Contacts of the helix formed by residues 4 - 26 (chain B) in PDB entry 1PVI
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 4 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B SER 3.8 5.6 - - - +
3B HIS* 1.3 99.9 - - + +
5B ASP* 1.3 63.4 + - - +
6B LEU 2.9 1.5 + - - -
7B ASN* 3.2 28.2 + - - +
8B LYS* 4.3 3.2 + - - +
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Residues in contact with ASP 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 4.0 7.3 - - + +
25A LYS* 3.4 20.4 + - - +
26A HIS* 2.8 36.6 + - + -
44A LEU* 3.8 11.8 - - + +
3B HIS* 2.9 21.9 + - - +
4B PRO* 1.3 73.3 - - - +
6B LEU* 1.3 63.6 + - - +
8B LYS* 2.8 53.9 + - + +
9B LEU 3.2 7.4 + - - -
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Residues in contact with LEU 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A GLN* 5.0 1.1 - - + +
44A LEU* 3.8 25.0 - - + +
45A ILE* 4.0 27.4 - - + -
2B SER* 3.7 25.1 - - - +
3B HIS 2.9 16.1 + - - +
5B ASP* 1.3 76.9 - - - +
7B ASN* 1.3 58.4 + - - +
9B LEU* 2.7 36.9 + - + +
10B LEU* 2.9 36.7 + - + +
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Residues in contact with ASN 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B HIS 5.3 0.4 + - - -
4B PRO* 3.2 22.1 + - - +
5B ASP 3.1 0.8 - - - -
6B LEU* 1.3 80.1 - - - +
8B LYS* 1.3 65.9 + - + +
10B LEU* 2.9 28.7 + - - +
11B GLU* 3.3 13.8 + - - +
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Residues in contact with LYS 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 4.6 17.0 - - + -
25A LYS* 4.0 16.2 - - - +
4B PRO 4.9 2.0 - - - +
5B ASP* 2.8 41.1 + - - +
7B ASN* 1.3 76.6 - - + +
9B LEU* 1.3 62.4 + - - +
11B GLU* 3.1 27.2 + - - +
12B LEU* 3.4 17.2 + - + +
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Residues in contact with LEU 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A TYR* 3.7 35.2 - - + +
22A LEU* 4.5 9.6 - - + +
40A LEU* 4.3 13.7 - - + -
41A GLN* 4.2 36.6 - - + +
44A LEU* 4.4 8.7 - - + -
5B ASP 3.2 6.4 + - - +
6B LEU* 2.7 27.5 + - + +
8B LYS* 1.3 73.1 - - - +
10B LEU* 1.3 71.2 + - + +
11B GLU 3.3 0.2 - - - -
12B LEU* 3.7 6.2 + - - +
13B TRP* 3.3 37.1 + - + +
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Residues in contact with LEU 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A GLN* 6.3 0.2 - - - +
6B LEU* 2.9 43.5 + - + +
7B ASN* 2.9 21.6 + - - +
9B LEU* 1.3 86.4 - - + +
11B GLU* 1.3 61.2 + - - +
13B TRP* 4.1 6.7 - - + +
14B PRO* 3.9 14.6 - - - +
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Residues in contact with GLU 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ASN 3.3 10.9 + - - +
8B LYS* 3.1 16.5 + - - +
10B LEU* 1.3 78.7 - - - +
12B LEU* 1.3 70.0 + - + +
13B TRP 3.6 0.2 + - - -
14B PRO* 3.8 11.5 - - - +
15B HIS* 3.8 12.8 + - - -
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Residues in contact with LEU 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A HIS* 4.2 15.7 - - + +
18A GLU* 3.8 32.8 - - + +
