Contacts of the strand formed by residues 18 - 22 (chain D) in PDB entry 1S9C
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 PHE 18 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16D PRO 4.0 9.4 - - - +
17D PRO* 1.3 76.4 - - + +
19D SER* 1.3 63.7 + - - +
64D ILE 3.7 11.4 - - - -
65D GLY* 4.0 14.8 - - - -
67D LYS* 3.3 47.6 - - + -
68D SER* 3.7 34.3 - - - -
107D LYS* 3.8 4.7 - - - +
108D CYS* 2.8 58.1 + - + +
110D ALA* 4.9 7.4 - - + -
128D VAL* 4.3 7.0 - - + -
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Residues in contact with SER 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D PHE* 1.3 80.4 - - - +
20D TYR* 1.3 58.4 + - - +
67D LYS* 2.3 39.8 + - - +
105D LYS* 6.3 1.3 - - - -
106D LEU 3.2 15.9 - - - -
107D LYS* 4.5 4.0 - - - -
108D CYS 4.6 0.2 - - - +
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Residues in contact with TYR 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D SER* 1.3 76.2 - - - +
21D ALA* 1.3 65.3 + - - +
22D TYR* 3.8 34.8 - + + -
26D GLU* 4.6 12.0 - - + +
60D PHE* 4.1 12.9 - + - -
63D ILE* 3.5 29.2 - - + +
64D ILE* 3.9 38.6 - - + +
67D LYS* 3.6 32.8 - - + +
104D GLY 3.9 0.5 - - - +
105D LYS* 3.4 1.5 - - - -
106D LEU* 2.7 40.7 + - + +
108D CYS* 4.7 4.0 - - - -
191D SER 4.8 2.8 + - - -
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Residues in contact with ALA 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D TYR* 1.3 84.1 - - - +
22D TYR* 1.3 64.5 + - - +
26D GLU* 5.1 2.8 - - - +
67D LYS* 5.5 0.4 - - - +
104D GLY 3.1 5.8 - - - +
105D LYS* 3.4 33.9 - - + -
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Residues in contact with TYR 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D TYR* 3.8 23.1 - + + -
21D ALA* 1.3 76.0 - - - +
23D THR* 1.3 78.0 + - - +
26D GLU* 3.8 22.0 - - + -
27D ALA* 4.9 2.2 - - + -
56D CYS* 4.6 4.7 - - - -
60D PHE* 3.6 32.5 - + + -
64D ILE* 3.9 16.0 - - + +
100D LEU* 4.2 6.9 - - - +
101D PRO* 2.8 42.8 + - + +
102D ARG 4.0 1.8 - - - -
103D ALA* 3.3 25.7 - - - +
104D GLY* 2.9 39.0 + - - +
106D LEU* 4.1 11.4 - - + +
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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