Contacts of the helix formed by residues 22 - 35 (chain A) in PDB entry 2ZUQ
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 ALA 22 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A MET 3.0 11.4 + - - +
20A PHE 3.1 0.2 - - - -
21A THR* 1.3 75.1 - - - +
23A LEU* 1.3 57.9 + - - +
24A ALA 3.2 0.7 - - - -
25A LEU* 3.7 1.3 + - - -
26A GLU* 3.1 30.5 + - - +
51A LEU* 3.9 31.5 - - + +
54A VAL* 4.6 4.0 - - + -
55A LEU* 3.3 33.9 - - + +
153A TYR* 4.1 6.7 - - - +
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Residues in contact with LEU 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 ALA 3.8 12.2 + - - +
20A PHE* 2.9 27.8 + - + +
22A ALA* 1.3 73.5 - - - +
24A ALA* 1.3 56.5 + - - +
25A LEU 2.9 11.6 + - - -
26A GLU* 4.5 6.7 - - + +
27A LEU* 3.2 59.3 + - + +
28A THR 4.1 0.7 + - - -
52A PHE* 5.7 5.4 - - + -
55A LEU* 4.8 16.6 - - + -
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Residues in contact with ALA 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 PHE* 3.0 24.4 + - + +
21A THR* 3.4 17.5 - - - +
22A ALA 3.2 0.8 - - - -
23A LEU* 1.3 74.8 - - - +
25A LEU* 1.3 72.9 + - - +
28A THR* 3.1 13.8 + - - -
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Residues in contact with LEU 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A THR* 3.7 11.4 - - - +
22A ALA 4.0 2.7 - - - +
23A LEU 2.9 2.0 + - - -
24A ALA* 1.3 94.7 - - - +
26A GLU* 1.3 58.0 + - - +
27A LEU 3.2 1.1 - - - -
28A THR* 3.0 10.8 + - + +
29A ALA* 2.6 36.7 + - - +
51A LEU* 3.7 19.1 - - + -
146A LEU* 5.3 4.3 - - + -
149A ILE* 3.6 38.6 - - + -
153A TYR* 4.3 10.3 - - + +
177A UQ1 3.5 20.9 - - + +
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Residues in contact with GLU 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 ALA 3.1 14.9 + - - +
23A LEU* 4.8 5.1 - - + +
25A LEU* 1.3 78.5 - - - +
27A LEU* 1.3 60.1 + - + +
29A ALA* 3.8 7.9 - - + +
30A LEU* 3.4 26.2 + - - +
48A ARG* 2.6 38.1 + - + +
51A LEU* 3.1 27.4 - - + +
52A PHE* 2.9 56.9 + - + -
55A LEU* 4.5 4.9 - - - +
123A VAL* 5.1 2.6 - - - +
177A UQ1 4.9 0.9 - - + -
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Residues in contact with LEU 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 3.2 43.5 + - + +
25A LEU 3.2 0.4 - - - -
26A GLU* 1.3 74.8 - - + +
28A THR* 1.3 60.1 + - - +
29A ALA 3.1 1.6 - - - -
30A LEU* 2.8 44.9 + - + +
31A TRP* 2.8 13.9 + - - +
52A PHE* 6.5 0.7 - - + -
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Residues in contact with THR 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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23A LEU 4.1 1.0 + - - -
24A ALA* 3.1 26.2 + - - -
25A LEU* 3.1 13.9 - - + -
27A LEU* 1.3 78.0 - - - +
29A ALA* 1.3 60.0 + - - +
31A TRP* 3.2 18.4 - - + +
32A PHE* 3.1 25.3 - - + -
177A UQ1 4.3 14.4 - - + -
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Residues in contact with ALA 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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25A LEU 2.6 18.0 + - - +
26A GLU* 3.8 9.0 - - + +
28A THR* 1.3 74.2 - - - +
30A LEU* 1.3 61.3 + - - +
32A PHE* 3.1 33.4 + - - +
33A GLN 3.6 2.9 + - - -
48A ARG* 4.1 18.4 + - - +
177A UQ1 3.5 39.8 - - + +
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Residues in contact with LEU 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 GLU 3.4 11.8 + - - +
27A LEU* 2.8 39.9 + - + +
29A ALA* 1.3 72.1 - - - +
31A TRP* 1.3 66.3 + - - +
33A GLN* 3.2 26.0 + - + +
34A HIS* 3.4 29.7 + - + +
48A ARG* 4.8 2.5 - - - +
52A PHE* 5.9 3.1 - - + -
122A GLN* 3.5 29.8 - - - +
123A VAL* 3.6 30.5 - - + -
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Residues in contact with TRP 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 LEU 2.8 10.0 + - - +
28A THR* 3.2 19.3 - - + +
30A LEU* 1.3 75.2 - - - +
32A PHE* 1.3 75.2 + + - +
34A HIS* 3.3 1.8 + - - +
35A VAL* 2.8 77.6 + - + +
36A MET* 3.6 28.7 - - + -
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Residues in contact with PHE 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 THR* 3.1 42.8 - - + -
29A ALA* 3.1 16.1 + - - +
31A TRP* 1.3 85.7 - + - +
33A GLN* 1.3 66.4 + - - +
34A HIS 3.0 0.9 + - - -
36A MET* 3.2 35.8 + - + +
37A LEU 2.9 24.3 + - - -
38A LEU* 3.1 35.0 - - + +
137A PHE* 5.6 4.5 - + - -
142A MET* 4.5 26.9 - - + -
177A UQ1 4.1 20.6 - - + +
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Residues in contact with GLN 33 (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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29A ALA 3.6 1.6 + - - -
30A LEU* 3.2 14.8 + - + +
32A PHE* 1.3 77.7 - - - +
34A HIS* 1.3 89.0 + - + +
37A LEU* 3.5 17.2 - - - +
38A LEU 3.0 17.5 - - - +
39A LYS* 3.7 19.9 + - + +
40A PRO 3.9 2.1 + - - -
45A ILE* 5.9 0.5 - - - +
48A ARG* 2.7 43.6 + - - +
122A GLN 4.6 4.1 - - - +
123A VAL* 4.7 2.9 - - - +
125A VAL* 5.3 8.6 - - + +
177A UQ1 3.3 24.4 - - - -
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Residues in contact with HIS 34 (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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30A LEU* 3.4 19.8 + - + +
31A TRP 3.3 2.5 + - - +
32A PHE 3.1 0.2 - - - -
33A GLN* 1.3 106.8 - - + +
35A VAL* 1.3 68.2 + - + +
37A LEU* 4.5 12.9 - - + +
122A GLN* 3.3 55.9 + - + +
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Residues in contact with VAL 35 (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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31A TRP* 2.8 78.4 + - + +
34A HIS* 1.3 77.8 - - + +
36A MET* 1.3 76.5 + - + +
37A LEU* 3.1 11.3 + - - +
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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