19A TYR* 3.6 46.9 - - + +
22A LEU* 5.5 5.4 - - + -
8B LYS* 3.4 15.8 + - + +
9B LEU* 3.7 4.4 + - - +
11B GLU* 1.3 84.7 - - + +
13B TRP* 1.3 66.0 + - - +
14B PRO 3.5 0.2 - - - -
15B HIS* 3.0 21.1 + - + +
16B ILE* 3.2 20.3 + - + +
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Residues in contact with TRP 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A TYR* 3.7 30.5 - + - -
37A GLY 5.1 0.9 - - - -
38A LYS* 6.1 0.7 - - + -
41A GLN* 4.1 24.4 - - - +
107A ILE* 3.2 45.6 + - + -
108A ALA* 4.9 6.9 - - - +
9B LEU* 3.3 33.5 + - + +
10B LEU* 4.1 8.7 - - + +
11B GLU 3.3 0.6 - - - -
12B LEU* 1.3 76.9 - - - +
14B PRO* 1.4 64.3 - - + +
16B ILE* 2.5 46.9 + - + +
17B GLN* 3.0 25.8 + - + -
32B PHE* 4.3 12.6 - + - -
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Residues in contact with PRO 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B LEU 3.9 7.9 - - - +
11B GLU 3.8 14.6 - - - +
12B LEU 3.8 0.4 - - - -
13B TRP* 1.4 90.2 - - + +
15B HIS* 1.3 76.5 + - + +
16B ILE 2.9 1.4 + - - -
17B GLN* 3.0 19.1 + - + +
18B GLU* 3.2 19.3 + - - +
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Residues in contact with HIS 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LEU* 4.0 17.2 - - + +
15A HIS* 3.9 54.8 + + + +
16A ILE* 5.9 1.3 - - - +
11B GLU 3.8 16.2 + - - -
12B LEU* 3.0 14.9 + - - +
14B PRO* 1.3 85.2 - - + +
16B ILE* 1.3 64.4 + - + +
18B GLU* 3.5 29.8 + - - +
19B TYR* 3.5 9.9 + - - +
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Residues in contact with ILE 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A HIS* 4.6 10.1 - - + +
16A ILE* 4.7 14.4 - - + -
19A TYR* 4.2 28.3 - - + -
107A ILE* 5.2 2.7 - - + -
12B LEU* 3.2 24.9 - - + +
13B TRP* 2.5 42.8 + - + +
15B HIS* 1.3 74.5 - - + +
17B GLN* 1.3 62.6 + - - +
19B TYR* 3.0 17.3 + - + +
20B GLN* 3.1 10.6 + - - +
31B ILE* 4.3 8.6 - - + +
32B PHE* 3.9 29.2 - - + -
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Residues in contact with GLN 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ILE* 4.3 22.0 - - - +
108A ALA* 4.6 11.8 + - - +
13B TRP* 3.0 23.8 + - + +
14B PRO* 3.6 11.0 - - + +
16B ILE* 1.3 76.5 - - - +
18B GLU* 1.3 51.2 + - + +
20B GLN* 3.0 20.2 + - - +
21B ASP* 2.7 59.3 + - - +
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Residues in contact with GLU 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 4.0 22.2 - - + +
14B PRO* 3.2 16.1 + - + +
15B HIS* 3.6 29.9 - - - +
16B ILE 3.1 0.8 - - - -
17B GLN* 1.3 73.2 - - + +
19B TYR* 1.3 55.6 + - - +
21B ASP* 3.1 11.0 + - - +
22B LEU* 2.7 36.7 + - - +
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Residues in contact with TYR 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LEU* 3.2 31.7 - - + +
12A LEU* 4.0 15.2 - - + +
13A TRP* 3.8 10.8 - + - -
16A ILE* 3.3 31.9 - - + -
32A PHE* 4.7 5.4 - + - -
15B HIS 3.5 8.0 + - - +
16B ILE* 3.0 12.9 + - + +
18B GLU* 1.3 76.9 - - - +
20B GLN* 1.3 52.4 + - - +
22B LEU* 3.0 7.0 + - + +
23B ALA* 2.7 35.5 + - - +
