Contacts of the helix formed by residues 0 - 20 (chain U) 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 U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-1U GLY* 1.3 81.5 - - - +
1U MET* 1.3 87.7 + - + +
3U GLU* 3.1 18.5 + - - +
4U GLN* 3.0 23.8 + - - +
21V GLU* 3.4 10.9 - - - +
4k GLN* 5.9 1.8 - - - +
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Residues in contact with MET 1 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-1U GLY* 4.4 5.2 - - - -
0U PRO* 1.3 100.2 - - + +
2U GLU* 1.3 70.3 + - + +
4U GLN* 3.2 7.8 + - - +
5U ARG* 2.9 45.7 + - - +
4k GLN* 4.8 19.0 + - + +
7k ILE* 4.7 1.2 - - + +
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Residues in contact with GLU 2 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-1U GLY 3.2 25.1 + - - +
0U PRO 3.1 0.4 - - - -
1U MET* 1.3 84.7 - - + +
3U GLU* 1.3 57.5 + - + +
5U ARG* 3.6 17.6 + - - +
6U GLU* 2.9 45.3 + - - +
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Residues in contact with GLU 3 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-1U GLY 2.9 19.4 + - - +
0U PRO* 3.3 14.8 - - - +
2U GLU* 1.3 77.4 - - + +
4U GLN* 1.3 57.8 + - - +
6U GLU* 3.1 8.5 + - - +
7U ILE* 2.9 34.9 + - + +
20V VAL* 6.1 1.1 - - - +
21V GLU* 2.9 28.6 - - - +
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Residues in contact with GLN 4 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0U PRO* 3.0 12.3 + - - +
1U MET* 3.7 9.0 - - - +
3U GLU* 1.3 76.5 - - - +
5U ARG* 1.3 57.8 + - - +
7U ILE* 3.5 9.0 + - - +
8U LEU* 3.0 26.3 + - - +
21V GLU* 3.0 35.6 + - + +
4k GLN* 5.3 14.0 + - - +
7k ILE* 4.5 16.0 - - + +
8k LEU* 5.1 16.4 - - - +
11k LEU* 3.8 18.4 - - + +
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Residues in contact with ARG 5 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1U MET* 2.9 41.4 + - - +
2U GLU* 3.6 21.1 - - - +
4U GLN* 1.3 73.0 - - - +
6U GLU* 1.3 61.3 + - - +
8U LEU* 3.2 5.9 + - - +
9U GLU* 2.9 28.1 + - - +
3k GLU* 4.9 16.6 + - - +
4k GLN* 5.9 0.6 - - - +
7k ILE* 3.3 30.1 - - + +
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Residues in contact with GLU 6 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2U GLU* 2.9 31.7 + - - +
3U GLU* 3.1 13.0 + - - +
5U ARG* 1.3 75.9 - - - +
7U ILE* 1.3 58.8 + - + +
9U GLU* 3.1 8.7 + - + +
10U GLN* 3.0 41.8 + - + +
17V MET* 5.1 12.4 - - + +
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Residues in contact with ILE 7 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3U GLU* 2.9 21.0 + - + +
4U GLN* 3.6 7.0 - - - +
6U GLU* 1.3 75.7 - - + +
8U LEU* 1.3 65.1 + - - +
10U GLN* 3.3 6.4 + - - +
11U LEU* 2.9 27.3 + - + +
14V THR* 4.7 4.6 - - + +
17V MET* 3.2 48.0 - - + +
18V LEU* 3.7 29.2 - - + +
21V GLU* 3.5 28.3 - - + +
11k LEU* 4.2 9.9 - - + -
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Residues in contact with LEU 8 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4U GLN 3.0 15.0 + - - +
5U ARG* 3.2 9.8 + - - +
7U ILE* 1.3 76.7 - - - +
9U GLU* 1.3 59.1 + - - +
11U LEU* 3.8 4.7 - - + +
12U LYS* 2.8 33.4 + - + +
7k ILE* 3.8 15.9 - - + +
10k GLN* 3.8 19.5 - - + +
11k LEU* 3.4 47.3 - - + +
14k THR* 4.0 18.2 - - - +
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Residues in contact with GLU 9 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5U ARG 2.9 13.8 + - - +
6U GLU* 3.1 12.7 + - + +
8U LEU* 1.3 78.7 - - - +
10U GLN* 1.3 64.9 + - - +
12U LYS* 3.1 8.2 + - - +
13U LYS* 2.9 27.9 + - - +
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Residues in contact with GLN 10 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6U GLU* 3.0 26.5 + - + +
7U ILE* 3.8 4.3 - - - +
9U GLU* 1.3 80.0 - - - +
11U LEU* 1.3 58.0 + - - +
13U LYS* 3.0 38.0 + - - +
14U THR* 2.9 32.1 + - - -
10V GLN* 3.2 10.4 + - - +
13V LYS* 5.3 4.7 - - - +
14V THR* 3.6 14.9 + - + +
17V MET* 3.8 33.5 - - + +
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Residues in contact with LEU 11 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7U ILE* 2.9 21.1 + - + +
8U LEU* 3.8 4.3 - - - +
10U GLN* 1.3 77.5 - - - +
12U LYS* 1.3 57.4 + - - +
