Contacts of the helix formed by residues 18 - 31 (chain I) in PDB entry 1JJ2
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 ILE 18 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12430 C 3.4 27.4 - - - +
12440 U 2.9 47.1 - - - +
17I CYS* 1.3 70.0 - - - +
19I MET* 1.3 65.5 + - - +
21I ARG* 2.8 38.1 + - + +
22I VAL* 3.1 11.9 + - - +
45I VAL* 3.3 9.0 - - + +
46I ILE* 5.5 0.7 - - - -
47I THR* 4.5 10.1 - - - +
118I GLY 5.4 0.7 - - - +
119I THR 2.7 19.1 + - - +
120I SER 5.0 3.1 - - - +
121I LEU* 4.6 23.1 - - + -
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Residues in contact with MET 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12420 A 4.7 3.6 - - - +
12430 C 4.0 5.6 - - - +
17I CYS 3.1 4.9 + - - -
18I ILE* 1.3 69.8 - - - +
20I GLY* 1.3 57.8 + - - +
22I VAL* 3.2 3.2 + - - +
23I ALA* 2.8 31.5 + - - +
44I ALA* 4.8 4.7 - - + -
45I VAL 3.1 17.4 + - - +
46I ILE* 4.8 5.6 - - + -
57I TYR* 4.6 11.9 - - - -
78I ILE* 3.4 16.6 - - + -
79I PHE* 3.4 52.0 - - + -
82I THR* 3.5 21.8 - - + +
132I LEU* 3.2 43.7 - - + -
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Residues in contact with GLY 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12420 A 3.1 33.4 + - - -
12430 C 2.9 16.7 + - - -
12470 A 3.4 9.0 + - - -
19I MET* 1.3 75.6 - - - +
21I ARG* 1.3 57.1 + - - +
23I ALA* 3.7 5.1 - - - +
24I SER* 2.9 30.3 + - - -
86I MET* 3.9 2.9 - - - +
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Residues in contact with ARG 21 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11090 U 2.8 64.7 + - + +
12430 C 3.1 29.3 + - - +
12440 U 2.8 24.4 + - - -
12460 A 3.6 15.5 + - - -
12470 A 3.0 30.8 + - - +
18I ILE* 2.8 31.0 + - + +
20I GLY* 1.3 70.3 - - - +
22I VAL* 1.3 65.0 + - - +
25I GLN* 3.4 22.9 + - - +
118I GLY 3.6 26.4 + - - +
119I THR* 4.1 7.6 - - + -
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Residues in contact with VAL 22 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I VAL* 3.9 13.7 - - + -
14I ALA* 5.3 4.3 - - + -
17I CYS* 3.7 26.9 - - + -
18I ILE 3.1 14.7 + - - +
19I MET* 3.6 6.5 - - - +
21I ARG* 1.3 75.0 - - - +
23I ALA* 1.3 55.5 + - - +
25I GLN* 2.9 5.2 + - - +
26I VAL* 2.7 52.4 + - + +
38I VAL* 4.9 4.3 - - + -
79I PHE* 3.9 18.6 - - + -
116I LEU* 3.8 14.6 - - + -
119I THR* 3.8 17.3 - - + +
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Residues in contact with ALA 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I MET 2.8 17.8 + - - +
20I GLY 3.7 4.0 - - - +
22I VAL* 1.3 77.6 - - - +
24I SER* 1.3 57.3 + - - +
26I VAL* 3.2 4.0 + - - +
27I ALA* 2.8 32.6 + - - +
79I PHE* 4.1 5.8 - - + -
82I THR* 3.8 21.3 - - + -
83I ILE* 3.8 29.5 - - + +
86I MET* 3.7 10.4 - - - +
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Residues in contact with SER 24 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11020 C 2.5 37.5 + - - +
11030 C 2.9 16.5 + - - +
11090 U 3.1 23.1 + - - -
20I GLY 2.9 13.8 + - - -
21I ARG 3.9 0.2 - - - -
22I VAL 3.2 0.2 - - - -
23I ALA* 1.3 76.0 - - - +
25I GLN* 1.3 59.4 + - - +
27I ALA* 3.7 2.8 - - - +
28I GLU* 3.3 22.2 + - - +
86I MET* 3.4 16.1 - - - -
