Contacts of the strand formed by residues 25 - 31 (chain A) in PDB entry 1CSN
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 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A ARG* 3.7 45.1 - - + +
19A GLY 3.7 11.7 - - - +
20A GLU* 4.5 9.6 - - + +
23A PHE 5.0 2.9 - - - +
24A GLY* 1.3 80.1 - - - +
26A ILE* 1.3 65.1 + - - +
27A PHE* 3.6 26.5 - - + -
40A ILE 3.6 1.7 - - - +
41A LYS* 3.6 0.7 - - - -
42A PHE* 2.9 37.4 + - + +
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Residues in contact with ILE 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ARG* 3.5 4.3 - - - +
18A ILE* 2.8 48.8 + - + -
19A GLY 2.9 15.3 + - - +
24A GLY 4.3 5.6 - - - +
25A VAL* 1.3 83.3 - - - +
27A PHE* 1.3 66.6 + - - +
39A ALA* 4.1 13.0 - - + -
40A ILE 3.3 7.4 - - - +
41A LYS* 4.0 27.4 - - + -
299A ATP 3.4 64.4 - - + +
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Residues in contact with PHE 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A VAL* 3.7 19.7 - - + -
15A GLY 3.2 22.9 - - - -
16A ARG* 3.3 16.4 - - - +
17A ARG* 3.5 30.7 - - + -
18A ILE* 4.1 4.5 - - - -
25A VAL* 3.6 21.3 - - + -
26A ILE* 1.3 77.7 - - - +
28A GLU* 1.3 67.3 + - - +
39A ALA* 3.2 6.6 - - - +
40A ILE* 2.8 37.3 + - + +
42A PHE* 3.5 33.4 - + + -
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Residues in contact with GLU 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A GLY* 2.8 31.0 + - - -
16A ARG* 3.0 49.2 + - + +
18A ILE* 3.8 24.2 - - + +
27A PHE* 1.3 74.3 - - - +
29A GLY* 1.3 67.2 + - - +
30A THR* 5.5 2.1 - - - +
37A GLN* 5.1 8.0 + - - -
38A VAL 3.5 5.6 - - - -
40A ILE* 5.0 0.7 - - - -
87A LEU* 4.0 21.2 - - + +
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Residues in contact with GLY 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LYS 3.1 16.2 - - - -
15A GLY* 4.1 1.8 - - - -
27A PHE 4.0 0.4 + - - -
28A GLU* 1.3 83.5 + - - +
30A THR* 1.3 69.9 + - - +
37A GLN* 3.4 4.2 - - - +
38A VAL* 2.9 32.6 + - - +
40A ILE* 4.3 9.1 - - - +
87A LEU* 5.6 0.2 - - - +
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Residues in contact with THR 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A TYR* 3.4 2.8 - - - +
13A LYS* 2.9 47.3 + - - +
28A GLU* 5.5 2.5 - - - +
29A GLY* 1.3 79.8 - - - +
31A ASN* 1.3 66.5 + - - +
32A LEU* 3.4 8.7 + - - +
35A ASN* 4.6 18.1 + - - +
36A GLN 3.1 13.0 - - - +
37A GLN* 4.2 16.8 - - + +
38A VAL* 4.0 6.6 - - - +
40A ILE* 5.3 0.2 - - - +
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Residues in contact with ASN 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A HIS* 2.8 35.4 + - - -
12A TYR* 3.7 26.1 + - + -
30A THR* 1.3 70.0 - - - +
32A LEU* 1.3 54.9 + - - +
33A LEU* 3.0 13.5 + - - +
34A ASN* 3.0 31.7 + - - +
35A ASN* 2.7 34.7 + - - -
36A GLN* 2.8 19.3 + - + +
38A VAL* 4.4 6.1 - - + +
72A TYR* 5.8 4.4 - - - -
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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