Contacts of the helix formed by residues 15 - 28 (chain A) in PDB entry 1ZMC
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 GLY 15 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A GLY 3.5 2.2 + - - -
14A SER* 1.3 79.3 - - - +
16A PRO* 1.4 77.3 - - - +
17A GLY 3.1 3.2 + - - -
18A GLY 3.1 1.3 + - - +
19A TYR* 2.8 23.7 + - - -
42A GLY 3.6 9.4 - - - -
43A GLY 3.7 0.2 - - - -
480A FAD 3.3 30.0 - - - -
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Residues in contact with PRO 16 (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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15A GLY* 1.4 82.8 - - - +
17A GLY* 1.3 60.3 + - - +
19A TYR* 3.9 12.6 - - + -
20A VAL* 3.2 28.6 + - - +
42A GLY 3.9 9.3 - - - +
45A CYS* 3.5 30.1 - - + -
328A ALA* 3.8 13.5 - - + +
331A ALA* 4.3 0.2 - - + -
332A GLU* 3.3 26.9 - - + +
480A FAD 3.1 36.1 - - - +
452B HIS* 5.7 0.2 - - - +
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Residues in contact with GLY 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A PRO* 1.3 75.3 - - - +
18A GLY* 1.3 56.6 + - - +
20A VAL* 4.0 1.0 - - - +
21A ALA* 3.0 31.7 + - - +
318A ILE* 3.6 15.7 - - - -
331A ALA* 3.5 27.4 - - - +
332A GLU* 4.3 0.2 - - - -
335A GLY* 4.1 2.8 - - - -
480A FAD 2.8 19.1 + - - -
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Residues in contact with GLY 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A VAL* 3.5 20.3 - - - +
13A GLY 3.1 24.2 - - - -
14A SER* 4.5 0.2 - - - -
15A GLY 3.1 5.6 + - - +
17A GLY* 1.3 74.4 - - - +
19A TYR* 1.3 56.1 + - - +
21A ALA* 3.2 2.1 + - - +
22A ALA* 2.9 27.1 + - - +
34A CYS* 4.8 0.4 - - - -
147A ALA* 3.7 14.3 - - - +
480A FAD 4.0 1.2 + - - -
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Residues in contact with TYR 19 (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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14A SER* 3.8 14.6 - - - +
15A GLY 2.8 29.8 + - - +
16A PRO* 3.9 12.3 - - + -
18A GLY* 1.3 69.3 - - - -
20A VAL* 1.3 83.4 + - + +
22A ALA* 3.4 1.9 + - - +
23A ILE* 3.1 50.7 + - + +
42A GLY* 5.1 1.1 - - - -
103A ILE* 3.6 45.4 - - + +
106A LEU* 4.6 2.5 - - + -
107A PHE* 3.8 23.9 - + + -
332A GLU* 4.3 7.2 + - - -
392B SER* 5.7 0.5 + - - -
452B HIS* 5.8 2.3 - - - -
472B ILE* 4.7 0.2 - - + -
473B ASN* 2.4 40.0 + - - -
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Residues in contact with VAL 20 (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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16A PRO 3.2 21.6 + - - +
17A GLY 4.0 0.7 - - - +
18A GLY 3.4 0.4 - - - -
19A TYR* 1.3 98.7 - - + +
21A ALA* 1.3 57.5 + - - +
23A ILE* 3.4 2.9 + - - +
24A LYS* 3.0 26.9 + - - +
332A GLU* 3.6 34.5 - - + +
336A ILE* 3.3 37.7 - - + -
472B ILE* 4.1 21.0 - - + +
473B ASN* 5.1 1.3 - - - +
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Residues in contact with ALA 21 (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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11A VAL* 4.6 2.7 - - + -
17A GLY 3.0 21.0 + - - +
18A GLY* 3.6 4.9 - - - +
20A VAL* 1.3 76.0 - - - +
22A ALA* 1.3 60.0 + - - +