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Residues in contact with GLN 25 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11090 U 4.2 20.1 - - + -
21I ARG 3.4 16.1 + - - +
22I VAL 2.9 7.4 + - - +
24I SER* 1.3 75.6 - - - +
26I VAL* 1.3 67.2 + - - +
27I ALA 3.1 1.6 - - - -
28I GLU* 3.3 7.6 + - + +
29I GLN* 2.9 38.9 + - - +
116I LEU* 3.9 30.8 - - + +
117I ASP* 3.4 26.3 + - - +
119I THR* 3.5 8.3 - - - +
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Residues in contact with VAL 26 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I VAL* 4.7 2.5 - - + -
22I VAL* 2.7 41.7 + - + +
23I ALA* 3.8 7.4 - - - +
25I GLN* 1.3 72.8 - - - +
27I ALA* 1.3 62.6 + - - +
29I GLN* 3.9 6.7 - - - +
30I ALA* 3.0 23.2 + - - +
36I VAL* 3.6 34.0 - - + +
38I VAL* 4.2 13.5 - - + -
83I ILE* 4.2 9.6 - - + -
101I VAL* 4.0 21.5 - - + -
116I LEU* 4.4 9.4 - - + -
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Residues in contact with ALA 27 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11030 C 3.4 22.7 - - - +
23I ALA 2.8 18.2 + - - +
24I SER 3.7 2.7 - - - +
26I VAL* 1.3 73.8 - - - +
28I GLU* 1.3 66.0 + - - +
30I ALA* 3.1 5.4 + - - +
31I LEU* 3.1 27.9 + - - +
83I ILE* 4.6 9.1 - - + +
86I MET* 3.8 18.8 - - + +
87I LEU* 3.9 14.0 - - + +
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Residues in contact with GLU 28 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11030 C 3.8 35.0 + - - +
11040 C 4.0 13.6 + - - -
11060 A 5.0 4.4 + - - -
24I SER 3.3 14.8 + - - +
25I GLN* 3.6 8.5 - - + +
27I ALA* 1.3 81.4 - - - +
29I GLN* 1.3 65.4 + - + +
31I LEU* 3.4 7.3 + - - +
32I ASP* 3.0 36.7 + - - +
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Residues in contact with GLN 29 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10I VAL* 3.8 28.1 - - - +
25I GLN* 2.9 32.5 + - + +
26I VAL* 4.0 5.7 - - - +
28I GLU* 1.3 78.1 - - + +
30I ALA* 1.3 62.1 + - - +
32I ASP* 3.0 23.9 + - - +
34I GLU* 3.1 33.4 + - + +
36I VAL* 4.5 8.1 - - + +
116I LEU* 4.2 23.2 - - - +
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Residues in contact with ALA 30 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26I VAL 3.0 18.1 + - - +
27I ALA* 3.7 5.2 - - - +
29I GLN* 1.3 76.5 - - - +
31I LEU* 1.3 57.9 + - - +
33I GLY* 3.1 17.2 + - - -
34I GLU 3.4 15.9 + - - +
36I VAL* 4.6 1.1 - - + +
87I LEU* 5.2 2.5 - - + -
97I ALA* 3.4 30.4 - - + +
100I SER* 4.5 1.4 + - - -
101I VAL* 3.5 27.1 - - + -
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Residues in contact with LEU 31 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11030 C 4.5 1.3 - - - +
11040 C 3.4 39.9 - - - +
27I ALA 3.1 12.6 + - - +
28I GLU* 3.7 7.2 - - - +
29I GLN 3.2 0.2 - - - -
30I ALA* 1.3 76.4 - - - +
32I ASP* 1.3 59.6 + - - +
33I GLY 3.2 2.0 + - - -
87I LEU* 3.4 27.4 - - + -
88I PRO* 4.5 4.5 - - + -
93I ARG* 4.2 49.5 + - + +
94I GLY* 4.5 5.8 - - - -
97I ALA* 3.7 17.5 - - + -
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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
------------------------------------------------------------
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