Contacts of the helix formed by residues 20 - 32 (chain F) in PDB entry 1OUQ
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 20 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21F ASP* 1.3 68.7 + - - +
22F GLU* 3.6 21.5 + - - +
23F VAL* 3.7 30.0 + - - +
24F ARG* 3.3 22.7 + - - +
104F LEU* 6.0 0.4 - - - -
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Residues in contact with ASP 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 SER* 1.3 74.4 + - - +
22F GLU* 1.3 70.7 + - + +
24F ARG* 2.9 32.7 + - - +
25F LYS* 3.1 13.1 + - - +
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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 SER* 3.7 14.5 + - - +
21F ASP* 1.3 83.8 + - + +
23F VAL* 1.3 63.4 + - + +
25F LYS* 3.1 7.6 + - - +
26F ASN* 3.0 34.8 + - - +
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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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20F SER* 3.7 26.7 + - - +
21F ASP 3.3 0.6 - - - -
22F GLU* 1.3 78.3 - - + +
24F ARG* 1.3 63.9 + - - +
26F ASN* 3.8 1.3 - - - +
27F LEU* 3.2 30.3 + - + +
64F PHE* 4.5 6.5 - - + -
102F SER* 3.8 26.9 + - - +
103F GLY 5.5 1.1 - - - +
104F LEU* 3.7 47.3 - - + -
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Residues in contact with ARG 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 SER 3.3 15.6 + - - +
21F ASP* 2.9 31.4 + - - +
23F VAL* 1.3 79.4 - - - +
25F LYS* 1.3 57.3 + - - +
27F LEU* 4.3 7.0 - - - +
28F MET* 3.1 61.5 + - + +
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Residues in contact with LYS 25 (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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69A GLU* 4.0 18.2 + - - -
112A ALA* 6.2 0.2 - - - -
21F ASP 3.1 10.6 + - - +
22F GLU* 3.1 11.2 + - - +
23F VAL 3.1 0.6 - - - -
24F ARG* 1.3 79.1 - - + +
26F ASN* 1.3 65.4 + - - +
27F LEU 3.3 0.4 - - - -
28F MET* 3.6 9.3 - - + +
29F ASP* 2.9 58.2 + - - +
32F ARG* 5.4 0.4 - - - +
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Residues in contact with ASN 26 (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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111A ASN* 3.4 25.4 + - - +
115A LEU* 5.8 0.2 - - - +
22F GLU* 3.0 24.4 + - - +
23F VAL* 3.8 1.5 - - - +
25F LYS* 1.3 79.7 - - - +
27F LEU* 1.3 65.4 + - - +
29F ASP* 3.2 19.2 - - - +
30F MET* 3.3 9.9 + - - +
101F ARG 3.8 15.6 - - - +
102F SER 3.0 30.5 + - - +
103F GLY* 4.3 5.5 - - - -
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Residues in contact with LEU 27 (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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23F VAL* 3.2 21.5 + - + +
24F ARG* 4.3 5.8 - - - +
26F ASN* 1.3 76.8 - - - +
28F MET* 1.3 66.1 + - - +
30F MET* 3.0 38.1 + - + +
31F PHE* 2.9 34.0 - - + -
64F PHE* 3.8 22.0 - - + -
98F LEU* 4.3 12.8 - - + +
101F ARG 5.0 0.2 - - - -
102F SER* 3.0 34.1 - - - +
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Residues in contact with MET 28 (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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24F ARG* 3.1 55.5 + - + +
25F LYS* 3.6 11.4 - - + +
27F LEU* 1.3 80.2 - - - +
29F ASP* 1.3 61.3 + - - +
31F PHE* 3.7 6.9 + - - +
32F ARG* 3.4 21.3 + - - +
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Residues in contact with ASP 29 (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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111A ASN* 3.7 14.4 - - + +
112A ALA* 3.4 35.3 + - - +
115A LEU* 3.7 13.5 - - + +
25F LYS* 2.9 49.6 + - - +
26F ASN* 3.2 14.8 - - - +
27F LEU 3.0 0.2 + - - -
28F MET* 1.3 76.9 - - - +
30F MET* 1.3 60.7 - - - +
32F ARG* 3.7 19.7 + - - +
33F ASP* 3.5 20.4 + - - +
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Residues in contact with MET 30 (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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115A LEU* 3.8 13.2 - - + +
26F ASN 3.3 7.1 + - - +
27F LEU* 3.0 37.2 + - + +
29F ASP* 1.3 77.6 - - - +
31F PHE* 1.3 77.1 + - + +
33F ASP 2.9 5.9 + - - -
34F ARG* 2.8 24.8 + - - -
37F PHE* 3.7 24.5 - - + -
42F TRP* 4.1 15.3 - - + -
45F LEU* 5.4 5.6 - - + -
97F MET* 5.0 5.4 - - - -
98F LEU* 4.7 11.4 - - + -
101F ARG* 3.4 35.4 - - + -
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Residues in contact with PHE 31 (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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27F LEU* 2.9 32.9 + - + -
28F MET* 4.1 7.9 - - - +
30F MET* 1.3 94.7 - - + +
32F ARG* 1.3 64.7 + - - +
33F ASP 3.0 1.0 + - - -
34F ARG* 3.1 40.3 + - - +
42F TRP* 3.8 29.2 - + - -
45F LEU* 6.1 1.3 - - + -
46F LEU* 5.9 2.7 - - + -
98F LEU* 5.9 3.8 - - + -
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Residues in contact with ARG 32 (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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69A GLU* 2.5 33.9 + - - +
72A ARG* 3.2 42.2 - - - +
73A ASP* 5.8 0.4 + - - -
112A ALA* 3.7 23.6 - - - +
119A ARG* 3.6 9.7 + - - -
25F LYS* 5.4 0.6 - - - +
28F MET 3.4 14.5 + - - +
29F ASP* 3.8 23.2 + - - +
30F MET 3.2 0.8 - - - -
31F PHE* 1.3 78.4 - - - +
33F ASP* 1.3 65.3 + - - +
34F ARG* 3.5 6.0 + - - +
35F GLN* 4.6 2.8 + - - -
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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