Contacts of the helix formed by residues 7 - 22 (chain F) in PDB entry 4P9U
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 7 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6F LYS* 1.3 80.7 - - - +
8F PRO* 1.4 75.2 - - - +
9F ALA 3.6 0.9 - - - -
10F GLY* 3.2 7.6 + - - -
11F PHE* 3.0 23.8 + - - +
13H G 5.8 0.2 - - - -
14H T 4.3 6.1 - - - -
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Residues in contact with PRO 8 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F LYS 4.6 0.9 - - - +
7F SER* 1.4 84.7 - - - +
9F ALA* 1.3 63.7 + - - +
11F PHE* 3.1 6.5 + - + +
12F ALA* 2.9 24.3 + - - +
43F VAL* 3.6 25.3 - - + +
47F THR* 4.3 2.2 - - + -
14H T 3.3 46.2 - - - +
15H T 4.2 14.6 - - - +
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Residues in contact with ALA 9 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F PRO* 1.3 78.5 - - - +
10F GLY* 1.3 63.6 + - - +
12F ALA* 3.4 0.6 + - - -
13F GLU* 2.9 21.8 + - - +
47F THR* 3.7 17.4 - - + +
50F GLU* 5.6 1.6 - - + +
51F VAL* 3.4 15.1 - - + +
54F ARG* 3.8 24.2 + - - +
14H T 3.1 27.3 + - - +
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Residues in contact with GLY 10 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F LYS* 4.7 8.7 - - - -
7F SER* 3.2 9.8 + - - -
8F PRO 3.1 1.0 - - - -
9F ALA* 1.3 77.6 - - - +
11F PHE* 1.3 62.3 + - - +
13F GLU* 2.9 12.7 + - - +
14F LYS* 2.9 33.8 - - - +
54F ARG* 4.8 2.2 - - - +
14H T 4.8 0.4 + - - -
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Residues in contact with PHE 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B PHE* 5.2 4.9 - + - -
15B TYR* 4.5 11.7 - + - -
24B ARG* 5.7 1.6 - - - -
40B LEU* 3.1 38.6 - - + -
41B ILE* 3.9 19.3 - - - -
6F LYS* 4.5 21.6 - - + +
7F SER 3.0 17.3 + - - +
8F PRO* 3.1 4.7 + - + +
10F GLY* 1.3 75.2 - - - +
12F ALA* 1.3 58.9 + - - +
14F LYS* 4.2 7.6 - - + -
15F TYR* 2.9 58.1 + + + +
41F ILE* 4.1 30.7 - - + -
43F VAL* 5.5 3.1 - - + -
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Residues in contact with ALA 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F PRO 2.9 16.8 + - - +
9F ALA* 3.6 4.9 - - - +
11F PHE* 1.3 78.7 - - - +
13F GLU* 1.3 56.1 + - - +
15F TYR* 3.5 1.3 - - - +
16F ILE* 2.9 34.1 + - - +
41F ILE* 4.2 17.5 - - + -
43F VAL* 4.1 25.4 - - + -
47F THR* 5.6 0.2 - - + -
48F LEU* 4.4 6.7 - - + -
51F VAL* 3.9 16.4 - - + -
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Residues in contact with GLU 13 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57E ARG* 3.0 30.6 + - - -
9F ALA 2.9 11.3 + - - +
10F GLY* 2.9 10.4 + - - +
12F ALA* 1.3 78.3 - - - +
14F LYS* 1.3 74.3 + - + +
16F ILE* 3.3 2.1 + - - +
17F ILE* 2.9 40.6 + - + +
51F VAL* 3.5 14.5 - - + +
54F ARG* 3.0 29.1 + - - -
55F LEU* 3.6 26.7 - - + +
58F ASP* 4.7 0.2 - - - +
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Residues in contact with LYS 14 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F LYS* 4.2 21.0 - - - +
10F GLY* 2.9 35.6 - - - +
11F PHE* 4.2 8.1 - - + +
13F GLU* 1.3 91.7 + - + +
15F TYR* 1.3 62.6 + - - +
17F ILE* 4.2 6.0 - - - +
18F GLU* 2.9 46.5 + - + +
277F ASP* 3.7 25.7 + - - -
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Residues in contact with TYR 15 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B PHE* 4.6 11.7 - + - -
