Contacts of the helix formed by residues 58 - 70 (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 SER 58 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57X PRO* 1.3 75.6 - - - +
59X GLN* 1.3 68.7 + - - +
60X GLU* 3.2 10.0 + - - +
61X THR* 2.9 17.7 + - - -
62X LEU* 3.0 22.0 + - - +
101X LEU* 4.3 1.1 - - - -
143X THR* 3.8 11.4 - - - +
147X ASP* 2.3 33.2 + - - -
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Residues in contact with GLN 59 (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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58X SER* 1.3 73.1 - - - +
60X GLU* 1.3 67.7 + - + +
62X LEU* 3.3 2.8 + - - +
63X GLU* 2.9 46.7 + - - +
94X SER* 3.2 12.5 + - - -
97X ALA* 3.1 29.0 - - - +
98X PHE* 3.2 31.0 - - - +
101X LEU* 3.7 20.2 - - + +
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Residues in contact with GLU 60 (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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58X SER* 3.1 8.2 - - - +
59X GLN* 1.3 81.8 - - + +
61X THR* 1.3 64.2 + - - +
63X GLU* 3.0 13.6 + - - +
64X THR* 2.9 25.6 + - - +
151X GLU* 5.8 0.7 - - - +
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Residues in contact with THR 61 (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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57X PRO* 4.7 0.4 - - - -
58X SER* 2.9 10.6 + - - -
60X GLU* 1.3 78.1 - - - +
62X LEU* 1.3 64.7 + - - +
64X THR* 3.0 8.1 + - - -
65X VAL* 2.9 24.9 + - + +
147X ASP* 2.6 38.3 + - - +
150X LEU* 3.7 35.7 - - + -
151X GLU* 2.6 31.4 + - + +
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Residues in contact with LEU 62 (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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1X MET* 3.9 14.1 - - + -
34X LEU* 4.1 26.2 - - + -
57X PRO* 4.6 13.8 - - + +
58X SER 3.0 16.3 + - - +
59X GLN 3.7 4.3 - - - +
61X THR* 1.3 77.7 - - - +
63X GLU* 1.3 53.2 + - - +
65X VAL* 3.3 4.6 + - + -
66X LEU* 2.7 59.5 + - + +
97X ALA* 3.9 22.2 - - + +
100X LEU* 4.1 6.5 - - + -
101X LEU* 3.8 27.4 - - + -
116X LEU* 4.9 5.4 - - + -
150X LEU* 6.0 2.2 - - + -
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Residues in contact with GLU 63 (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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59X GLN* 2.9 41.5 + - - +
60X GLU* 3.0 13.4 + - - +
62X LEU* 1.3 76.9 - - - +
64X THR* 1.3 61.9 + - - +
66X LEU* 3.7 1.4 - - - +
67X ALA* 2.9 26.9 + - - +
93X ILE* 3.9 15.8 - - + +
94X SER* 2.6 42.9 + - - -
97X ALA* 3.7 10.3 - - + -
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Residues in contact with THR 64 (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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60X GLU* 2.9 16.8 + - - +
61X THR* 3.0 9.7 + - - -
63X GLU* 1.3 75.7 - - - +
65X VAL* 1.3 59.7 + - + +
67X ALA* 3.7 4.3 - - - +
68X THR* 2.9 30.1 + - - +
151X GLU* 5.2 12.7 + - + +
154X ARG* 4.2 27.1 - - + +
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Residues in contact with VAL 65 (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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61X THR* 2.9 19.3 + - + +
62X LEU* 3.8 6.7 - - + +
64X THR* 1.3 77.8 - - + +
66X LEU* 1.3 61.0 + - - +
68X THR* 3.3 8.7 - - + -
69X ARG* 2.7 30.1 + - + +
70X ALA 3.8 0.5 + - - -
116X LEU* 3.6 28.5 - - + -
118X LEU* 4.0 22.0 - - + -
150X LEU* 3.7 44.9 - - + +
151X GLU* 5.4 0.2 - - - -
154X ARG* 4.9 4.9 - - + -
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Residues in contact with LEU 66 (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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34X LEU* 4.8 0.4 - - + -
62X LEU* 2.7 45.9 + - + +
63X GLU 3.2 3.8 + - - +
65X VAL* 1.3 71.6 - - - +
67X ALA* 1.3 60.5 + - - +
70X ALA* 2.8 41.8 + - + +
79X VAL* 4.1 4.8 - - + +
93X ILE* 4.0 13.9 - - + -
96X LEU* 4.4 11.9 - - + -
97X ALA* 3.9 22.2 - - + +
100X LEU* 3.8 23.1 - - + -
107X LEU* 4.1 25.1 - - + -
112X LEU* 5.5 0.2 - - + -
116X LEU* 4.2 16.8 - - + -
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Residues in contact with ALA 67 (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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63X GLU 2.9 15.7 + - - +
64X THR* 3.7 4.5 - - - +
66X LEU* 1.3 79.5 - - - +
68X THR* 1.3 60.6 - - - +
70X ALA 4.5 1.7 + - - +
78X ASP* 5.8 1.2 - - - +
79X VAL 3.6 16.5 + - - +
80X ASP* 5.7 0.2 - - - -
93X ILE* 3.3 30.2 - - + +
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Residues in contact with THR 68 (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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567A U 5.3 1.0 + - - -
64X THR* 2.9 27.1 + - - +
65X VAL* 3.2 15.3 - - - +
67X ALA* 1.3 79.5 - - - +
69X ARG* 1.3 77.1 + - + +
70X ALA 3.8 1.0 - - - +
154X ARG* 3.2 43.7 + - + +
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Residues in contact with ARG 69 (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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566A A 3.4 11.6 + - - -
567A U 2.7 30.1 + - - -
1263A C 3.1 40.3 + - - -
1264A U 4.5 6.5 + - - -
65X VAL* 2.7 18.2 + - + +
68X THR* 1.3 87.3 + - + +
70X ALA* 1.3 62.2 + - - +
71X GLU* 3.9 8.2 + - - +
115X THR 4.4 0.9 - - - +
116X LEU* 3.8 18.1 - - + -
117X ARG* 3.5 20.3 + - - +
118X LEU* 4.0 27.4 - - + -
119X HIS* 3.6 19.3 - - - +
154X ARG* 2.7 26.8 + - - +
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Residues in contact with ALA 70 (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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65X VAL 3.8 0.2 + - - -
66X LEU* 2.8 45.6 + - + +
67X ALA 4.5 1.5 + - - +
68X THR 3.8 1.1 - - - +
69X ARG* 1.3 76.5 - - - +
71X GLU* 1.3 65.4 + - - +
77X ALA 4.6 1.7 - - - +
78X ASP* 5.3 0.5 - - - -
79X VAL* 3.5 34.0 + - + +
107X LEU* 5.5 0.2 - - + -
112X LEU* 4.6 8.5 - - + -
116X LEU* 4.0 9.6 - - + -
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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