Contacts of the helix formed by residues 16 - 33 (chain A) in PDB entry 1ZX1
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 SER 16 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A HIS* 3.2 31.6 + - - -
13A GLU* 2.5 29.1 + - - +
15A LYS* 1.3 84.5 - - - +
17A PHE* 1.3 57.2 + - - +
18A ASN 3.5 0.7 + - - -
19A GLY* 3.0 16.1 + - - -
20A SER* 3.0 25.8 + - - -
232A FAD 3.0 25.6 - - - -
64B VAL* 5.2 1.3 - - - -
65B PHE 5.5 0.2 - - - -
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Residues in contact with PHE 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A SER* 1.3 70.5 - - - +
18A ASN* 1.3 66.1 + - - +
20A SER* 3.2 3.6 + - - -
21A LEU* 3.0 42.2 + - + +
147A THR* 3.9 10.5 - - + -
189A SER* 3.9 15.0 - - - -
192A PRO* 3.6 24.2 - - + -
200A ARG* 3.7 22.2 - - + -
203A MET* 3.8 24.2 - - + -
204A VAL* 3.4 30.5 - - + -
232A FAD 3.3 64.0 + + - +
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Residues in contact with ASN 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A TYR* 3.7 6.2 - - + -
11A HIS* 3.6 31.5 - - + -
16A SER 3.3 0.2 - - - -
17A PHE* 1.3 74.4 - - - +
19A GLY* 1.3 58.5 + - - +
21A LEU* 3.2 4.1 + - - +
22A LYS* 2.9 28.6 + - - +
100A GLN* 2.6 33.7 + - - +
101A PHE* 3.2 18.0 + - - -
102A PRO* 3.8 8.2 - - - +
147A THR* 2.7 29.5 + - - +
232A FAD 2.8 27.4 + - - +
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Residues in contact with GLY 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A TYR* 3.4 22.1 + - - -
14A PRO* 3.7 17.3 - - - -
16A SER* 3.0 16.9 + - - -
18A ASN* 1.3 76.0 - - - +
20A SER* 1.3 56.0 - - - +
22A LYS* 3.3 4.9 + - - +
23A ASN* 2.9 35.8 + - - +
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Residues in contact with SER 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PRO 4.5 0.2 + - - -
15A LYS* 4.8 1.2 + - - -
16A SER 3.0 5.6 + - - -
17A PHE* 3.2 8.7 + - - -
19A GLY* 1.3 73.7 - - - +
21A LEU* 1.3 61.6 + - - +
23A ASN* 3.9 7.5 - - - +
24A VAL* 3.0 35.0 + - - +
204A VAL* 4.7 9.6 - - - -
232A FAD 2.6 49.5 + - - -
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Residues in contact with LEU 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A PHE* 3.0 28.9 + - + +
18A ASN* 3.6 5.4 - - - +
20A SER* 1.3 76.0 - - - +
22A LYS* 1.3 62.2 + - - +
24A VAL* 3.5 1.1 + - - -
25A ALA* 3.1 12.8 + - - +
100A GLN* 3.5 33.7 - - - +
145A SER* 4.2 6.3 - - - +
146A VAL 5.6 0.4 - - - +
147A THR* 3.7 21.3 - - + -
187A GLN* 6.1 0.9 - - + -
189A SER* 4.0 10.8 - - - +
203A MET 4.3 2.5 - - - +
204A VAL* 4.1 25.4 - - + -
207A TRP* 3.0 51.9 + - + -
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Residues in contact with LYS 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ILE* 4.1 19.1 - - + -
9A TYR* 3.8 49.8 + - + -
14A PRO* 6.2 3.4 - - - +
18A ASN 2.9 13.0 + - - +
19A GLY* 3.5 8.3 + - - +
20A SER 3.3 0.2 - - - -
21A LEU* 1.3 75.7 - - - +
23A ASN* 1.3 79.8 + - - +
25A ALA* 3.1 7.6 + - - +
26A VAL* 3.0 45.5 + - + +
38A VAL* 4.3 14.4 - - + -
40A ASP* 5.2 3.7 + - - -
100A GLN* 4.5 6.2 - - + +
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Residues in contact with ASN 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PRO 4.7 7.5 + - - -
19A GLY 2.9 24.2 + - - +
20A SER* 3.4 7.1 + - - +
22A LYS* 1.3 106.8 + - - +
24A VAL* 1.3 58.0 + - + +
26A VAL* 3.7 5.9 - - - +
27A ASP* 2.9 43.1 + - - +
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Residues in contact with VAL 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A SER* 3.0 20.6 + - - +
21A LEU* 3.8 3.1 - - - +
22A LYS 3.3 0.2 - - - -
23A ASN* 1.3 74.8 - - + +