15B TYR* 3.4 37.1 - + - -
24B ARG* 5.6 2.5 - - - +
11F PHE* 2.9 41.1 + + + +
12F ALA* 3.5 5.4 - - - +
14F LYS* 1.3 77.3 - - - +
16F ILE* 1.3 56.6 + - + +
18F GLU* 3.9 6.5 - - - +
19F SER* 2.5 51.6 + - - -
24F ARG* 2.4 34.5 + - - -
25F PHE* 4.5 13.2 - + - -
37F LEU* 4.7 4.0 - - + -
40F LEU* 4.3 10.3 - - + +
41F ILE* 3.6 34.3 - - + -
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Residues in contact with ILE 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F ALA 2.9 22.7 + - - +
13F GLU 3.8 2.9 - - - +
15F TYR* 1.3 77.4 - - + +
17F ILE* 1.3 62.4 + - - +
19F SER* 3.2 6.7 + - - -
20F ILE* 2.9 44.6 + - + +
25F PHE* 4.8 3.4 - - + -
31F LEU* 4.6 16.8 - - + -
37F LEU* 4.8 10.5 - - + -
41F ILE* 4.1 12.6 - - + -
48F LEU* 3.8 28.0 - - + -
51F VAL* 4.1 4.0 - - + -
52F LEU* 3.8 18.4 - - + -
55F LEU* 3.7 23.1 - - + -
61F LEU* 5.1 2.0 - - + -
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Residues in contact with ILE 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F GLU* 2.9 31.3 + - + +
14F LYS* 4.2 5.6 - - - +
16F ILE* 1.3 75.0 - - - +
18F GLU* 1.3 59.4 + - + +
20F ILE* 3.2 10.9 + - + +
21F TRP* 2.9 26.3 + - - +
55F LEU* 3.6 31.4 - - + -
58F ASP* 5.9 0.4 - - - +
60F TRP* 3.9 34.6 - - + +
85F THR* 4.1 13.5 - - + +
89F LEU* 3.8 28.9 - - + -
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Residues in contact with GLU 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ARG* 2.4 49.3 + - - +
14F LYS* 2.9 34.4 + - + +
15F TYR* 4.0 3.3 - - - +
17F ILE* 1.3 77.8 - - + +
19F SER* 1.3 57.6 + - - +
21F TRP* 3.2 8.2 + - + +
22F ASN* 2.9 40.3 + - - +
88F THR 5.8 0.2 - - - +
89F LEU* 3.9 19.5 - - + +
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Residues in contact with SER 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F TYR* 2.5 44.6 + - - -
16F ILE 3.5 4.3 - - - -
18F GLU* 1.3 73.4 - - - +
20F ILE* 1.3 62.9 + - - +
22F ASN* 2.8 23.4 + - - +
24F ARG* 2.9 30.3 + - - -
25F PHE* 3.0 28.4 + - - -
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Residues in contact with ILE 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F ILE* 2.9 38.7 + - + +
17F ILE* 3.5 8.7 - - + +
19F SER* 1.3 77.8 - - - +
21F TRP* 1.3 63.4 + - - +
23F GLY* 3.8 4.7 + - - -
25F PHE* 3.3 34.1 - - + +
27F PRO* 3.9 16.1 - - + +
60F TRP* 4.3 34.3 - - + +
61F LEU* 4.2 21.1 - - + -
71F VAL* 3.8 17.0 - - + -
72F ASN 5.3 0.2 - - - +
74F PHE* 4.5 16.3 - - + -
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Residues in contact with TRP 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F ILE 2.9 16.8 + - - +
18F GLU* 3.6 7.0 - - + +
20F ILE* 1.3 81.3 - - - +
22F ASN* 1.3 68.6 + - + +
23F GLY* 3.5 0.7 + - - -
60F TRP* 5.9 2.5 - + + -
74F PHE* 4.1 27.8 - + - -
86F LEU* 3.8 22.2 - - + -
89F LEU* 3.0 52.6 + - + -
90F ASP* 3.3 41.6 - - + +
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Residues in contact with ASN 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B ASN* 3.4 53.7 + - + +
23B GLY 6.0 0.7 - - - -
24B ARG* 5.0 12.5 - - + +
18F GLU* 2.9 26.0 + - - +
19F SER* 2.8 20.4 + - - +
21F TRP* 1.3 84.5 - - + +
23F GLY* 1.3 74.8 + - - +
24F ARG* 3.2 9.2 + - - +
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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