Contacts of the helix formed by residues 20 - 29 (chain F) in PDB entry 4O9U
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 VAL 20 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17F VAL* 4.0 8.5 - - + -
19F LEU* 1.3 74.7 - - - +
21F PRO* 1.4 75.5 - - + +
22F GLU* 4.1 12.8 - - + +
23F VAL* 3.0 39.4 + - + +
24F VAL* 3.3 9.4 + - - +
46F HIS* 3.4 28.9 - - + +
51F TYR* 3.9 2.5 - - - -
320F VAL 5.0 0.4 - - - +
323F SER* 3.9 26.9 - - - +
324F GLU* 4.0 17.3 - - + +
327F ALA* 3.6 7.7 - - + +
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Residues in contact with PRO 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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20F VAL* 1.4 86.0 - - + +
22F GLU* 1.3 60.1 + - - +
24F VAL* 3.5 3.8 + - + +
25F ALA* 3.3 19.2 + - - +
46F HIS* 3.4 34.8 - - + +
50F ALA* 3.7 32.1 - - + +
51F TYR* 3.6 41.0 - - + -
54F ALA* 3.6 13.9 - - + +
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Residues in contact with GLU 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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20F VAL* 3.1 11.5 + - + +
21F PRO* 1.3 79.8 - - - +
23F VAL* 1.3 66.9 + - - +
25F ALA* 3.9 14.1 - - - +
26F ARG* 3.9 29.5 + - - +
46F HIS* 6.2 1.6 - - + -
324F GLU* 5.1 7.3 - - - +
328F LYS* 4.4 16.8 - - - -
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Residues in contact with VAL 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* 3.8 16.6 - - + -
20F VAL* 3.0 17.4 + - + +
22F GLU* 1.3 83.4 - - - +
24F VAL* 1.3 66.2 + - - +
25F ALA 3.1 2.0 - - - -
26F ARG* 2.9 25.0 + - - +
27F LEU* 3.3 13.8 + - + +
324F GLU 5.0 0.2 - - - +
327F ALA* 3.7 35.7 - - + +
328F LYS* 4.1 17.0 - - + +
331F TYR* 3.6 27.1 - - + -
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Residues in contact with VAL 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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6F VAL* 5.0 1.1 - - + -
19F LEU* 3.8 34.8 - - + -
20F VAL 3.3 5.9 + - - +
21F PRO* 3.7 9.4 - - + +
23F VAL* 1.3 77.1 - - - +
25F ALA* 1.3 51.3 + - - +
27F LEU* 3.0 11.6 + - - +
28F VAL* 2.7 42.1 + - + +
34F VAL* 3.8 32.5 - - + -
51F TYR* 4.6 15.3 - - + +
54F ALA* 4.4 8.5 - - + -
56F ALA* 4.2 14.4 - - + -
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Residues in contact with ALA 25 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21F PRO 3.3 12.9 + - - +
22F GLU* 3.9 10.1 - - - +
23F VAL 3.1 0.6 - - - -
24F VAL* 1.3 80.2 - - - +
26F ARG* 1.3 57.1 + - + +
28F VAL* 4.1 5.7 - - - +
29F LYS* 2.9 31.2 + - - +
54F ALA* 4.0 21.3 - - + +
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Residues in contact with ARG 26 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281D ASP* 5.9 2.8 + - - +
284D ASP* 4.4 17.0 + - - -
22F GLU* 3.9 29.8 + - - +
23F VAL* 2.9 15.4 + - - +
25F ALA* 1.3 76.8 - - - +
27F LEU* 1.3 57.1 + - - +
29F LYS* 3.8 4.0 - - - +
30F GLY* 2.8 22.3 + - - -
328F LYS* 4.6 27.5 - - - +
331F TYR* 3.4 57.0 + - + +
332F ASN* 5.2 4.2 + - - +
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Residues in contact with LEU 27 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4F VAL* 5.2 7.4 - - + -
19F LEU* 3.8 30.5 - - + -
23F VAL* 3.7 19.5 - - + +
24F VAL* 3.0 11.5 + - - +
26F ARG* 1.3 77.7 - - - +
28F VAL* 1.3 54.7 + - - +
30F GLY* 3.1 4.9 + - - +
31F GLY 2.9 8.3 + - - -
32F ALA* 2.7 36.7 + - + +
34F VAL* 4.3 13.5 - - + -
72F PHE* 5.8 2.9 - - + -
331F TYR* 3.6 17.5 - - + -
334F SER* 3.6 31.0 - - - +
338F ILE* 4.2 17.9 - - + -
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Residues in contact with VAL 28 (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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24F VAL* 2.7 37.3 + - + +
25F ALA* 4.1 3.1 - - - +
27F LEU* 1.3 72.3 - - - +
29F LYS* 1.3 61.2 + - - +
31F GLY* 3.5 10.4 + - - -
32F ALA 3.3 19.1 - - - +
34F VAL* 4.3 7.9 - - + +
54F ALA 4.1 8.7 - - - +
55F GLY* 3.4 39.5 - - - +
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Residues in contact with LYS 29 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25F ALA 2.9 18.2 + - - +
26F ARG* 3.8 4.0 - - - +
28F VAL* 1.3 74.8 - - - +
30F GLY* 1.3 56.4 + - - +
31F GLY* 3.2 5.7 + - - -
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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