31B ILE* 3.4 30.5 - - + -
37B GLY* 2.6 48.1 + - - -
40B LEU* 3.4 23.0 - - + +
41B GLN 4.4 1.2 + - - -
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Residues in contact with GLN 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A GLY* 6.0 0.6 - - - -
107A ILE* 3.5 30.8 - - + +
16B ILE 3.1 10.2 + - - +
17B GLN* 3.0 22.3 + - - +
19B TYR* 1.3 77.5 - - - +
21B ASP* 1.3 63.5 + - - +
23B ALA* 3.0 1.7 + - - +
24B LEU* 2.9 36.9 + - + +
28B ILE 4.0 6.3 + - - -
29B ASN 3.2 32.9 + - - -
30B ASP* 3.8 0.4 - - - +
31B ILE* 2.8 51.1 + - + +
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Residues in contact with ASP 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B GLN* 2.7 45.6 + - - +
18B GLU* 3.5 11.6 - - - +
20B GLN* 1.3 73.1 - - - +
22B LEU* 1.3 61.8 + - - +
24B LEU* 3.5 14.4 + - - +
25B LYS* 3.4 19.4 + - - +
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Residues in contact with LEU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ASP* 3.6 33.4 - - + +
8A LYS* 3.9 30.7 - - + -
9A LEU* 4.1 15.3 - - + +
12A LEU* 4.2 15.3 - - + -
18B GLU 2.7 17.7 + - - +
19B TYR* 3.3 6.5 - - + +
21B ASP* 1.3 76.6 - - - +
23B ALA* 1.3 64.5 + - - +
25B LYS* 3.4 11.4 + - + +
26B HIS* 3.0 32.0 + - + -
40B LEU* 4.1 15.7 - - + +
44B LEU* 5.1 3.4 - - + -
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Residues in contact with ALA 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B TYR 2.7 12.3 + - - +
20B GLN* 3.0 3.6 + - - +
22B LEU* 1.3 73.8 - - - +
24B LEU* 1.3 53.4 + - - +
25B LYS 3.1 0.2 - - - -
26B HIS* 2.8 23.4 + - - +
27B GLY 3.4 0.2 + - - -
28B ILE* 3.0 36.1 + - + +
31B ILE* 3.3 34.3 - - + -
40B LEU* 3.4 20.4 - - + +
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Residues in contact with LEU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B GLN* 2.9 27.7 + - + +
21B ASP* 3.7 15.3 - - - +
23B ALA* 1.3 75.9 - - - +
25B LYS* 1.3 57.2 + - - +
26B HIS 3.1 1.6 + - - -
27B GLY* 3.9 7.7 + - - -
28B ILE 3.2 18.3 + - - +
29B ASN* 3.5 28.7 - - - +
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Residues in contact with LYS 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A HIS* 6.1 1.6 - - - -
5A ASP* 3.6 32.6 + - - +
8A LYS* 4.4 7.1 - - - +
21B ASP 3.4 10.3 + - - +
22B LEU* 3.5 16.2 - - + +
23B ALA 3.1 0.6 - - - -
24B LEU* 1.3 76.9 - - - +
26B HIS* 1.3 66.3 + - + +
27B GLY 3.6 0.9 - - - -
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Residues in contact with HIS 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A HIS* 3.7 19.5 + + - -
5A ASP* 2.8 32.2 + - - -
22B LEU* 3.0 27.4 + - + +
23B ALA 2.8 8.0 + - - +
25B LYS* 1.3 91.2 + - + +
27B GLY* 1.3 58.2 + - - +
28B ILE* 3.5 3.6 + - + +
40B LEU* 4.1 14.7 - - + +
43B LEU* 4.3 18.4 - - + +
44B LEU* 3.4 30.4 - - + +
48B LEU 6.0 1.6 - - - -
49B THR* 6.0 1.0 - - - +
50B VAL* 3.2 19.0 + - - +
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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