Contacts of the helix formed by residues 14 - 24 (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 HIS 14 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1066A U 3.3 35.8 + - - -
1067A A 4.3 5.1 - - - -
3084B G 3.4 30.4 + - - -
3085B A 3.0 31.3 + - - -
12X ASN 3.7 3.5 + - - -
13X MET* 1.3 77.0 - - - +
15X THR* 1.3 65.3 + - - +
16X ASP* 3.3 19.7 - - - +
17X ILE* 3.2 21.0 + - + +
18X GLN* 3.0 18.9 + - - +
51X PHE* 5.8 0.4 - + - -
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Residues in contact with THR 15 (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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943A A 4.9 1.3 - - - +
1066A U 5.0 0.4 + - - -
1067A A 2.6 34.1 + - - -
13X MET 3.4 3.4 + - - -
14X HIS* 1.3 74.6 + - - +
16X ASP* 1.3 58.4 + - - +
17X ILE 3.0 0.2 - - - -
18X GLN* 3.0 10.7 + - + +
19X ASP* 2.8 47.9 + - - +
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Residues in contact with ASP 16 (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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943A A 4.1 13.9 - - - +
944A G 3.5 28.0 + - - +
14X HIS* 3.3 19.8 - - - +
15X THR* 1.3 75.6 - - - +
17X ILE* 1.3 68.9 + - - +
19X ASP* 4.0 1.1 - - - -
20X THR* 2.9 23.9 + - - -
47X LYS* 3.2 27.7 + - - -
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Residues in contact with ILE 17 (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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3084B G 4.1 15.0 - - - +
13X MET* 3.1 20.7 - - + +
14X HIS* 3.5 32.1 - - + +
15X THR 3.0 0.6 - - - -
16X ASP* 1.3 93.7 + - - +
18X GLN* 1.3 64.7 + - - +
20X THR* 3.2 7.3 + - - -
21X LEU* 3.1 19.4 + - - +
47X LYS* 3.8 37.0 - - + +
48X VAL* 3.9 9.8 - - + +
51X PHE* 3.7 31.6 - - + -
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Residues in contact with GLN 18 (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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1068A C 5.5 1.4 + - - -
6X GLN* 6.1 0.7 - - - +
10X GLU* 3.0 48.1 + - + +
13X MET* 3.1 27.8 - - + +
14X HIS 3.0 12.6 + - - +
15X THR* 3.6 13.3 + - + +
17X ILE* 1.3 74.4 - - - +
19X ASP* 1.3 67.2 + - - +
21X LEU* 3.4 6.5 + - + +
22X GLU* 3.1 42.9 + - + +
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Residues in contact with ASP 19 (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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943A A 2.5 48.3 + - + +
944A G 4.8 0.2 - - - +
15X THR* 2.8 32.9 + - - +
16X ASP 4.3 3.4 - - - +
18X GLN* 1.3 76.9 - - - +
20X THR* 1.3 61.3 + - - +
22X GLU* 3.2 18.4 + - - +
23X MET* 2.9 46.9 + - + +
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Residues in contact with THR 20 (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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944A G 2.5 32.9 + - - +
16X ASP 2.9 17.9 + - - -
17X ILE* 3.2 12.0 + - - -
19X ASP* 1.3 76.5 - - - +
21X LEU* 1.3 67.3 + - - +
23X MET* 2.8 19.3 + - - +
24X LEU* 3.0 15.4 + - + +
44X MET* 3.8 31.4 - - + +
47X LYS* 3.7 5.6 - - + +
48X VAL* 3.8 17.9 - - + -
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Residues in contact with LEU 21 (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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4X LEU* 4.7 10.3 - - + -
6X GLN* 3.6 25.6 - - + +
13X MET* 3.8 20.0 - - + -
17X ILE 3.1 10.7 + - - +
18X GLN* 3.7 8.3 - - + +
19X ASP 3.3 0.2 - - - -
20X THR* 1.3 76.0 - - - +
22X GLU* 1.3 57.9 + - - +
24X LEU* 3.0 15.8 + - + +
25X ASN 3.3 0.2 + - - -
26X ILE* 3.0 60.6 + - + +
48X VAL* 3.1 42.8 - - + -
51X PHE* 5.1 4.7 - - + +
52X VAL* 4.8 1.6 - - + -
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Residues in contact with GLU 22 (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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943A A 5.7 6.1 - - + -
1025A C 4.2 9.6 + - - +
18X GLN* 3.1 40.6 + - + +
19X ASP* 3.5 21.2 - - - +
20X THR 3.0 0.6 - - - -
21X LEU* 1.3 79.1 - - + +
23X MET* 1.3 61.4 + - - +
24X LEU 3.0 0.2 - - - -
25X ASN* 3.1 13.0 + - - +
26X ILE 3.7 8.7 - - - +
27X HIS* 3.3 39.4 + - + +
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Residues in contact with MET 23 (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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943A A 3.4 45.1 - - + +
944A G 3.2 56.3 - - + +
1024A G 2.6 51.8 + - + +
1025A C 3.2 29.1 - - - +
19X ASP* 2.9 23.0 + - + +
20X THR* 2.8 8.6 + - - +
22X GLU* 1.3 77.0 - - + +
24X LEU* 1.3 59.1 + - + +
25X ASN* 3.1 1.7 + - - -
44X MET* 5.1 4.9 - - - +
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Residues in contact with LEU 24 (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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1024A G 4.5 0.4 - - - +
4X LEU* 3.5 27.4 - - + -
20X THR* 3.0 20.0 + - + +
21X LEU* 3.0 11.8 + - + +
23X MET* 1.3 81.4 - - - +
25X ASN* 1.3 74.0 + - - +
26X ILE* 3.3 15.8 + - + +
33X THR* 3.5 19.1 + - + +
35X VAL* 5.1 5.4 - - + -
41X TYR* 3.7 34.5 - - + -
44X MET* 3.9 31.6 - - + -
45X VAL* 4.7 10.5 - - + +
48X VAL* 5.4 0.9 - - + -
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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