Contacts of the helix formed by residues 21 - 38 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18K LEU* 2.7 50.6 + - + +
20K PRO* 1.3 76.8 - - + +
22K ALA* 1.3 56.8 + - - +
23K ASP 3.2 2.9 - - - -
24K GLN* 2.5 40.8 + - + -
25K VAL* 2.8 17.4 + - + +
147K ALA* 3.6 17.7 - - + +
148K VAL* 4.2 13.9 - - + -
151K CYS* 3.5 26.2 - - + -
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Residues in contact with ALA 22 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4K ARG 5.7 0.9 - - - +
6K LEU* 4.3 18.0 - - + +
18K LEU 3.3 4.5 + - - -
19K GLU* 3.0 23.5 + - + +
20K PRO 3.4 0.4 - - - -
21K VAL* 1.3 74.4 - - - +
23K ASP* 1.3 64.8 + - - +
25K VAL* 3.0 26.1 - - - +
26K ALA* 3.1 13.2 + - - +
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Residues in contact with ASP 23 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20K PRO 5.0 3.5 + - - +
21K VAL 3.2 1.2 - - - -
22K ALA* 1.3 81.1 - - - +
24K GLN* 1.3 57.1 + - - +
26K ALA* 3.5 8.0 - - - +
27K HIS* 3.0 25.6 + - - +
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Residues in contact with GLN 24 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20K PRO 5.5 0.2 + - - -
21K VAL* 2.5 32.9 + - + +
23K ASP* 1.3 72.9 - - - +
25K VAL* 1.3 62.3 + - - +
27K HIS* 3.2 21.9 - - - +
28K MET* 3.1 29.1 + - - +
144K GLY* 3.0 30.4 + - - -
147K ALA* 4.1 18.8 - - + +
148K VAL* 4.7 4.3 - - + +
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Residues in contact with VAL 25 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4K ARG 6.1 0.2 - - - +
6K LEU* 3.9 22.4 - - + -
9K LEU* 4.7 10.3 - - + -
18K LEU* 6.1 1.1 - - + -
21K VAL* 2.8 23.5 + - + +
22K ALA* 3.0 26.5 - - - +
24K GLN* 1.3 68.9 - - - +
26K ALA* 1.3 59.7 + - - +
28K MET* 3.1 12.2 + - - +
29K GLY* 2.9 24.6 + - - -
50K LEU* 4.6 27.6 - - + -
145K TRP* 5.1 5.3 - - + -
148K VAL* 4.4 16.7 - - + +
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Residues in contact with ALA 26 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4K ARG* 5.3 11.9 - - + +
22K ALA 3.1 17.6 + - - +
23K ASP* 3.5 11.4 - - - +
25K VAL* 1.3 76.1 - - - +
27K HIS* 1.3 65.8 + - - +
29K GLY* 3.0 13.5 + - - -
30K GLN* 3.0 12.9 + - - +
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Residues in contact with HIS 27 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23K ASP 3.0 14.9 + - - +
24K GLN* 3.2 30.1 - - - +
26K ALA* 1.3 74.4 - - - +
28K MET* 1.3 73.1 + - - +
30K GLN* 3.1 13.2 + - + +
31K PHE* 2.9 34.2 + - + +
143K LYS 4.9 6.0 + - - -
144K GLY* 5.4 1.1 - - - -
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Residues in contact with MET 28 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24K GLN* 3.3 21.3 - - - +
25K VAL* 3.1 12.0 + - - +
27K HIS* 1.3 79.4 - - - +
29K GLY* 1.3 67.3 + - - +
31K PHE* 3.0 25.2 + - + +
32K LEU* 2.9 27.8 + - - +
143K LYS 3.2 28.0 - - - +
144K GLY* 3.4 20.2 - - - +
145K TRP* 3.5 65.3 - - + +
148K VAL* 4.7 0.9 - - + -
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Residues in contact with GLY 29 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25K VAL 2.9 13.5 + - - -
26K ALA* 3.0 5.5 + - - -
28K MET* 1.3 77.5 - - - +
30K GLN* 1.3 62.5 + - - +
32K LEU* 3.0 13.6 + - - +
33K ARG* 2.9 37.0 + - - +
