Contacts of the helix formed by residues 17 - 27 (chain A) in PDB entry 1W7L
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 PRO 17 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A TYR* 3.7 34.1 - - + +
16A ASN* 1.3 87.8 - - - +
18A TRP* 1.3 68.1 + - + +
20A GLU* 4.2 7.1 + - - +
21A PHE* 3.3 25.3 - - + -
126A ASP* 5.3 5.8 - - + +
364A ARG* 4.3 11.2 - - - +
383A ILE* 3.8 37.0 - - + +
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Residues in contact with TRP 18 (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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16A ASN* 3.0 36.5 - - - +
17A PRO* 1.3 82.5 - - + +
19A VAL* 1.3 67.7 + - - +
21A PHE* 2.9 20.9 + - + +
22A VAL* 3.2 26.1 + - + +
34A GLY 4.8 2.2 - - - -
101A TYR* 5.3 6.0 + - - -
125A PHE* 5.7 5.6 - + - -
126A ASP* 3.3 36.4 + - - -
379A ILE* 3.6 34.5 - - + -
383A ILE* 3.9 20.1 - - + +
384A PHE* 4.3 9.6 - + - -
398A ARG* 4.3 18.4 - - - -
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Residues in contact with VAL 19 (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 TYR* 6.1 0.9 - - + -
16A ASN* 3.1 36.1 + - + +
18A TRP* 1.3 73.6 - - - +
20A GLU* 1.3 64.7 + - - +
21A PHE 3.1 0.3 + - - -
22A VAL* 3.1 8.9 + - + +
23A LYS* 2.8 30.2 + - + +
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Residues in contact with GLU 20 (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 TYR* 4.0 19.1 + - - +
16A ASN 4.9 0.4 + - - -
17A PRO 4.2 8.1 + - - +
18A TRP 3.3 0.4 - - - -
19A VAL* 1.3 78.0 - - - +
21A PHE* 1.3 69.3 + - + +
23A LYS* 3.6 7.2 + - - +
24A LEU* 3.1 27.5 + - + +
360A GLU* 4.7 3.3 - - - +
364A ARG* 5.8 1.9 - - - -
368A LYS* 3.2 40.0 + - + -
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Residues in contact with PHE 21 (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 PRO* 3.3 26.0 - - + -
18A TRP* 2.9 8.9 + + + +
20A GLU* 1.3 84.0 - - + +
22A VAL* 1.3 57.1 - - + +
23A LYS 3.1 1.6 - - - -
24A LEU* 3.2 4.8 + - + +
25A ALA* 2.8 36.7 + - - +
364A ARG* 3.5 50.3 - - + -
367A VAL* 3.6 26.2 - - + -
368A LYS* 3.7 26.5 - - + -
371A ILE* 4.5 10.6 - - + +
377A VAL* 5.8 4.5 - - + -
378A ALA 5.6 2.2 - - - +
379A ILE* 5.6 8.7 - - + -
380A PRO* 3.7 22.4 - - + -
383A ILE* 5.3 3.1 - - + -
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Residues in contact with VAL 22 (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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18A TRP* 3.5 32.3 - - + +
19A VAL* 3.1 8.2 + - + +
21A PHE* 1.3 76.4 - - + +
23A LYS* 1.3 61.0 + - - +
25A ALA* 3.7 5.8 + - - +
26A SER* 3.3 23.1 + - - -
32A ASN* 6.1 3.4 - - - +
35A GLN* 6.1 2.9 - - - +
379A ILE* 6.5 0.4 - - + -
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Residues in contact with LYS 23 (chain A).
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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19A VAL* 2.8 21.3 + - + +
20A GLU* 3.7 6.3 - - - +
22A VAL* 1.3 76.3 - - - +
24A LEU* 1.3 63.5 + - + +
26A SER* 2.7 23.7 + - - +
27A GLU* 3.4 38.5 + - - +
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Residues in contact with LEU 24 (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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20A GLU* 3.1 19.4 + - + +
21A PHE* 3.2 6.7 + - + +
23A LYS* 1.3 74.3 - - + +
25A ALA* 1.3 64.9 + - - +
27A GLU* 3.3 23.8 - - - +
28A HIS* 3.1 39.1 - - + +
368A LYS* 3.9 50.9 - - + +
371A ILE* 4.0 17.2 - - + +
372A LYS* 4.4 16.4 - - + -
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Residues in contact with ALA 25 (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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21A PHE 2.8 20.4 + - - +
22A VAL* 4.0 7.6 - - + +
24A LEU* 1.3 73.5 - - - +
26A SER* 1.3 61.3 + - - +
27A GLU 3.3 0.3 + - - -
28A HIS* 3.3 20.6 + - - +
30A VAL* 3.5 12.4 - - + +
32A ASN* 4.2 13.2 - - - +
371A ILE* 4.2 12.0 - - + +
377A VAL* 3.8 30.5 - - + -
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Residues in contact with SER 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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22A VAL* 3.3 13.0 + - - -
23A LYS* 2.7 25.6 + - - +
25A ALA* 1.3 79.0 - - - +
27A GLU* 1.3 58.1 + - - +
28A HIS 3.4 4.7 + - - +
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Residues in contact with GLU 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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23A LYS* 3.4 40.7 + - - +
24A LEU* 3.3 33.3 - - - +
25A ALA 3.2 0.2 - - - -
26A SER* 1.3 79.2 + - - +
28A HIS* 1.3 74.3 + - + +
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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