Contacts of the helix formed by residues 24 - 36 (chain S) 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 24 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1370A G 2.8 40.2 + - - -
2052A U 4.9 10.6 + - - -
23S MET* 1.3 75.2 - - - +
25S PHE* 1.3 53.0 - - - +
26S LYS 3.2 0.9 + - - -
27S HIS* 2.8 47.6 + - - +
28S SER* 2.7 31.4 + - - -
83S LYS* 5.6 0.4 - - - +
84S ALA* 4.7 1.5 - - - +
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Residues in contact with PHE 25 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523A C 3.4 26.5 - - - -
524A A 3.7 10.5 - - - -
1370A G 4.2 4.4 + - - -
23S MET 3.2 3.8 + - - -
24S SER* 1.3 72.5 - - - +
26S LYS* 1.3 65.0 + - + +
28S SER* 3.2 2.1 + - - -
29S LYS* 2.9 56.5 + - + +
116S ALA* 3.6 22.7 - - + -
117S HIS* 3.6 2.2 - - - -
118S LYS* 3.3 44.0 - - + -
139S PRO* 4.4 8.9 - - + +
141S VAL* 3.7 26.5 - - + -
8506S CL 4.1 23.6 - - + -
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Residues in contact with LYS 26 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1367A A 5.3 7.8 + - - -
1368A U 4.5 2.4 + - - -
1369A A 3.0 27.5 + - - +
1370A G 2.8 58.9 + - + +
24S SER* 3.2 6.7 + - - +
25S PHE* 1.3 80.5 - - + +
27S HIS* 1.3 64.2 + - + +
29S LYS* 3.6 8.0 + - - +
30S ALA* 3.5 18.5 + - - +
59S PHE* 5.7 0.3 - - - -
62S HIS* 3.5 51.1 - - + +
8506S CL 4.0 23.1 - - + -
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Residues in contact with HIS 27 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1370A G 3.8 25.2 + + - +
2050A G 5.9 0.7 - - - -
2051A G 3.6 28.1 + - - -
2052A U 5.1 6.0 + - - -
2053A G 5.7 1.8 - - - -
24S SER* 2.8 33.0 + - - +
26S LYS* 1.3 78.1 - - + +
28S SER* 1.3 60.1 + - - +
30S ALA* 3.4 6.5 + - - +
31S ILE* 3.0 34.8 + - - +
59S PHE* 3.7 29.2 - + - -
79S ARG* 5.6 3.8 + - - -
81S PRO* 3.8 27.2 - - + +
83S LYS* 6.2 0.2 - - - +
84S ALA* 3.9 10.3 + - + +
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Residues in contact with SER 28 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23S MET* 3.2 25.2 - - - +
24S SER 2.7 19.7 + - - -
25S PHE* 3.2 12.2 + - - -
27S HIS* 1.3 75.5 - - - +
29S LYS* 1.3 66.5 + - - +
31S ILE* 3.2 1.5 + - - +
32S ALA* 2.8 26.5 + - - +
84S ALA* 4.3 2.0 - - - +
88S PHE* 3.8 19.4 - - - -
116S ALA* 3.6 22.0 - - - -
141S VAL* 4.2 1.5 - - - +
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Residues in contact with LYS 29 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523A C 3.5 8.7 + - - -
524A A 3.0 40.5 + - - +
525A G 4.7 11.6 + - - +
1367A A 5.6 2.2 + - - -
25S PHE* 2.9 55.4 + - + +
26S LYS* 4.0 4.7 - - - +
27S HIS 3.4 0.4 - - - -
28S SER* 1.3 75.1 - - - +
30S ALA* 1.3 57.6 + - - +
32S ALA* 3.7 5.5 - - - +
33S ARG* 2.8 43.6 + - - +
61S GLN* 4.5 5.1 + - + +
62S HIS* 3.0 38.8 + - + +
116S ALA* 4.3 4.2 - - + +
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Residues in contact with ALA 30 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26S LYS 3.5 9.9 + - - +
27S HIS 3.4 9.6 + - - +
28S SER 3.1 0.4 - - - -
