Contacts of the helix formed by residues 0 - 22 (chain K) in PDB entry 5JHC
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 PRO 0 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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-1K GLY* 1.3 80.8 - - - +
1K MET* 1.3 83.6 + - + +
2K GLU 3.2 0.2 - - - -
3K GLU* 3.1 17.2 + - - +
4K GLN* 3.0 26.1 + - - +
10M GLN* 3.3 38.4 - - + +
14M THR* 4.6 11.7 - - - +
17M MET* 4.3 5.2 - - + +
14N THR* 4.8 10.1 - - + +
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Residues in contact with MET 1 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-1K GLY* 3.9 8.1 - - - -
0K PRO* 1.3 99.7 - - + +
2K GLU* 1.3 65.1 + - - +
4K GLN* 3.1 21.1 + - - +
5K ARG* 3.0 27.4 + - - +
10M GLN* 5.6 0.7 - - - +
0f PRO* 6.5 1.3 - - + -
4f GLN* 4.2 5.4 + - - +
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Residues in contact with GLU 2 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-1K GLY* 3.0 35.5 + - - +
1K MET* 1.3 83.3 - - - +
3K GLU* 1.3 56.3 + - - +
5K ARG* 3.2 8.1 + - - +
6K GLU* 3.0 54.2 + - + +
10N GLN* 4.2 10.7 + - - -
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Residues in contact with GLU 3 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-1K GLY 3.1 17.5 + - - +
0K PRO* 3.1 12.0 + - - +
2K GLU* 1.3 77.1 - - - +
4K GLN* 1.3 63.2 + - - +
6K GLU* 3.3 3.0 + - - +
7K ILE* 3.0 29.6 + - - +
14M THR* 4.5 1.0 + - - +
17M MET* 3.6 14.4 - - + +
7N ILE* 5.4 2.7 - - + -
10N GLN* 2.8 60.6 - - + +
11N LEU* 2.9 26.7 - - + +
14N THR* 3.1 20.7 + - - +
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Residues in contact with GLN 4 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0K PRO 3.0 10.5 + - - +
1K MET* 3.1 22.9 + - - +
3K GLU* 1.3 77.2 - - - +
5K ARG* 1.3 62.2 + - - +
7K ILE* 3.4 2.4 + - - +
8K LEU* 3.0 24.8 + - + +
18L LEU* 4.7 6.1 - - + +
21L GLU* 3.1 31.3 + - - +
22L LEU* 3.1 31.4 - - + +
13M LYS* 5.5 1.4 - - - +
17M MET* 3.8 16.5 - - - -
1f MET* 4.2 15.6 - - - +
4f GLN* 3.4 18.1 + - - +
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Residues in contact with ARG 5 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1K MET 3.0 11.6 + - - +
2K GLU* 3.2 9.8 + - - +
4K GLN* 1.3 74.5 - - - +
6K GLU* 1.3 64.5 + - + +
8K LEU* 3.2 4.2 + - - +
9K GLU* 3.0 24.5 + - - +
4f GLN* 3.1 25.7 + - - +
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Residues in contact with GLU 6 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2K GLU* 3.0 45.5 + - + +
3K GLU 3.6 4.5 - - - +
5K ARG* 1.3 76.3 - - + +
7K ILE* 1.3 64.0 + - - +
9K GLU* 3.2 15.3 + - - +
10K GLN* 3.0 20.4 + - - +
3N GLU* 4.4 10.5 - - - +
6N GLU* 4.8 6.5 - - - +
7N ILE* 3.4 28.0 - - + +
10N GLN* 2.8 35.1 + - - +
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Residues in contact with ILE 7 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3K GLU 3.0 16.7 + - - +
4K GLN* 4.0 3.4 - - - +
6K GLU* 1.3 73.6 - - - +
8K LEU* 1.3 66.6 + - - +
10K GLN* 3.0 9.5 + - - +
11K LEU* 3.0 24.4 + - + +
18L LEU* 3.6 22.9 - - + -
17M MET* 3.9 31.4 - - + +
20M VAL* 4.0 14.8 - - + -
21M GLU* 3.0 35.4 - - + +
7N ILE* 3.7 24.9 - - + -
11N LEU* 4.3 2.5 - - + -
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Residues in contact with LEU 8 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4K GLN* 3.0 18.0 + - + +
5K ARG* 3.7 5.4 - - - +
7K ILE* 1.3 75.7 - - - +
9K GLU* 1.3 66.8 + - - +
11K LEU* 3.1 8.7 + - - +
12K LYS* 3.0 20.1 + - + +
18L LEU* 4.1 10.9 - - + +
22L LEU* 4.4 4.7 - - + -
4f GLN* 3.4 47.8 - - + +
7f ILE* 4.5 11.2 - - + -
8f LEU* 3.9 26.5 - - + -
11f LEU* 4.2 21.9 - - + +
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Residues in contact with GLU 9 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5K ARG 3.0 13.2 + - - +
6K GLU* 3.4 15.3 - - - +
8K LEU* 1.3 80.2 - - - +
10K GLN* 1.3 57.3 + - - +
12K LYS* 2.8 29.0 + - + +
13K LYS* 3.1 26.3 + - + +
3N GLU* 4.7 8.5 - - - +
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Residues in contact with GLN 10 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6K GLU 3.0 11.4 + - - +
7K ILE* 3.0 10.0 + - + +
9K GLU* 1.3 77.4 + - - +
11K LEU* 1.3 67.4 + - + +
13K LYS* 3.3 13.7 + - + +
14K THR* 3.1 30.6 + - - +
21M GLU* 3.4 27.2 + - - +
0N PRO* 4.4 6.7 + - - +
3N GLU* 4.3 13.9 - - + +
4N GLN* 4.1 26.1 - - - +
7N ILE* 3.6 16.7 - - + +
