Contacts of the helix formed by residues 19 - 24 (chain F) in PDB entry 5M73
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 TYR 19 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149E A 2.7 29.7 + - - -
150E G 2.9 22.1 - - - -
197E G 3.9 9.7 - - - -
17F CYS* 4.6 4.9 - - + -
18F ILE* 1.4 80.8 - - - +
20F PRO* 1.3 72.5 - - + +
21F ALA 4.2 4.7 - - - +
22F TYR* 2.9 58.5 + + + +
23F LEU* 4.2 0.9 + - - +
49F ILE* 4.7 0.9 - - - +
66F LYS 5.8 0.4 - - - -
67F MET 4.5 4.7 - - - -
68F TYR* 3.6 48.9 - + + -
80F GLY 3.9 13.0 - - - -
81F ARG* 3.6 35.1 + - + -
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Residues in contact with PRO 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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18F ILE 4.4 1.3 - - - +
19F TYR* 1.3 87.2 - - + +
21F ALA* 1.3 56.9 + - - +
23F LEU* 2.9 19.9 + - - +
24F ASN* 3.4 7.1 + - - -
44F PRO* 3.3 32.9 - - + +
45F THR* 4.5 1.1 - - - -
46F ALA* 4.1 14.8 - - + +
49F ILE* 4.1 14.1 - - + -
68F TYR* 5.6 1.8 - - + -
77F GLN 4.7 2.7 - - - +
78F TYR* 4.1 17.3 - - + +
79F ARG 4.0 15.7 - - - +
80F GLY 3.2 26.0 - - - +
81F ARG* 4.9 0.2 - - - -
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Residues in contact with ALA 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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19F TYR* 3.0 1.2 + - + +
20F PRO* 1.3 79.9 - - - +
22F TYR* 1.3 64.6 + - + +
23F LEU 2.9 1.4 + - - -
24F ASN* 3.0 22.0 + - - +
27F LYS* 3.9 15.4 - - + +
31F GLU 3.9 13.7 - - - +
32F GLY* 3.9 2.7 - - - -
33F ARG* 3.4 14.9 + - - +
68F TYR* 3.7 35.6 - - + -
71F GLU* 5.7 1.6 - - + +
78F TYR* 6.2 1.3 - - - -
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Residues in contact with TYR 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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149E A 4.0 0.3 + - - -
150E G 2.2 37.1 + - - -
17F CYS* 4.4 7.3 - - - +
18F ILE* 4.0 9.6 - - + -
19F TYR* 2.9 50.3 + + + +
21F ALA* 1.3 76.9 - - + +
23F LEU* 1.3 65.6 + - + +
32F GLY* 3.1 20.2 - - - -
33F ARG* 3.8 1.6 - - - +
34F ARG* 3.2 51.8 + - + +
35F ILE* 3.7 9.5 + - - +
68F TYR* 4.1 13.7 - + - -
105F MET* 3.4 33.0 - - + -
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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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18F ILE* 5.7 1.6 - - + -
19F TYR 4.9 0.9 - - - +
20F PRO 2.9 5.9 + - - +
22F TYR* 1.3 88.3 - - + +
24F ASN* 1.3 59.3 + - - +
25F ASN 3.2 0.2 + - - -
33F ARG* 5.2 0.4 - - - -
35F ILE* 3.7 17.3 - - + -
40F ALA* 3.6 3.8 - - - +
41F VAL* 2.9 31.5 + - + +
44F PRO* 3.6 21.1 - - + +
49F ILE* 4.2 22.9 - - + -
105F MET* 3.4 41.3 - - + +
108F ALA* 3.7 29.2 - - + -
109F ALA* 4.0 8.7 - - + +
112F ILE* 4.8 1.3 - - + -
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Residues in contact with ASN 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 PRO 3.4 2.3 + - - +
21F ALA* 3.0 18.7 + - - +
23F LEU* 1.3 74.9 - - - +
25F ASN* 1.3 57.4 + - - +
26F LYS* 3.1 16.2 + - - +
27F LYS* 3.0 58.9 + - + +
33F ARG* 3.4 13.9 - - - +
41F VAL 3.5 1.6 - - - -
43F ASN* 2.8 36.1 + - - +
44F PRO* 3.6 7.4 - - + -
78F TYR* 3.4 19.4 + - + -
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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