Contacts of the helix formed by residues 13 - 25 (chain F) in PDB entry 5K58
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 GLU 13 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10F ASN* 3.1 35.2 + - - +
11F ARG 3.1 0.4 - - - -
12F ARG* 1.3 78.8 - - - +
14F GLU* 1.3 61.9 + - - +
15F ILE 3.6 0.9 - - - -
16F LEU* 4.2 10.6 - - + +
17F GLN* 3.0 52.4 + - - +
375M PHE* 3.8 17.8 - - - -
377M ARG* 3.4 27.4 + - - +
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Residues in contact with GLU 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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10F ASN 3.3 8.0 + - - +
11F ARG* 3.4 56.1 + - - +
13F GLU* 1.3 79.9 - - - +
15F ILE* 1.3 67.7 + - + +
17F GLN* 3.4 5.7 + - - +
18F SER* 2.9 27.5 + - - -
41F VAL* 4.4 16.9 - - + +
43F VAL* 5.2 1.0 - - - +
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Residues in contact with ILE 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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11F ARG* 3.6 19.1 - - + +
13F GLU 5.5 0.2 - - - +
14F GLU* 1.3 77.6 - - + +
16F LEU* 1.3 57.9 + - + +
18F SER* 2.9 5.5 + - - -
19F LEU* 2.7 34.8 + - + +
37F LEU* 3.9 20.8 - - + +
41F VAL* 4.0 19.5 - - + -
47F ALA 4.4 9.6 - - - +
48F LEU* 3.8 31.9 - - + -
51F HIS* 5.1 4.5 - - + -
52F PHE* 3.8 28.0 - - + -
58F MET* 4.3 20.0 - - + -
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Residues in contact with LEU 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 ARG* 3.3 28.9 - - - +
13F GLU* 4.2 16.6 - - + +
14F GLU 3.4 0.2 - - - -
15F ILE* 1.3 80.3 - - + +
17F GLN* 1.3 52.4 + - - +
19F LEU* 3.1 8.9 + - + +
20F ALA* 2.8 36.0 + - - +
52F PHE* 4.4 16.8 - - + -
58F MET* 3.4 28.7 - - + +
61F SER* 4.0 22.4 - - - +
62F LEU* 3.6 22.3 - - + +
375M PHE* 3.9 12.1 - - + -
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Residues in contact with GLN 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* 3.0 39.7 + - - +
14F GLU* 3.4 7.6 + - - +
16F LEU* 1.3 74.8 - - - +
18F SER* 1.3 65.9 + - - +
20F ALA* 3.6 2.1 + - - +
21F LEU* 3.2 26.4 + - - +
375M PHE* 2.6 58.1 + - - +
376M LEU* 3.8 19.5 - - - +
377M ARG* 3.9 16.1 - - - +
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Residues in contact with SER 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14F GLU 2.9 14.1 + - - -
15F ILE 2.9 9.2 + - - -
17F GLN* 1.3 77.1 - - - +
19F LEU* 1.3 61.2 + - - +
21F LEU* 3.6 7.5 + - - +
22F MET* 3.1 25.9 + - - +
37F LEU* 4.1 3.6 + - - +
40F SER* 3.4 29.9 + - - -
41F VAL* 3.6 25.5 + - - +
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Residues in contact with LEU 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 ILE* 2.7 17.0 + - + +
16F LEU* 3.5 10.3 - - + +
18F SER* 1.3 71.3 - - - +
20F ALA* 1.3 62.1 + - - +
22F MET* 2.8 29.0 + - + +
23F LEU* 3.2 27.6 - - + +
32F ILE* 4.1 30.1 - - + -
37F LEU* 4.4 15.0 - - + +
58F MET* 4.4 28.0 - - + +
59F PHE* 4.1 28.0 - - + -
62F LEU* 4.0 19.7 - - + -
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Residues in contact with ALA 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 LEU 2.8 20.2 + - - +
17F GLN* 3.9 4.3 - - - +
19F LEU* 1.3 74.7 - - - +
21F LEU* 1.3 61.7 + - - +
22F MET 3.3 0.5 + - - -
23F LEU* 3.4 16.5 + - - +
24F GLU* 3.6 2.3 + - - +
62F LEU* 4.6 8.3 - - + +
104F GLY* 3.6 22.1 - - - -
105F LEU* 5.0 5.4 - - + -
375M PHE* 3.5 30.1 - - + -
376M LEU* 5.2 8.3 - - + -
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Residues in contact with LEU 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 GLN 3.2 15.6 + - - +
18F SER* 3.7 8.1 - - - +
20F ALA* 1.3 78.2 - - - +
22F MET* 1.3 61.8 + - + +
24F GLU* 3.0 28.4 + - + +
25F SER* 3.1 16.2 + - - +
376M LEU* 5.0 15.8 - - + +
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Residues in contact with MET 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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18F SER* 3.1 21.4 + - - +
19F LEU* 2.8 17.4 + - + +
21F LEU* 1.3 72.5 - - + +
23F LEU* 1.3 60.7 + - - +
24F GLU 3.0 6.0 + - - -
25F SER* 2.9 30.0 + - - +
27F ASP* 4.2 4.6 - - + -
28F GLY* 3.6 5.7 + - - -
32F ILE* 4.3 37.9 - - + -
36F LYS* 3.4 32.3 - - + +
37F LEU* 4.3 14.4 - - - -
40F SER* 3.6 20.9 - - - +
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Residues in contact with LEU 23 (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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19F LEU* 3.2 50.6 + - + +
20F ALA* 3.8 7.2 - - - +
21F LEU 3.4 0.2 - - - -
22F MET* 1.3 76.0 - - - +
24F GLU* 1.3 56.5 + - - +
25F SER 3.9 0.7 - - - -
28F GLY* 4.0 10.3 - - - +
32F ILE* 5.3 6.5 - - + +
59F PHE* 4.8 6.5 - - + -
62F LEU* 4.6 9.9 - - + -
104F GLY* 3.3 33.2 - - - +
107F ARG* 2.8 36.6 + - + +
108F ILE* 3.9 13.2 - - + -
113F ALA* 3.5 32.5 - - + -
178F PHE* 3.9 3.6 - - - -
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Residues in contact with GLU 24 (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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20F ALA 3.6 6.0 + - - +
21F LEU* 3.0 24.8 + - + +
22F MET 3.0 0.6 - - - -
23F LEU* 1.3 77.8 - - - +
25F SER* 1.3 66.6 + - - +
26F SER 3.6 0.9 + - - -
103F PRO* 4.3 21.4 - - + +
104F GLY* 4.5 5.5 + - - +
107F ARG* 4.1 2.1 + - - -
178F PHE* 3.3 40.7 - - + -
376M LEU* 4.2 21.9 - - - +
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Residues in contact with SER 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F LEU* 3.1 15.2 + - - +
22F MET* 2.9 20.9 + - - +
24F GLU* 1.3 80.5 - - - +
26F SER* 1.3 53.5 + - - +
27F ASP* 2.8 26.2 + - - +
28F GLY* 2.5 29.8 + - - -
107F ARG* 3.6 1.7 + - - -
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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
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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