Contacts of the helix formed by residues 21 - 32 (chain A) in PDB entry 3Q2K
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 ILE 21 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A ARG* 1.3 76.9 - - - +
22A SER* 1.3 69.7 + - - +
23A LYS 3.2 2.9 - - - -
24A ASN* 3.1 31.5 + - - +
25A HIS* 3.4 19.6 + - + +
79A ALA* 4.1 10.5 - - + -
102A GLU* 4.1 0.4 - - - +
301A HIS* 3.7 28.3 - - + +
500A NAI 3.0 78.0 + - + +
550A HP7 4.6 9.2 - - - +
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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
----------------------------------------------------------
15A LEU* 3.8 13.2 - - - -
17A GLY 3.4 25.8 + - - -
18A CYS* 3.3 14.0 + - - +
19A GLY 2.7 21.3 + - - -
21A ILE* 1.3 84.4 - - - +
23A LYS* 1.3 61.1 + - - +
25A HIS* 2.8 25.6 + - - +
26A ILE* 2.8 23.7 + - - +
52A ALA* 5.8 0.3 - - - +
79A ALA* 5.1 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
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A GLY 3.9 4.0 - - - -
20A ARG* 2.6 50.8 + - - +
21A ILE 3.2 0.2 - - - -
22A SER* 1.3 80.8 + - - +
24A ASN* 1.3 68.2 + - - +
26A ILE* 3.7 14.3 - - + +
27A GLY* 2.7 26.0 + - - -
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Residues in contact with ASN 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 ARG 4.7 2.2 + - - -
21A ILE* 3.1 32.7 + - + +
23A LYS* 1.3 94.4 - - - +
25A HIS* 1.3 57.3 + - - +
27A GLY* 5.1 0.7 - - - -
28A ALA* 3.0 29.8 + - - +
298A GLY 3.5 9.2 - - - +
299A PHE* 3.3 36.9 - - + +
301A HIS* 3.9 18.9 + - + +
302A PRO* 5.2 1.1 - - + +
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Residues in contact with HIS 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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15A LEU* 4.2 14.4 - - + -
21A ILE* 3.4 30.8 + - + -
22A SER* 2.8 8.3 + - - +
24A ASN* 1.3 75.3 - - - +
26A ILE* 1.3 65.5 + - - +
28A ALA* 3.1 3.3 + - - +
29A ILE* 2.9 34.1 + - + +
77A VAL* 3.4 20.5 - - + +
79A ALA* 4.4 7.4 - - + -
102A GLU* 2.8 37.7 + - + +
129A VAL* 4.3 9.6 - - + -
301A HIS* 3.5 18.6 + + - -
305A TYR* 2.7 36.3 + + - +
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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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15A LEU* 4.0 12.3 - - + +
22A SER* 2.8 33.0 + - - +
23A LYS* 3.7 11.4 - - + +
25A HIS* 1.3 76.5 - - - +
27A GLY* 1.3 64.1 + - - +
29A ILE* 3.3 3.0 + - - +
30A ALA* 3.1 24.2 + - + +
38A LEU* 3.8 26.5 - - + -
41A ILE* 6.2 0.4 - - + -
52A ALA* 5.1 11.7 - - + -
55A ALA* 5.7 6.3 - - + +
56A THR* 4.0 27.6 - - + -
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Residues in contact with GLY 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 2.7 20.9 + - - -
24A ASN* 4.1 0.9 - - - -
26A ILE* 1.3 73.9 - - - +
28A ALA* 1.3 56.0 + - - +
30A ALA* 3.7 7.2 - - - +
31A GLN* 2.8 31.9 + - - +
302A PRO* 5.5 1.6 - - - -
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Residues in contact with ALA 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 ASN 3.0 20.8 + - - +
25A HIS 3.1 3.8 + - - +
27A GLY* 1.3 77.1 - - - +
29A ILE* 1.3 62.6 + - - +
31A GLN* 3.5 1.4 + - - +
32A HIS* 3.1 31.1 + - - -
301A HIS* 3.8 2.2 - - + -
302A PRO* 3.7 33.1 - - + +
305A TYR* 3.6 27.6 - - + -
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Residues in contact with ILE 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 PHE* 3.9 31.4 - - + -
15A LEU* 6.1 1.8 - - + -
25A HIS* 2.9 23.1 + - + +
26A ILE* 3.8 4.0 - - - +
28A ALA* 1.3 73.8 - - - +
30A ALA* 1.3 56.3 + - - +
32A HIS* 2.7 28.2 + - - +
33A GLY* 2.8 10.2 + - - -
36A ALA* 4.3 6.2 - - + +
37A GLU* 3.9 15.9 - - - +
38A LEU* 3.8 42.4 - - + +
77A VAL* 4.9 2.9 - - + -
305A TYR* 3.8 32.1 - - + +
309A ILE* 5.9 0.7 - - + -
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Residues in contact with ALA 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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26A ILE* 3.1 18.9 + - + +
27A GLY* 3.7 8.3 - - - +
29A ILE* 1.3 76.5 - - - +
31A GLN* 1.3 55.1 + - - +
33A GLY* 2.5 30.0 + - - +
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Residues in contact with GLN 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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27A GLY 2.8 21.1 + - - +
28A ALA* 3.8 6.5 - - - +
30A ALA* 1.3 71.7 - - - +
32A HIS* 1.3 72.7 + - + +
33A GLY 3.5 0.5 + - - -
34A ASP* 4.4 4.7 - - - +
302A PRO* 3.5 32.3 - - - +
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Residues in contact with HIS 32 (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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28A ALA 3.1 22.2 + - - +
29A ILE 2.7 16.0 + - - +
31A GLN* 1.3 92.2 + - + +
33A GLY* 1.3 50.0 + - - +
34A ASP* 2.6 24.4 + - - +
35A ARG* 2.6 48.0 + - - +
36A ALA* 3.3 6.7 + - + -
302A PRO* 3.1 26.5 + - + -
305A TYR* 4.3 11.2 - - + -
306A ASP* 3.8 15.6 + - + -
309A ILE* 3.7 20.9 - - + -
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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