Contacts of the helix formed by residues 19 - 28 (chain A) in PDB entry 4Q1U
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 19 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A ASP* 1.3 74.1 - - - +
20A GLN* 1.3 54.1 + - - +
21A LYS* 3.1 6.7 - - - +
22A SER* 3.6 16.1 + - - +
23A SER* 3.3 21.5 + - - -
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Residues in contact with GLN 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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18A ASP* 3.5 5.8 - - + +
19A ARG* 1.3 75.3 - - - +
21A LYS* 1.3 56.9 + - - +
22A SER 3.5 0.4 - - - -
23A SER* 4.1 9.5 - - - +
24A PHE* 3.3 23.6 + - - +
403A LMT 6.0 2.0 - - - +
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Residues in contact with LYS 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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18A ASP* 4.4 18.4 - - + +
19A ARG* 3.1 1.2 - - - +
20A GLN* 1.3 76.7 - - - +
22A SER* 1.3 59.1 + - - +
23A SER 3.4 0.2 - - - -
24A PHE* 3.4 6.6 + - - +
25A GLN* 3.1 39.3 + - + +
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Residues in contact with SER 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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19A ARG* 3.6 20.1 + - - +
21A LYS* 1.3 77.1 - - - +
23A SER* 1.3 54.9 + - - +
25A GLN* 3.5 8.6 + - - +
26A THR* 2.5 41.8 + - - +
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Residues in contact with SER 23 (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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19A ARG 3.3 14.7 + - - -
20A GLN* 4.5 7.0 - - - -
21A LYS 3.4 0.2 - - - -
22A SER* 1.3 74.6 - - - +
24A PHE* 1.3 67.0 + - - +
26A THR* 3.3 6.4 + - - +
27A ARG* 3.0 43.4 + - - +
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Residues in contact with PHE 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 GLN 3.3 19.6 + - - +
21A LYS* 3.4 6.7 + - - +
22A SER 3.3 0.6 - - - -
23A SER* 1.3 78.7 - - - +
25A GLN* 1.3 72.3 + - + +
27A ARG* 4.7 5.2 - - - +
28A PHE* 3.0 56.6 + + - +
30A VAL* 3.8 20.0 - - + -
197A HIS* 4.5 13.7 - + - -
289A MET* 3.9 22.4 - - - -
293A PHE* 4.0 21.8 - + - -
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Residues in contact with GLN 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 LYS* 3.1 26.0 + - - +
22A SER* 3.5 8.2 + - - +
23A SER 3.2 0.4 - - - -
24A PHE* 1.3 84.2 - - + +
26A THR* 1.3 60.2 + - + +
29A ASN* 2.9 21.3 + - - -
30A VAL* 3.0 36.0 + - + +
31A HIS* 3.6 29.9 + - + +
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Residues in contact with THR 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 SER* 2.5 35.9 - - - +
23A SER* 3.8 6.5 + - - +
25A GLN* 1.3 78.0 - - + +
27A ARG* 1.3 62.7 + - - +
29A ASN* 3.0 9.7 + - - +
243A HIS* 2.8 26.3 + - - -
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Residues in contact with ARG 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 SER* 3.0 36.6 + - - +
24A PHE* 4.9 3.6 - - - +
26A THR* 1.3 78.8 + - - +
28A PHE* 1.3 85.0 + - + +
196A MET* 2.8 32.3 + - - +
197A HIS* 4.2 8.7 + - - +
199A GLY* 3.8 19.3 - - - -
201A ALA 5.8 0.2 - - - +
221A ASP* 2.9 36.9 + - - +
241A LEU* 3.6 48.0 - - + +
243A HIS* 2.7 24.2 - - - -
267A LEU* 3.9 1.2 - - - +
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Residues in contact with PHE 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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24A PHE* 3.0 53.0 + + + +
25A GLN 3.8 0.2 - - - -
27A ARG* 1.3 99.4 - - + +
29A ASN* 1.3 63.6 + - - +
30A VAL* 3.1 15.0 + - + -
196A MET* 4.0 22.7 - - + -
197A HIS* 4.7 4.5 - + - -
241A LEU* 4.0 22.0 - - + -
267A LEU* 4.4 0.4 - - - -
288A GLY* 2.6 38.5 + - - -
289A MET* 3.6 8.3 + - + +
292A PHE* 3.6 45.1 - + + -
293A PHE* 4.8 7.0 - + - -
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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