25A ALA* 1.3 59.4 + - - +
27A ASP* 3.9 6.8 - - - +
28A GLU* 2.9 30.0 + - - +
204A VAL* 3.7 24.9 - - + +
207A TRP* 3.9 15.3 - - + -
208A SER* 3.4 36.8 - - - +
211A LEU* 4.6 0.2 - - + -
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Residues in contact with ALA 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ILE* 3.9 16.6 - - + -
21A LEU 3.1 14.1 + - - +
22A LYS* 3.4 10.3 - - - +
24A VAL* 1.3 75.5 - - - +
26A VAL* 1.3 65.4 + - - +
29A LEU* 3.0 37.1 + - + +
98A ILE* 4.9 2.9 - - + -
207A TRP* 4.0 11.9 - - + +
211A LEU* 3.5 23.6 - - + -
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Residues in contact with VAL 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ILE* 3.9 10.5 - - + -
22A LYS* 3.0 25.9 + - + +
23A ASN* 3.7 9.9 - - - +
25A ALA* 1.3 76.3 - - - +
27A ASP* 1.3 63.2 + - - +
29A LEU* 4.3 0.3 - - - +
30A SER* 2.9 39.7 + - - -
36A VAL* 4.5 14.8 - - + +
38A VAL* 3.7 29.6 - - + -
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Residues in contact with ASP 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ASN* 2.9 33.8 + - - +
24A VAL* 3.9 6.8 - - - +
26A VAL* 1.3 80.1 - - - +
28A GLU* 1.3 57.8 + - - +
30A SER* 3.7 4.0 - - - -
31A ARG* 2.9 30.7 + - - +
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Residues in contact with GLU 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A VAL 2.9 19.5 + - - +
25A ALA 4.2 1.6 - - - +
27A ASP* 1.3 75.9 - - - +
29A LEU* 1.3 64.1 + - - +
31A ARG* 2.5 37.3 + - - +
32A GLN* 3.1 32.0 + - - +
208A SER* 3.9 16.8 - - - +
211A LEU* 3.8 28.9 - - + -
212A GLN* 3.4 30.1 + - + +
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Residues in contact with LEU 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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5A VAL* 4.0 22.7 - - + -
7A ILE* 4.6 4.7 - - + -
25A ALA* 3.0 28.6 + - + +
28A GLU* 1.3 72.7 - - - +
30A SER* 1.3 65.6 + - - +
32A GLN* 3.2 30.6 + - - +
33A GLY 3.3 0.2 + - - -
34A CYS* 3.0 36.9 + - + +
36A VAL* 3.8 15.0 - - + -
96A LEU* 5.1 1.1 - - + -
98A ILE* 3.9 26.7 - - + -
211A LEU* 4.5 12.8 - - + -
214A ILE* 4.1 21.5 - - + -
215A TRP* 4.4 0.4 - - + +
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Residues in contact with SER 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 VAL* 2.9 27.3 + - - -
27A ASP* 3.7 4.9 - - - -
29A LEU* 1.3 78.1 - - - +
31A ARG* 1.3 57.0 + - - +
33A GLY* 3.0 20.3 + - - -
34A CYS 4.2 10.8 - - - +
36A VAL* 4.1 7.3 - - - +
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Residues in contact with ARG 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 ASP 2.9 19.0 + - - +
28A GLU* 2.5 46.1 + - - +
29A LEU 3.3 0.2 - - - -
30A SER* 1.3 76.5 + - - +
32A GLN* 1.3 70.2 + - - +
33A GLY* 3.3 1.0 + - - -
212A GLN* 5.1 2.2 - - - +
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Residues in contact with GLN 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 GLU* 3.1 37.2 + - - +
29A LEU* 3.2 16.0 + - - +
31A ARG* 1.3 83.7 - - - +
33A GLY* 1.3 57.7 + - - +
34A CYS* 3.6 9.7 - - - -
211A LEU 2.8 30.5 + - - -
212A GLN* 3.5 12.7 + - - +
215A TRP* 3.2 30.7 + - - -
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Residues in contact with GLY 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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2A GLY* 5.6 4.2 + - - -
3A LYS 4.9 1.7 + - - +
30A SER 3.0 13.1 + - - -
31A ARG 3.2 1.8 + - - -
32A GLN* 1.3 78.3 - - - +
34A CYS* 1.3 66.5 + - - +
35A THR* 3.8 2.3 + - - -
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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