Contacts of the helix formed by residues 21 - 38 (chain A) in PDB entry 2ZHX
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 21 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LEU* 2.6 53.6 + - + +
20A PRO* 1.3 78.0 - - + +
22A ALA* 1.3 50.8 + - - -
23A ASP 3.3 2.7 - - - -
24A GLN* 2.9 22.1 + - + +
25A VAL* 2.5 40.9 + - + +
147A ALA* 3.8 15.3 - - + +
148A VAL* 4.2 13.7 - - + -
151A CYS* 3.7 26.2 - - + -
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Residues in contact with ALA 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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6A LEU* 4.2 18.2 - - + +
18A LEU 3.4 2.7 + - - -
19A GLU* 3.1 19.8 + - + +
20A PRO 3.4 0.8 - - - -
21A VAL* 1.3 75.8 - - - +
23A ASP* 1.3 58.9 - - - +
25A VAL* 3.3 10.8 + - - +
26A ALA* 2.8 33.0 + - - +
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Residues in contact with ASP 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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20A PRO 5.2 1.5 + - - +
21A VAL 3.3 0.6 - - - -
22A ALA* 1.3 79.7 - - - +
24A GLN* 1.3 58.3 + - - +
26A ALA* 3.8 5.7 - - - +
27A HIS* 3.0 29.5 + - - +
160C ALA* 5.3 2.9 - - - +
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Residues in contact with GLN 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 PRO 5.4 0.4 - - - +
21A VAL* 2.9 26.2 + - + +
23A ASP* 1.3 80.3 - - - +
25A VAL* 1.3 61.2 + - - +
27A HIS* 3.4 19.3 - - - +
28A MET* 3.3 23.1 + - - +
144A GLY* 2.5 41.3 + - - -
147A ALA* 3.9 18.7 - - + +
148A VAL* 4.2 5.3 - - + +
160C ALA* 5.4 2.4 - - - +
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Residues in contact with VAL 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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4A ARG 6.0 0.2 - - - +
6A LEU* 4.1 19.3 - - + -
9A LEU* 4.4 22.4 - - + -
18A LEU* 5.4 1.8 - - + -
21A VAL* 2.5 49.2 + - + +
22A ALA* 3.3 14.6 - - - +
24A GLN* 1.3 67.5 - - - +
26A ALA* 1.3 68.3 + - - +
27A HIS 3.0 1.3 - - - -
28A MET* 2.8 26.6 + - + +
29A GLY* 3.3 4.0 + - - -
50A LEU* 4.6 16.6 - - + -
145A TRP* 5.2 4.0 - - + -
148A VAL* 4.3 15.8 - - + +
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Residues in contact with ALA 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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4A ARG* 4.8 24.7 - - + +
9A LEU* 6.2 1.3 - - - -
22A ALA 2.8 22.6 + - - +
23A ASP* 3.8 6.1 - - - +
25A VAL* 1.3 74.9 - - - +
27A HIS* 1.3 62.4 + - - +
29A GLY* 3.1 16.2 + - - -
30A GLN* 3.7 5.4 + - - +
33A ARG* 5.2 1.9 + - - -
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Residues in contact with HIS 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 ASP 3.0 18.3 + - - +
24A GLN* 3.4 22.9 - - - +
25A VAL 3.0 0.2 - - - -
26A ALA* 1.3 74.1 - - - +
28A MET* 1.3 85.2 + - - +
29A GLY 3.0 1.2 + - - -
30A GLN* 3.1 26.2 + - - +
31A PHE* 3.2 17.3 + - + +
143A LYS 4.4 8.6 + - - -
144A GLY* 5.3 1.5 - - - -
158C ALA 3.4 17.9 + - - -
159C ARG* 3.6 7.9 - - + -
160C ALA* 3.0 46.2 + - + -
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Residues in contact with MET 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 GLN* 3.3 16.6 - - - +
25A VAL* 2.8 13.3 + - - +
27A HIS* 1.3 92.3 - - - +
29A GLY* 1.3 60.8 + - - +
31A PHE* 3.3 28.0 + - + +
32A LEU* 3.0 27.4 + - - +
143A LYS 3.5 15.7 - - - +
144A GLY* 3.6 27.1 - - - -
145A TRP* 3.8 63.7 - - + +
148A VAL* 4.6 0.7 - - + -
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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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25A VAL 3.3 3.6 + - - -
26A ALA 3.1 9.2 + - - -
27A HIS 3.0 1.4 - - - -
28A MET* 1.3 78.4 - - - +
30A GLN* 1.3 51.1 + - - +
32A LEU* 2.9 12.8 + - - +