14U THR* 3.8 2.7 - - - -
15U LEU* 2.9 27.9 + - - +
11V LEU* 5.8 0.2 - - + -
14V THR* 3.5 23.5 - - + +
15V LEU* 5.9 3.1 - - + -
18V LEU* 5.6 5.6 - - + -
11k LEU* 4.1 17.0 - - + +
14k THR* 3.5 28.9 - - + -
15k LEU* 3.6 31.9 - - + +
18k LEU* 3.5 30.6 - - + +
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Residues in contact with LYS 12 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8U LEU* 2.8 28.2 + - + +
9U GLU* 3.3 9.0 - - - +
11U LEU* 1.3 74.9 - - - +
13U LYS* 1.3 59.3 + - - +
15U LEU* 3.2 6.1 + - - +
16U GLN* 2.9 31.8 + - - +
14k THR* 4.2 10.7 - - + +
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Residues in contact with LYS 13 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9U GLU 2.9 12.4 + - - +
10U GLN* 3.0 33.0 + - - +
12U LYS* 1.3 73.8 - - - +
14U THR* 1.3 66.0 + - - +
16U GLN* 2.8 24.0 + - - +
17U MET* 3.0 24.0 + - + +
10V GLN* 2.3 42.3 + - - +
-1X GLY* 5.0 4.5 - - - -
0X PRO* 4.3 26.2 - - + -
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Residues in contact with THR 14 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10U GLN 2.9 9.5 + - - -
11U LEU* 3.8 6.3 - - - -
13U LYS* 1.3 76.8 - - - +
15U LEU* 1.3 62.9 + - - +
17U MET* 3.4 7.7 + - - +
18U LEU* 3.0 34.4 - - + +
7V ILE* 4.7 1.8 - - + +
10V GLN* 2.9 20.6 + - + +
11V LEU* 3.7 41.1 - - + +
14V THR* 2.7 27.3 + - - -
18k LEU* 4.8 7.2 - - + -
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Residues in contact with LEU 15 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11U LEU 2.9 18.7 + - - +
12U LYS* 3.5 6.7 - - - +
13U LYS 3.2 0.2 - - - -
14U THR* 1.3 77.3 - - - +
16U GLN* 1.3 63.4 + - - +
18U LEU* 3.6 4.3 + - - +
19U THR* 2.7 41.4 + - + +
14k THR* 3.7 11.2 - - + +
17k MET* 3.6 28.5 - - + +
18k LEU* 3.2 52.0 - - + +
21k GLU* 4.9 7.6 - - + +
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Residues in contact with GLN 16 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12U LYS* 2.9 14.7 + - - +
13U LYS* 2.8 16.8 + - - +
15U LEU* 1.3 78.4 - - - +
17U MET* 1.3 62.5 + - - +
19U THR* 3.0 17.4 + - - -
20U VAL* 3.2 13.0 + - - +
0X PRO* 3.9 25.2 - - + +
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Residues in contact with MET 17 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13U LYS* 3.0 21.3 + - + +
14U THR* 3.4 7.2 + - - +
15U LEU 3.4 0.4 - - - -
16U GLN* 1.3 75.7 - - - +
18U LEU* 1.3 63.0 + - + +
20U VAL* 3.2 9.1 - - - +
6V GLU* 4.6 24.5 - - + +
7V ILE* 3.7 20.6 - - + +
10V GLN* 4.4 28.5 - - + +
20W VAL* 5.0 1.4 - - - +
-1X GLY* 3.4 14.4 - - - +
0X PRO* 3.3 44.2 - - + -
3X GLU* 3.1 40.3 - - + +
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Residues in contact with LEU 18 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14U THR* 3.0 35.4 + - + +
15U LEU* 4.0 4.5 - - - +
16U GLN 3.2 0.4 - - - -
17U MET* 1.3 80.0 - - - +
19U THR* 1.3 59.9 + - - +
20U VAL* 3.5 3.0 + - - +
7V ILE* 3.5 34.8 - - + -
11V LEU* 6.2 2.0 - - + -
20W VAL* 5.1 3.6 - - - +
21W GLU* 4.0 27.5 + - + +
22W LEU* 5.0 11.0 - - + +
10Z GLN* 5.9 2.4 - - - +
18k LEU* 4.6 9.9 - - + -
21k GLU* 3.4 48.7 - - + +
22k LEU* 4.6 12.6 - - + -
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Residues in contact with THR 19 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15U LEU* 2.7 30.6 + - + +
16U GLN* 3.0 8.6 + - - -
18U LEU* 1.3 76.2 - - - +
20U VAL* 1.3 52.0 + - - +
21U GLU* 2.3 30.4 + - + +
21k GLU* 4.0 18.0 + - - +
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Residues in contact with VAL 20 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16U GLN 3.2 8.1 + - - +
17U MET* 3.2 11.7 - - - +
18U LEU 3.5 3.2 - - - +
19U THR* 1.3 66.6 - - - +
21U GLU* 1.3 61.3 + - - +
22U LEU* 4.5 10.0 - - - +
18W LEU* 4.5 15.2 - - + +
20W VAL* 5.6 6.2 - - + +
0X PRO* 5.7 3.4 - - + +
3X GLU* 3.0 28.3 - - - +
4X GLN* 4.0 37.9 - - + +
7X ILE* 4.4 17.7 - - + +
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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
------------------------------------------------------------
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