Contacts of the helix formed by residues 21 - 38 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ARG* 6.0 1.3 - - - +
18C LEU* 2.6 54.9 + - + +
20C PRO* 1.3 77.6 - - + +
22C ALA* 1.3 63.9 + - - -
23C ASP 3.2 3.1 - - - -
24C GLN* 2.7 28.1 + - + -
25C VAL* 2.8 15.6 + - + +
147C ALA* 3.9 14.6 - - + +
148C VAL* 4.0 16.2 - - + -
151C CYS* 3.6 25.1 - - + -
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Residues in contact with ALA 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B PRO* 4.3 26.2 - - + +
64B GLU* 6.0 0.2 - - - -
6C LEU* 4.1 16.1 - - + +
18C LEU 3.2 3.7 + - - -
19C GLU 2.8 18.7 + - - +
20C PRO 3.5 0.2 - - - -
21C VAL* 1.3 74.6 - - - +
23C ASP* 1.3 54.4 + - - +
25C VAL* 3.1 13.1 - - - +
26C ALA* 2.8 36.4 + - - +
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Residues in contact with ASP 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B PRO 5.5 3.4 - - - +
20C PRO 5.2 2.1 + - - +
21C VAL 3.2 1.0 - - - -
22C ALA* 1.3 79.2 - - - +
24C GLN* 1.3 58.5 + - - +
26C ALA* 3.4 7.3 + - - +
27C HIS* 2.8 28.2 + - - +
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Residues in contact with GLN 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C VAL* 2.7 30.7 + - + +
23C ASP* 1.3 71.9 - - - +
25C VAL* 1.3 59.8 + - - +
27C HIS* 3.2 26.2 + - - +
28C MET* 2.9 28.4 + - - +
144C GLY* 2.8 34.7 + - - +
147C ALA* 3.4 23.5 - - + +
148C VAL* 4.6 4.7 - - + +
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Residues in contact with VAL 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C LEU* 4.0 22.2 - - + -
9C LEU* 4.6 12.1 - - + -
18C LEU* 5.6 1.3 - - + -
21C VAL* 2.8 23.8 + - + +
22C ALA* 3.1 26.0 - - - +
24C GLN* 1.3 68.9 - - - +
26C ALA* 1.3 65.5 + - - +
28C MET* 3.3 7.1 + - - +
29C GLY* 3.2 15.9 + - - -
50C LEU* 4.3 32.1 - - + -
145C TRP* 4.8 5.1 - - + -
148C VAL* 4.3 21.8 - - + +
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Residues in contact with ALA 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C ARG 4.8 14.6 - - - +
9C LEU* 6.6 0.4 - - - -
22C ALA 2.8 17.9 + - - +
23C ASP* 3.5 9.9 - - - +
25C VAL* 1.3 78.4 - - - +
27C HIS* 1.3 58.2 + - - +
29C GLY* 2.9 21.8 + - - -
30C GLN* 3.5 7.0 + - - +
33C ARG* 5.3 1.6 + - - -
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Residues in contact with HIS 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C ASP 2.8 17.4 + - - +
24C GLN* 3.3 27.4 - - - +
26C ALA* 1.3 72.4 - - - +
28C MET* 1.3 76.1 + - - +
29C GLY 2.8 1.4 + - - -
30C GLN* 3.0 47.7 + - + +
31C PHE* 3.1 14.8 + - + +
143C LYS 4.8 6.6 + - - -
144C GLY* 5.7 1.1 - - - -
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Residues in contact with MET 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C GLN* 2.9 23.4 + - - +
25C VAL* 3.5 8.7 - - - +
27C HIS* 1.3 81.1 - - - +
29C GLY* 1.3 63.5 + - - +
31C PHE* 3.4 25.6 + - + +
32C LEU* 3.3 27.2 + - - +
143C LYS 3.3 28.0 - - - +
144C GLY* 3.4 22.7 - - - +
145C TRP* 3.2 67.5 - - + +
148C VAL* 4.6 0.9 - - + -
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Residues in contact with GLY 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C VAL 3.2 8.2 + - - -
26C ALA 2.9 12.3 + - - -
27C HIS 2.8 1.4 + - - -
28C MET* 1.3 74.8 - - - +
30C GLN* 1.3 55.5 + - - -