29S LYS* 1.3 79.7 - - - +
31S ILE* 1.3 57.5 + - - +
33S ARG* 3.3 18.1 - - - +
34S GLU* 2.9 29.1 + - - +
57S VAL* 3.7 12.9 - - + +
58S PRO 3.7 21.3 - - - +
59S PHE* 4.0 16.4 - - + -
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Residues in contact with ILE 31 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27S HIS 3.0 14.0 + - - +
28S SER 3.2 3.1 + - - +
30S ALA* 1.3 73.4 - - - +
32S ALA* 1.3 70.9 + - - +
34S GLU* 3.0 11.2 + - - +
35S ILE* 3.0 18.0 + - + +
46S TYR* 5.8 0.2 - - + -
47S LEU* 4.0 18.8 - - + -
57S VAL* 4.4 22.4 - - + -
81S PRO* 4.2 8.7 - - + +
84S ALA* 3.5 34.1 - - + +
85S SER* 3.6 24.2 - - - +
88S PHE* 3.8 29.2 - - + -
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Residues in contact with ALA 32 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525A G 6.1 2.9 - - - -
28S SER 2.8 20.4 + - - +
29S LYS* 3.7 5.6 - - - +
31S ILE* 1.3 75.2 - - - +
33S ARG* 1.3 68.1 + - - +
34S GLU 3.0 0.2 + - - -
35S ILE* 3.0 10.8 + - - +
36S LYS* 3.1 10.2 + - - +
88S PHE* 4.1 9.1 - - + -
114S VAL* 3.7 44.4 - - + +
115S ALA* 4.3 8.3 - - - -
116S ALA 4.5 2.9 - - - +
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Residues in contact with ARG 33 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A U 4.8 8.0 + - - -
13A G 5.8 0.8 + - - -
525A G 3.4 29.4 + - - +
29S LYS* 2.8 27.2 + - - +
30S ALA* 3.3 28.4 - - - +
32S ALA* 1.3 78.5 - - - +
34S GLU* 1.3 61.3 + - + +
35S ILE 3.6 0.2 + - - -
36S LYS* 3.8 13.6 + - - +
58S PRO* 5.2 2.4 + - - -
60S LYS* 4.4 31.0 - - - +
61S GLN* 4.0 35.9 - - - +
62S HIS* 6.2 0.6 - - - -
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Residues in contact with GLU 34 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30S ALA 2.9 17.8 + - - +
31S ILE* 3.0 6.2 + - - +
33S ARG* 1.3 80.4 - - - +
35S ILE* 1.3 59.0 + - - +
36S LYS 3.8 3.6 + - - +
38S LYS* 3.7 16.7 + - - +
46S TYR* 3.1 43.2 + - + +
56S PRO 5.0 0.3 - - - +
57S VAL* 4.8 1.3 - - + -
58S PRO* 3.7 33.0 - - + +
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Residues in contact with ILE 35 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31S ILE* 3.0 13.4 + - + +
32S ALA* 3.6 9.6 - - - +
34S GLU* 1.3 73.9 - - - +
36S LYS* 1.3 71.0 + - - +
37S GLY 3.4 0.3 + - - -
38S LYS* 3.0 31.5 + - + +
43S ALA* 4.4 10.3 - - + -
46S TYR* 3.8 30.5 - - + -
47S LEU* 4.3 14.1 - - + -
88S PHE* 4.2 24.9 - - + -
92S LEU* 4.6 10.8 - - + -
111S ILE* 3.5 26.9 - - + +
114S VAL* 4.4 12.1 - - + -
145S LEU* 5.7 1.8 - - + -
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Residues in contact with LYS 36 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525A G 3.9 6.6 + - - +
526A U 3.0 40.3 + - - +
32S ALA 3.1 9.5 + - - +
33S ARG* 4.1 9.8 - - - +
34S GLU 3.5 5.3 - - - +
35S ILE* 1.3 79.8 - - - +
37S GLY* 1.3 64.1 + - - +
38S LYS* 3.3 3.5 + - - +
111S ILE* 3.9 9.6 - - - +
112S LYS 3.5 20.9 + - - +
113S HIS* 4.9 5.5 - - + +
114S VAL* 3.5 32.3 - - + +
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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