Contacts of the helix formed by residues 20 - 37 (chain C) in PDB entry 3GZN
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 TYR 20 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C LYS* 3.1 32.8 + - + +
18C GLN 3.4 0.2 - - - -
19C LYS* 1.3 96.7 + - + +
21C ASP* 1.3 63.7 + - - +
22C ARG 3.5 2.2 - - - -
23C GLN* 3.2 29.8 - - + +
24C LEU* 3.0 32.7 + - + +
32C GLN* 3.8 14.6 - - + +
36C GLU* 3.5 21.2 + - - -
58C LEU 3.5 15.5 - - - -
59C PRO 3.4 15.5 - - - -
60C GLY* 3.6 3.6 - - - -
104C ASN* 2.7 31.4 + - - -
106C ASP* 3.6 16.0 + - - +
110D ASN* 3.9 15.7 - - + -
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Residues in contact with ASP 21 (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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17C GLU* 3.5 14.4 + - - +
18C GLN* 3.4 17.9 + - - +
19C LYS 3.3 3.4 + - - -
20C TYR* 1.3 76.8 - - - +
22C ARG* 1.3 92.4 + - - +
24C LEU* 3.0 19.1 + - - +
25C ARG* 2.9 55.3 + - - +
107D SER* 4.6 1.3 - - - -
300D ARG* 4.4 10.9 + - - +
303D GLN* 3.9 12.7 - - - +
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Residues in contact with ARG 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C LYS 5.3 0.2 + - - -
20C TYR 3.5 0.4 - - - -
21C ASP* 1.3 110.0 + - - +
23C GLN* 1.3 59.4 + - - +
25C ARG* 3.8 10.9 - - - +
26C LEU* 4.0 2.1 - - - +
105D ASP* 5.1 1.6 + - - -
107D SER* 3.1 37.5 + - - +
108D ASN* 5.7 1.4 - - - +
110D ASN* 4.2 5.9 - - - +
111D ARG* 3.9 26.9 - - - +
303D GLN* 5.7 1.8 + - - -
307D LYS* 4.1 21.0 - - - +
309D ILE* 3.5 40.3 - - - +
310D ILE 3.7 10.2 + - - +
311D PRO* 3.6 10.7 - - - +
312D ALA* 3.4 37.7 + - + +
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Residues in contact with GLN 23 (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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20C TYR* 3.2 23.5 - - - +
22C ARG* 1.3 74.5 - - - +
24C LEU* 1.3 56.7 + - - +
25C ARG 3.0 2.0 - - - -
26C LEU* 2.8 23.7 + - - +
27C TRP* 3.2 31.8 + - + -
32C GLN* 2.9 20.5 + - - +
59C PRO* 2.9 46.6 + - - +
110D ASN* 2.8 31.7 + - - +
312D ALA 3.7 2.6 + - - -
313D VAL* 3.6 27.6 - - + +
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Residues in contact with LEU 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C GLU* 3.6 34.3 - - + +
20C TYR* 3.0 25.9 + - + +
21C ASP* 3.0 9.3 + - - +
23C GLN* 1.3 77.2 - - - +
25C ARG* 1.3 57.9 + - - +
26C LEU 3.0 1.0 + - - -
27C TRP* 4.7 0.4 - - - -
28C GLY* 2.9 51.1 + - - +
29C ASP* 3.7 16.8 - - - +
32C GLN* 3.7 27.1 - - + +
300D ARG* 4.0 34.2 + - - +
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Residues in contact with ARG 25 (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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21C ASP* 2.9 43.7 + - - +
22C ARG* 3.8 11.7 - - - +
23C GLN 3.0 0.4 - - - -
24C LEU* 1.3 76.9 - - - +
26C LEU* 1.3 62.9 + - - +
300D ARG* 3.2 52.5 + - - +
301D LEU* 4.5 4.9 - - - +
303D GLN* 3.9 5.7 + - - +
304D GLY* 3.4 24.3 - - - +
309D ILE* 3.5 32.3 - - - +
311D PRO* 4.4 18.7 - - + +
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Residues in contact with LEU 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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22C ARG 4.0 9.9 - - - +
23C GLN* 2.8 10.2 + - - +
25C ARG* 1.3 82.1 - - - +
27C TRP* 1.3 61.3 + - + +
28C GLY 3.7 0.4 - - - -
182C HIS* 3.5 22.2 + - - -
520C PHE* 3.6 9.4 - - + -
205D GLY* 4.1 23.1 - - - -
206D PHE* 3.9 33.2 - - + -
311D PRO* 3.7 26.2 - - + -
312D ALA 4.2 3.1 - - - +
313D VAL* 3.6 28.9 - - + -
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Residues in contact with TRP 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C GLN* 3.2 44.4 + - + +
24C LEU* 4.6 0.6 - - - +
26C LEU* 1.3 74.9 - - + +
28C GLY* 1.3 74.2 + - - +
30C HIS* 3.7 5.0 - - - -
31C GLY* 3.1 23.8 + - - -
32C GLN* 3.2 30.5 + - - +
35C LEU* 4.1 14.1 - - + -
59C PRO* 4.2 4.3 - - + -
182C HIS* 4.9 0.2 - - - -
510C GLN* 4.0 12.3 - - - -
513C ILE* 3.5 45.5 - - + -
517C THR* 5.0 5.4 - - + -
519C GLN* 3.1 34.3 + - - +
520C PHE* 4.3 10.3 - + + -