33A ARG* 2.7 49.8 + - - +
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Residues in contact with GLN 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 ALA 3.7 4.8 + - - +
27A HIS* 3.1 23.8 + - - +
29A GLY* 1.3 71.2 - - - +
31A PHE* 1.3 60.6 + - - +
33A ARG* 3.1 33.4 - - - +
34A ALA* 2.8 29.7 + - - +
157C ALA 4.4 2.9 - - - +
158C ALA* 3.9 20.1 - - - +
159C ARG 3.9 11.1 + - - +
160C ALA* 4.1 13.5 + - - +
183C ASN* 3.8 19.9 + - - +
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Residues in contact with PHE 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 HIS* 3.2 23.3 + - + +
28A MET* 3.3 32.3 - - + +
29A GLY 3.1 0.4 - - - -
30A GLN* 1.3 75.9 - - - +
32A LEU* 1.3 68.7 + - + +
34A ALA* 3.0 6.3 + - + +
35A GLU* 2.7 61.5 + - + +
131A THR* 4.7 0.4 - - - -
140A HIS* 3.7 31.2 - + + -
143A LYS* 3.4 45.3 - - + -
158C ALA* 4.6 16.4 - - + +
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Residues in contact with LEU 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 MET 3.0 14.1 + - - +
29A GLY* 2.9 9.7 + - - +
31A PHE* 1.3 96.0 - - + +
33A ARG* 1.3 57.6 + - + +
35A GLU* 2.6 27.1 + - + +
36A ILE* 3.0 13.2 + - - +
42A TYR* 3.5 48.8 - - + +
49A VAL* 4.5 8.1 - - + -
131A THR* 3.7 38.6 - - + +
140A HIS* 4.3 2.2 - - + -
145A TRP* 4.3 11.4 - - + +
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Residues in contact with ARG 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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3A ALA 5.0 9.9 + - - +
26A ALA 5.2 1.6 + - - -
29A GLY* 2.7 22.2 + - - +
30A GLN* 3.1 42.4 - - - +
32A LEU* 1.3 72.1 - - + +
34A ALA* 1.3 57.6 + - - +
36A ILE* 3.2 14.4 + - + +
37A ALA* 2.9 27.9 + - - +
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Residues in contact with ALA 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 GLN 2.8 25.5 + - - +
31A PHE* 3.0 4.9 + - + +
33A ARG* 1.3 72.6 - - - +
35A GLU* 1.3 57.6 + - - +
37A ALA* 3.3 9.7 + - - +
38A ALA* 2.9 29.6 + - - +
154C ARG* 5.7 0.6 - - - +
158C ALA* 3.9 24.9 - - + -
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Residues in contact with GLU 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 PHE* 2.7 44.6 + - + +
32A LEU* 2.6 20.6 + - - +
34A ALA* 1.3 71.0 - - - +
36A ILE* 1.3 61.1 + - - +
38A ALA* 3.2 9.8 + - - -
39A GLY 3.4 4.2 + - - -
40A ARG* 2.5 72.0 + - - +
41A ARG 5.2 2.2 - - - +
42A TYR* 5.0 9.0 - - + -
133A ARG* 4.7 4.9 - - - +
140A HIS* 3.3 23.8 + - + +
143A LYS* 5.5 1.6 + - - -
20C PRO* 4.7 5.2 - - - +
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Residues in contact with ILE 36 (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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32A LEU 3.0 11.0 + - - +
33A ARG* 3.7 13.5 - - + +
35A GLU* 1.3 74.7 - - - +
37A ALA* 1.3 55.6 + - - +
39A GLY* 2.7 26.4 + - - -
40A ARG 3.2 11.9 - - - +
41A ARG* 4.9 7.6 - - + -
42A TYR* 3.8 33.4 - - + +
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Residues in contact with ALA 37 (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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33A ARG 2.9 14.3 + - - +
34A ALA* 3.3 14.6 - - - +
36A ILE* 1.3 76.6 - - - +
38A ALA* 1.3 58.0 + - - +
39A GLY* 3.2 4.9 + - - -
154C ARG* 5.6 1.4 + - - -
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Residues in contact with ALA 38 (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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34A ALA 2.9 15.4 + - - +
35A GLU 3.8 3.8 - - - +
36A ILE 3.2 0.6 - - - -
37A ALA* 1.3 74.9 - - - +
39A GLY* 1.3 57.0 + - - +
40A ARG* 3.4 39.5 + - - +
154C ARG* 3.9 30.7 - - + +
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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