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Residues in contact with LEU 11 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7K ILE* 3.0 18.8 + - + +
8K LEU* 3.1 8.3 + - - +
10K GLN* 1.3 82.8 - - + +
12K LYS* 1.3 63.2 + - - +
14K THR* 3.3 6.5 + - - +
15K LEU* 2.9 23.9 + - - +
11L LEU* 4.6 19.5 - - + +
14L THR* 3.6 44.4 - - + +
15L LEU* 3.9 20.4 - - + -
18L LEU* 4.4 19.1 - - + -
20M VAL* 4.9 4.5 - - + -
8f LEU* 5.2 2.7 - - + -
11f LEU* 3.9 13.9 - - + +
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Residues in contact with LYS 12 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8K LEU* 3.0 13.9 + - + +
9K GLU* 2.8 17.6 + - + +
11K LEU* 1.3 76.9 - - - +
13K LYS* 1.3 64.6 + - + +
15K LEU* 3.1 7.4 + - + +
16K GLN* 3.0 51.4 + - + +
11f LEU* 3.9 24.3 - - + +
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Residues in contact with LYS 13 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9K GLU* 3.1 26.5 + - + +
10K GLN* 3.7 13.9 - - + +
12K LYS* 1.3 77.2 - - + +
14K THR* 1.3 64.2 + - - +
16K GLN* 3.1 17.3 + - - +
17K MET* 3.1 22.5 + - - +
0N PRO* 5.4 10.5 - - - +
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Residues in contact with THR 14 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10K GLN* 3.1 17.0 + - - +
11K LEU* 3.8 10.0 - - - +
13K LYS* 1.3 78.1 - - - +
15K LEU* 1.3 56.7 + - - +
17K MET* 3.4 21.2 + - + +
18K LEU* 2.9 37.4 + - + +
7L ILE* 6.1 1.1 - - + -
11L LEU* 3.4 28.0 - - + -
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Residues in contact with LEU 15 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11K LEU 2.9 13.9 + - - +
12K LYS* 3.1 13.9 + - + +
14K THR* 1.3 77.6 - - - +
16K GLN* 1.3 55.4 + - + +
18K LEU* 3.3 1.6 + - + +
19K THR* 2.7 41.6 + - - +
11L LEU* 3.7 25.5 - - + +
15L LEU* 5.8 1.1 - - + -
11f LEU* 4.1 26.5 - - + +
14f THR* 3.9 28.3 - - + -
15f LEU* 4.6 9.2 - - + -
18f LEU* 3.9 26.0 - - + -
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Residues in contact with GLN 16 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12K LYS* 3.0 45.7 + - + +
13K LYS* 3.5 16.2 - - - +
15K LEU* 1.3 75.9 - - + +
17K MET* 1.3 67.9 + - - +
19K THR* 3.0 17.4 + - - -
20K VAL* 3.0 19.4 + - + +
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Residues in contact with MET 17 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13K LYS 3.1 8.7 + - - +
14K THR* 3.8 24.9 - - + +
16K GLN* 1.3 78.3 - - - +
18K LEU* 1.3 69.5 + - - +
20K VAL* 3.2 9.8 + - + +
21K GLU* 2.9 39.4 + - - +
16Y GLN* 4.5 31.4 - - + +
18Y LEU 6.0 0.4 - - - +
16l GLN* 6.4 0.2 - - - -
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Residues in contact with LEU 18 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14K THR* 2.9 24.4 + - + +
15K LEU* 3.7 5.4 - - - +
17K MET* 1.3 87.6 - - - +
19K THR* 1.3 65.4 + - - +
21K GLU* 3.3 16.0 + - + +
22K LEU* 3.2 24.4 + - - +
4L GLN* 5.8 1.8 - - - +
7L ILE* 3.6 48.9 - - + +
8L LEU* 4.3 10.1 - - + +
11L LEU* 4.1 26.9 - - + -
18f LEU* 4.5 13.8 - - + +
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Residues in contact with THR 19 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15K LEU* 2.7 27.4 + - - +
16K GLN* 3.0 8.7 + - - -
18K LEU* 1.3 76.7 - - - +
20K VAL* 1.3 63.5 + - - +
22K LEU* 3.1 19.5 + - - +
14f THR* 5.0 5.5 - - + +
18f LEU* 4.0 30.0 - - + +
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Residues in contact with VAL 20 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16K GLN 3.0 18.1 + - - +
17K MET* 3.5 10.5 - - - +
19K THR* 1.3 75.6 - - - +
21K GLU* 1.3 68.3 + - - +
22K LEU* 3.1 9.7 - - - +
16Y GLN* 6.5 0.7 - - + -
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Residues in contact with GLU 21 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17K MET* 2.9 27.6 + - - +
18K LEU* 3.3 17.1 + - + +
20K VAL* 1.3 79.2 - - - +
22K LEU* 1.3 61.2 + - - +
-1L GLY* 3.3 30.3 + - - +
4L GLN* 6.3 2.7 - - + -
7L ILE* 5.1 11.4 - - - +
16Y GLN* 3.9 26.2 - - + +
16l GLN* 5.5 6.4 + - - -
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Residues in contact with LEU 22 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18K LEU 3.2 14.0 + - - +
19K THR* 3.1 15.1 - - - +
20K VAL 3.1 12.8 - - - +
21K GLU* 1.3 83.1 - - - +
4L GLN* 5.3 14.8 - - + -
8L LEU* 6.1 4.9 - - + -
18f LEU* 5.9 6.3 - - + -
21f GLU* 6.0 6.7 - - + -
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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