145K TRP* 5.4 0.6 - - - -
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Residues in contact with GLN 30 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26K ALA 3.0 10.5 + - - +
27K HIS* 3.3 14.6 - - + +
29K GLY* 1.3 73.2 - - - +
31K PHE* 1.3 51.0 + - - +
33K ARG* 3.4 24.3 + - - +
34K ALA* 2.8 35.6 + - - +
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Residues in contact with PHE 31 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27K HIS* 2.9 21.2 + - + +
28K MET* 3.0 37.0 + - + +
30K GLN* 1.3 73.4 - - - +
32K LEU* 1.3 68.2 + - + +
34K ALA* 3.3 9.6 - - + +
35K GLU* 2.8 62.9 + - + +
131K THR* 4.4 0.7 - - - -
140K HIS* 3.7 31.6 - + + -
143K LYS* 3.5 41.7 - - + +
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Residues in contact with LEU 32 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28K MET 2.9 18.1 + - - +
29K GLY* 3.4 13.5 - - - +
31K PHE* 1.3 84.2 - - + +
33K ARG* 1.3 62.6 + - + +
35K GLU* 2.8 23.5 + - - +
36K ILE* 2.9 15.2 + - - +
42K TYR* 3.6 46.2 - - + +
49K VAL* 4.8 7.6 - - + -
131K THR* 3.7 32.1 - - + +
140K HIS* 4.8 1.1 - - + -
145K TRP* 4.2 18.6 - - + -
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Residues in contact with ARG 33 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3K ALA 5.1 8.5 + - - -
26K ALA 5.6 0.2 + - - -
29K GLY* 2.9 23.2 + - - +
30K GLN* 3.7 26.1 - - - +
32K LEU* 1.3 74.9 - - + +
34K ALA* 1.3 63.7 + - - +
36K ILE* 3.1 14.0 + - + +
37K ALA* 3.0 24.4 + - - +
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Residues in contact with ALA 34 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30K GLN 2.8 16.6 + - - +
31K PHE* 3.3 14.6 - - + +
33K ARG* 1.3 74.7 - - - +
35K GLU* 1.3 63.1 + - + +
37K ALA* 3.6 7.0 + - - +
38K ALA* 3.1 26.0 + - - +
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Residues in contact with GLU 35 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31K PHE* 2.8 46.4 + - + +
32K LEU* 2.8 22.3 + - - +
34K ALA* 1.3 70.0 - - - +
36K ILE* 1.3 59.8 + - - +
38K ALA* 3.3 6.7 + - - +
40K ARG* 2.6 78.6 + - - +
41K ARG 6.1 0.9 - - - -
42K TYR* 4.9 10.5 - - + +
133K ARG* 4.6 4.3 - - - -
140K HIS* 4.0 20.4 + - + -
143K LYS* 6.2 0.7 - - - -
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Residues in contact with ILE 36 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32K LEU 2.9 13.8 + - - +
33K ARG* 3.1 13.0 + - + +
35K GLU* 1.3 73.5 - - - +
37K ALA* 1.3 57.7 + - - +
39K GLY* 2.8 30.7 + - - -
40K ARG 3.3 11.5 + - - +
41K ARG* 5.1 7.4 - - + -
42K TYR* 4.3 26.5 - - + +
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Residues in contact with ALA 37 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33K ARG 3.0 15.0 + - - +
34K ALA* 3.8 7.9 - - - +
36K ILE* 1.3 78.7 - - - +
38K ALA* 1.3 56.7 + - - +
39K GLY* 3.0 7.1 + - - -
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Residues in contact with ALA 38 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34K ALA 3.1 19.3 + - - +
35K GLU* 3.6 6.5 - - - +
36K ILE 3.0 0.8 + - - -
37K ALA* 1.3 73.1 - - - +
39K GLY* 1.3 54.6 - - - +
40K ARG* 3.4 41.9 + - - +
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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