Contacts of the strand formed by residues 4 - 9 (chain C) in PDB entry 1DXO
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 ARG 4 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C ARG* 1.3 90.2 - - + +
5C ALA* 1.3 61.2 - - - +
34C TRP* 3.5 2.9 - - - -
35C GLU* 2.8 38.5 + - + +
37C VAL* 6.3 2.5 - - - -
93C ALA* 3.6 51.5 + - + +
94C ALA* 4.4 2.9 - - - -
95C ASP* 2.8 35.8 + - - +
96C LEU 3.2 5.9 + - - -
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Residues in contact with ALA 5 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C ARG* 1.3 76.3 - - - +
6C LEU* 1.3 62.3 + - - +
7C ILE* 5.1 2.7 - - + -
29C LEU* 3.6 31.4 - - + -
34C TRP* 3.7 11.9 - - + -
35C GLU 2.8 14.5 + - - +
36C VAL* 4.6 2.5 - - + -
37C VAL* 2.8 30.8 + - - +
94C ALA* 4.4 3.4 - - - -
96C LEU* 3.2 14.4 - - + +
98C ILE* 5.6 0.7 - - + -
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Residues in contact with LEU 6 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ALA* 1.3 74.5 - - - +
7C ILE* 1.3 65.7 + - - +
8C VAL* 4.2 17.5 - - + -
37C VAL* 3.0 22.0 - - + +
38C GLU 4.0 5.8 - - - -
39C SER* 3.7 23.1 - - - +
90C LYS* 3.9 36.6 - - + +
91C LEU* 4.1 28.0 - - + +
94C ALA* 3.7 15.7 - - + +
96C LEU 3.0 7.0 + - - +
97C VAL* 3.2 7.5 - - + +
98C ILE* 2.8 25.6 + - - +
115C TRP* 4.7 6.5 - - + -
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Residues in contact with ILE 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C ALA 5.1 0.9 - - - -
6C LEU* 1.3 80.0 - - - +
8C VAL* 1.3 65.6 + - - +
9C LEU* 3.6 2.1 + - - +
22C LYS* 3.8 27.7 - - + +
25C ALA* 4.2 10.8 - - + -
26C ALA* 3.9 25.4 - - + +
29C LEU* 4.8 3.1 - - + -
36C VAL* 3.4 33.2 - - + -
37C VAL 2.8 10.3 + - - +
38C GLU* 3.5 10.3 - - + +
39C SER 2.9 24.7 + - - -
98C ILE* 3.5 33.4 - - + +
100C GLN* 4.8 5.2 - - + -
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Residues in contact with VAL 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C LEU* 4.2 12.1 - - + -
7C ILE* 1.3 74.1 - - - +
9C LEU* 1.3 60.2 + - - +
39C SER* 3.5 11.4 - - - -
41C LEU* 4.0 22.2 - - + -
97C VAL* 4.3 4.5 - - + -
98C ILE 2.7 13.1 + - - +
99C PHE* 3.5 16.4 - - + -
100C GLN* 2.8 28.8 + - - +
112C LEU* 3.9 31.6 - - + +
115C TRP* 3.9 30.1 - - + -
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Residues in contact with LEU 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C ILE 3.6 2.3 + - - +
8C VAL* 1.3 73.5 - - - +
10C ALA* 1.3 66.7 + - - +
11C HIS* 4.0 19.5 + - + +
18C ASN* 4.1 20.2 - - + +
19C TYR* 3.7 32.3 - - + +
22C LYS* 3.8 27.8 - - + -
39C SER 3.0 9.4 + - - +
40C ASP* 3.8 22.4 - - - +
41C LEU* 3.3 28.5 + - - +
42C TYR 4.6 0.2 + - - -
100C GLN* 3.4 29.4 - - + +
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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