Contacts of the helix formed by residues 33 - 46 (chain T) 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 33 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1673A U 3.6 23.3 - - - -
1674A C 3.3 14.8 - - - -
31T ARG 3.8 1.6 + - - -
32T ALA* 1.3 72.4 - - - +
34T LYS* 1.3 65.8 + - - +
35T GLY* 3.3 5.4 + - - -
36T GLU* 2.9 36.3 + - - +
37T VAL* 2.9 25.3 + - - +
54T THR* 5.2 0.9 - - - -
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Residues in contact with LYS 34 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1448A A 2.7 41.6 + - - +
1449A G 4.9 3.0 + - - -
1673A U 3.6 31.8 + - - +
1674A C 2.9 35.7 + - - +
33T SER* 1.3 73.6 - - - +
35T GLY* 1.3 57.7 + - - +
37T VAL* 3.1 5.1 + - - +
38T ALA* 2.8 30.6 + - - +
52T VAL* 3.4 39.4 + - + +
54T THR* 3.6 26.0 - - + +
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Residues in contact with GLY 35 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1672A G 5.9 2.9 - - - -
1673A U 4.9 4.4 + - - -
33T SER* 3.1 6.5 + - - -
34T LYS* 1.3 79.7 - - - +
36T GLU* 1.3 56.9 + - - +
38T ALA* 3.2 7.1 + - - +
39T ASP* 3.0 37.9 + - - -
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Residues in contact with GLU 36 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2T TRP* 4.1 11.2 - - - -
4T VAL* 3.9 12.4 - - + +
31T ARG 3.5 5.9 - - - +
32T ALA* 3.0 18.4 - - + +
33T SER* 2.9 35.9 + - - +
35T GLY* 1.3 75.0 - - - +
37T VAL* 1.3 58.2 + - - +
39T ASP* 3.5 6.8 + - - +
40T ALA* 3.0 31.4 + - - +
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Residues in contact with VAL 37 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4T VAL* 4.0 7.6 - - + -
5T ILE* 5.9 0.2 - - + -
26T PHE* 5.7 0.2 - - + -
28T VAL* 4.2 25.8 - - + -
32T ALA* 4.2 17.5 - - + +
33T SER 2.9 21.4 + - - +
34T LYS* 3.4 9.0 - - - +
36T GLU* 1.3 74.1 - - - +
38T ALA* 1.3 65.7 + - - +
40T ALA* 4.0 0.2 - - - +
41T VAL* 3.0 35.6 + - + +
52T VAL* 3.9 7.2 - - + -
54T THR* 4.9 3.6 - - + -
64T ALA* 3.9 16.6 - - + -
66T VAL* 3.9 26.9 - - + -
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Residues in contact with ALA 38 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34T LYS 2.8 13.6 + - - +
35T GLY* 3.5 11.2 - - - +
37T VAL* 1.3 79.1 - - - +
39T ASP* 1.3 70.1 + - - +
41T VAL* 3.4 0.4 + - - -
42T GLU* 3.1 27.8 + - - +
49T VAL* 3.6 26.9 - - + +
52T VAL* 3.9 10.5 - - + +
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Residues in contact with ASP 39 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35T GLY 3.0 23.0 + - - +
36T GLU* 3.9 5.4 - - - +
37T VAL 3.3 0.2 - - - -
38T ALA* 1.3 75.8 - - - +
40T ALA* 1.3 67.8 + - - +
42T GLU* 2.9 26.1 + - - +
43T GLU* 3.1 31.5 + - - +
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Residues in contact with ALA 40 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4T VAL* 3.8 30.5 - - + -
5T ILE* 4.0 12.6 - - + -
36T GLU 3.0 18.6 + - - +
37T VAL 4.0 2.2 - - - +
39T ASP* 1.3 75.5 - - - +
41T VAL* 1.3 62.5 - - - +
43T GLU* 3.3 9.4 + - - +
44T GLN* 3.0 28.1 + - + +
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Residues in contact with VAL 41 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5T ILE* 3.9 20.6 - - + -
24T LEU* 5.3 2.7 - - + -
26T PHE* 4.1 25.1 - - + -
37T VAL* 3.0 36.0 + - + +
38T ALA 3.7 3.8 - - - +
39T ASP 3.0 0.2 + - - -
40T ALA* 1.3 76.8 - - - +
42T GLU* 1.3 62.8 + - - +
45T TYR* 3.1 33.9 + - + +
47T VAL* 4.2 9.8 - - + +
49T VAL* 3.9 17.3 - - + -
66T VAL* 4.2 11.4 - - + -
68T LEU* 4.9 3.4 - - + -
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Residues in contact with GLU 42 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38T ALA* 3.1 17.3 - - - +
39T ASP* 2.9 19.1 + - - +
41T VAL* 1.3 75.9 - - - +
43T GLU* 1.3 59.2 + - + +
46T ASP* 2.7 35.2 + - - -
47T VAL* 3.4 22.4 - - - +
48T THR* 3.4 10.4 - - - +
49T VAL* 2.7 42.9 + - + +
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Residues in contact with GLU 43 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39T ASP* 3.1 31.3 + - - +
40T ALA* 3.7 7.3 + - - +
42T GLU* 1.3 79.1 - - + +
44T GLN* 1.3 66.1 + - + +
46T ASP* 4.4 1.8 + - - +
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Residues in contact with GLN 44 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5T ILE* 4.3 11.9 - - + -
40T ALA* 3.0 17.8 + - + +
42T GLU 3.2 0.2 - - - -
43T GLU* 1.3 86.5 - - + +
45T TYR* 1.3 85.6 + - + +
46T ASP 3.7 0.2 - - - -
24W LYS 6.2 0.4 - - - -
25W THR* 4.5 17.7 + - - +
28W LEU* 3.3 28.5 - - + +
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Residues in contact with TYR 45 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5T ILE* 4.0 18.4 - - + +
8T PRO* 4.7 4.0 - - - +
24T LEU* 5.6 0.9 - - + -
26T PHE* 3.5 29.0 - + - -
41T VAL* 3.1 24.4 + - + +
44T GLN* 1.3 97.7 - - + +
46T ASP* 1.3 72.5 + - - +
47T VAL* 3.4 10.0 - - + +
77T VAL* 3.7 34.8 - - + -
80T ARG* 2.8 32.9 + - + +
81T ILE* 3.9 32.5 - - + +
28W LEU* 4.1 19.2 - - + +
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Residues in contact with ASP 46 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42T GLU 2.7 20.9 + - - -
43T GLU 4.4 2.1 + - - +
44T GLN 3.7 1.2 - - - -
45T TYR* 1.3 78.1 - - - +
47T VAL* 1.3 59.2 + - - +
72T ASP* 4.6 3.1 - - - +
80T ARG* 4.9 1.4 + - - +
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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