32C LEU* 3.0 13.2 + - - +
33C ARG* 3.0 40.8 + - - +
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Residues in contact with GLN 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C ALA 3.5 5.2 + - - +
27C HIS* 3.0 43.6 + - + +
29C GLY* 1.3 69.8 - - - +
31C PHE* 1.3 60.9 + - - +
33C ARG* 3.4 28.4 - - - +
34C ALA* 2.8 30.0 + - - +
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Residues in contact with PHE 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C HIS* 3.1 22.4 + - + +
28C MET* 3.5 34.8 - - + +
29C GLY 3.2 0.4 - - - -
30C GLN* 1.3 78.8 - - - +
32C LEU* 1.3 68.5 + - + +
34C ALA* 3.2 10.2 + - + +
35C GLU* 2.9 54.0 + - + +
140C HIS* 3.7 35.9 - + - -
143C LYS* 3.8 42.2 - - + -
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Residues in contact with LEU 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C MET 3.4 14.4 - - - +
29C GLY* 3.0 9.7 + - - +
31C PHE* 1.3 93.1 - - + +
33C ARG* 1.3 66.7 + - + +
35C GLU* 3.1 7.2 + - + +
36C ILE* 3.1 27.3 + - - +
42C TYR* 3.5 45.0 - - + +
49C VAL* 4.5 7.4 - - + -
131C THR* 3.9 35.0 - - + +
140C HIS* 4.1 4.0 - - + -
145C TRP* 4.1 11.7 - - + +
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Residues in contact with ARG 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C ALA 4.9 9.7 + - - -
26C ALA 5.3 1.4 + - - -
29C GLY* 3.0 26.1 + - - +
30C GLN* 3.4 31.3 - - - +
32C LEU* 1.3 76.7 - - + +
34C ALA* 1.3 61.4 + - - +
36C ILE* 3.6 10.8 + - + +
37C ALA* 3.4 21.7 + - - +
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Residues in contact with ALA 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C GLN 2.8 18.6 + - - +
31C PHE* 3.2 12.3 - - + +
33C ARG* 1.3 76.5 - - - +
35C GLU* 1.3 65.7 + - - +
37C ALA* 3.3 6.9 + - - +
38C ALA* 3.0 24.0 + - - +
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Residues in contact with GLU 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C PHE* 2.9 48.4 + - + +
32C LEU* 3.1 15.0 + - + +
34C ALA* 1.3 77.7 - - - +
36C ILE* 1.3 59.9 + - - +
38C ALA* 3.2 17.9 + - - +
39C GLY 3.4 1.6 + - - -
40C ARG* 2.8 63.5 + - - +
41C ARG 5.1 4.5 - - - +
42C TYR* 4.7 9.9 - - + -
133C ARG* 5.2 2.1 - - - +
140C HIS* 4.4 14.9 + - + -
143C LYS* 5.6 1.3 + - - -
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Residues in contact with ILE 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C LEU 3.1 14.2 + - - +
33C ARG* 4.1 10.1 - - + +
34C ALA 3.4 0.4 - - - -
35C GLU* 1.3 73.9 - - - +
37C ALA* 1.3 57.9 - - - +
39C GLY* 3.0 22.2 + - - -
40C ARG 3.5 8.7 - - - +
41C ARG* 5.3 6.5 - - + -
42C TYR* 3.9 29.6 - - + +
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Residues in contact with ALA 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C ARG 3.4 10.7 + - - +
34C ALA* 3.3 10.5 + - - +
35C GLU 3.3 0.2 - - - -
36C ILE* 1.3 74.4 - - - +
38C ALA* 1.3 54.1 + - - +
39C GLY* 2.8 16.6 + - - -
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Residues in contact with ALA 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C ALA 3.0 13.6 + - - +
35C GLU* 3.4 13.9 - - - +
37C ALA* 1.3 72.9 - - - +
39C GLY* 1.3 54.1 + - - +
40C ARG* 3.4 43.8 + - - +
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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