206D PHE* 4.2 20.0 - + - -
313D VAL* 4.0 19.3 - - + -
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Residues in contact with GLY 28 (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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24C LEU* 2.9 27.5 + - - +
26C LEU 3.7 0.8 - - - -
27C TRP* 1.3 87.1 - - - +
29C ASP* 1.3 64.3 + - - -
30C HIS* 3.3 9.6 - - - -
32C GLN* 3.2 15.9 + - - +
300D ARG* 4.7 4.9 - - - -
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Residues in contact with ASP 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C GLU* 4.7 2.8 - - - +
24C LEU* 3.7 15.6 - - - +
28C GLY* 1.3 72.3 - - - -
30C HIS* 1.3 60.7 + - - +
32C GLN* 3.5 3.8 + - - +
33C GLU* 3.0 27.7 + - - +
300D ARG* 3.2 36.1 + - - +
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Residues in contact with HIS 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C TRP 3.7 13.4 + - - -
28C GLY* 4.4 4.9 - - - -
29C ASP* 1.3 81.4 + - - +
31C GLY* 1.3 71.9 + - - +
33C GLU* 3.5 7.8 + - - +
34C ALA* 3.3 19.6 + - - +
180C GLU* 2.7 36.6 + - - -
385C LYS* 5.1 13.9 - - - +
389C LEU* 4.6 16.8 - - + +
517C THR 6.0 0.4 - - - -
519C GLN* 3.7 9.5 + - + -
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Residues in contact with GLY 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 TRP* 3.1 26.1 + - - -
30C HIS* 1.3 75.3 - - - +
32C GLN* 1.3 66.0 + - - +
34C ALA* 3.0 7.6 + - - +
35C LEU* 2.9 22.1 + - - +
517C THR* 3.6 17.0 - - - +
519C GLN* 3.4 14.1 - - - -
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Residues in contact with GLN 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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20C TYR* 3.8 15.1 - - + -
23C GLN* 2.9 25.3 + - - +
24C LEU* 3.7 17.8 - - + +
27C TRP* 3.2 17.1 + - - +
28C GLY 3.2 15.3 + - - +
29C ASP* 3.5 9.4 - - - +
31C GLY* 1.3 74.9 - - - +
33C GLU* 1.3 50.8 + - - +
35C LEU* 3.2 8.7 + - - +
36C GLU* 2.7 78.2 + - - +
59C PRO 3.2 22.2 + - - -
60C GLY 4.4 0.4 + - - -
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Residues in contact with GLU 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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29C ASP 3.0 17.1 + - - +
30C HIS* 3.7 9.6 - - - +
31C GLY 3.2 0.4 - - - -
32C GLN* 1.3 73.2 - - - +
34C ALA* 1.3 65.0 + - - +
36C GLU* 3.1 7.8 + - - +
37C SER* 3.1 28.7 + - - -
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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 HIS 3.3 9.6 + - - +
31C GLY* 3.0 9.7 + - - +
33C GLU* 1.3 78.3 - - - +
35C LEU* 1.3 63.4 + - - +
37C SER* 3.6 7.7 + - - -
38C ALA* 3.4 14.2 + - - +
516C ILE* 3.4 19.5 - - - +
517C THR* 4.0 25.1 - - - +
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Residues in contact with LEU 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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27C TRP* 4.1 13.7 - - + -
31C GLY 2.9 10.6 + - - +
32C GLN* 3.3 14.8 - - - +
34C ALA* 1.3 73.8 - - - +
36C GLU* 1.3 57.9 + - - +
37C SER 3.1 8.0 + - - -
38C ALA* 3.2 11.1 + - - +
59C PRO* 3.8 46.0 - - + +
60C GLY 4.2 4.5 - - - +
61C ILE* 3.7 12.5 - - + +
62C GLY 3.0 18.8 + - - -
513C ILE* 3.7 35.9 - - + -
516C ILE* 3.8 17.9 - - + +
517C THR* 3.9 12.3 - - + -
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Residues in contact with GLU 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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16C LYS* 5.7 2.8 - - - +
20C TYR* 3.5 26.8 + - - -
32C GLN* 2.7 50.0 + - - +
33C GLU* 3.1 6.9 + - - +
35C LEU* 1.3 69.8 - - - +
37C SER* 1.3 59.4 + - - +
38C ALA 3.6 0.4 - - - -
60C GLY* 3.5 17.5 - - - +
62C GLY* 3.4 15.2 - - - +
106C ASP* 4.9 8.8 - - - +
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Residues in contact with SER 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C GLU 3.1 17.7 + - - -
34C ALA* 3.8 7.0 + - - -
35C LEU 3.1 0.2 - - - -
36C GLU* 1.3 78.6 - - - +
38C ALA* 1.3 61.9 + - - +
62C GLY* 4.7 0.4 - - - -
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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