* 3.5 27.5 + - - -
158C VAL* 4.1 10.0 - - - +
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Residues in contact with LYS 77 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721 GLU* 3.4 47.3 + - + +
731 THR 3.6 12.1 - - - +
741 VAL* 3.7 13.5 - - + +
751 ALA 3.0 0.2 - - - -
761 GLY* 1.3 73.8 - - - +
781 ALA* 1.3 65.3 + - - +
791 VAL 3.1 2.3 + - - -
801 MET* 3.3 32.3 + - + +
811 LYS* 3.7 18.1 + - - +
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Residues in contact with ALA 78 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741 VAL 3.6 9.8 + - - +
751 ALA* 3.1 12.8 + - - +
771 LYS* 1.3 79.3 - - - +
791 VAL* 1.3 63.3 + - + +
811 LYS* 3.3 21.6 + - + +
821 ALA* 3.3 22.9 + - - +
104C PRO* 5.1 7.6 - - + -
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Residues in contact with VAL 79 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
751 ALA 3.4 15.3 - - - +
761 GLY* 3.3 12.6 - - - +
771 LYS 3.1 0.6 - - - -
781 ALA* 1.3 75.9 - - - +
801 MET* 1.3 69.8 + - + +
811 LYS 3.1 1.0 + - - -
821 ALA 3.5 15.6 + - - -
90C PRO* 3.9 27.4 - - + -
103C VAL* 5.7 1.5 - - + +
104C PRO* 4.2 21.0 - - + +
156C ILE* 4.9 5.2 - - + -
157C GLY* 4.1 15.9 - - - +
158C VAL* 4.0 28.5 - - + +
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Residues in contact with MET 80 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721 GLU* 3.6 21.8 - - - +
761 GLY 3.7 9.9 - - - +
771 LYS* 3.3 38.1 + - + +
791 VAL* 1.3 79.5 - - + +
811 LYS* 1.3 67.5 + - + +
821 ALA 4.4 0.3 - - - -
90C PRO* 5.9 3.4 - - - -
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Residues in contact with LYS 81 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
771 LYS* 3.8 21.4 - - - +
781 ALA* 3.5 16.8 - - + +
791 VAL 3.1 1.0 + - - -
801 MET* 1.3 79.7 - - + +
821 ALA* 1.3 74.6 + - - +
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Residues in contact with ALA 82 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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781 ALA 3.3 11.5 + - - +
791 VAL 3.7 9.2 - - - +
801 MET 4.4 0.4 - - - -
811 LYS* 1.3 87.9 - - - +
102C GLY 3.4 25.1 - - - +
103C VAL* 4.5 18.6 - - - +
104C PRO* 3.9 16.4 - - + -
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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