24A LYS* 3.4 1.9 + - - -
25A ALA* 2.8 33.5 + - - +
145A LEU* 3.7 29.4 - - + -
335A GLY* 3.7 24.2 - - - +
339A VAL* 3.8 4.7 - - + +
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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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11A VAL* 4.1 6.9 - - + +
18A GLY 2.9 17.2 + - - +
19A TYR 3.7 5.4 - - - +
20A VAL 3.3 0.2 - - - -
21A ALA* 1.3 76.4 - - - +
23A ILE* 1.3 60.5 + - - +
25A ALA 3.4 0.2 + - - -
26A ALA* 3.0 24.1 + - - +
32A THR* 3.6 26.8 - - + +
34A CYS* 4.0 23.8 - - + -
107A PHE* 4.2 4.9 - - + -
112A VAL* 3.7 11.3 - - + +
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Residues in contact with ILE 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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19A TYR* 3.1 47.7 + - + +
20A VAL 3.8 3.4 - - - +
22A ALA* 1.3 71.9 - - - +
24A LYS* 1.3 62.3 + - - +
26A ALA* 3.2 3.0 + - - +
27A GLN* 2.8 59.3 + - - +
106A LEU* 4.1 15.0 - - + -
107A PHE* 4.1 16.6 - - + -
110A ASN* 3.6 18.6 - - - +
112A VAL* 4.3 7.4 - - + -
472B ILE* 3.9 30.7 - - + +
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Residues in contact with LYS 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 VAL 3.0 17.6 + - - +
21A ALA* 3.9 4.7 - - - +
23A ILE* 1.3 78.4 - - - +
25A ALA* 1.3 62.2 + - - +
27A GLN* 3.1 11.0 + - - +
28A LEU* 2.9 49.7 + - + +
336A ILE* 4.0 30.0 - - + +
339A VAL* 3.9 5.2 - - + -
340A GLU* 4.0 20.3 + - - -
464B LEU* 4.1 18.6 - - - +
468B PHE* 3.8 44.6 - - - +
472B ILE* 3.8 19.3 - - + -
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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
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9A VAL* 4.5 9.0 - - + -
21A ALA 2.8 20.4 + - - +
22A ALA 3.8 1.8 - - - +
24A LYS* 1.3 76.5 - - - +
26A ALA* 1.3 61.8 + - - +
28A LEU* 3.0 9.9 + - - +
29A GLY 3.2 0.2 + - - -
30A PHE* 3.0 32.8 + - + +
32A THR* 3.5 20.4 - - + +
339A VAL* 3.2 27.3 - - + +
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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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22A ALA 3.0 17.9 + - - +
23A ILE 3.6 3.8 - - - +
25A ALA* 1.3 76.4 - - - +
27A GLN* 1.3 58.0 + - - +
29A GLY* 3.0 20.3 + - - -
30A PHE 3.5 13.8 + - - +
32A THR* 3.4 7.2 + - - +
110A ASN* 3.1 31.1 - - + +
111A LYS* 5.0 2.2 - - + +
112A VAL* 3.8 11.4 - - + +
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Residues in contact with GLN 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 ILE* 2.8 34.3 + - - +
24A LYS* 3.1 9.9 + - - +
26A ALA* 1.3 75.6 - - - +
28A LEU* 1.3 59.4 + - - +
29A GLY 3.2 1.3 + - - -
109A GLN* 5.9 1.6 - - - +
110A ASN* 3.2 28.2 + - - +
464B LEU* 6.0 0.2 - - - +
468B PHE* 3.9 32.0 - - + -
470B LYS* 4.0 33.3 + - + +
471B SER 3.0 29.0 + - - +
472B ILE* 3.9 13.4 + - - +
474B PHE* 5.4 0.2 + - - -
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Residues in contact with LEU 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 LYS* 2.9 28.1 + - + +
25A ALA 3.0 8.4 + - - +
27A GLN* 1.3 76.7 - - - +
29A GLY* 1.3 58.3 + - - +
30A PHE* 3.6 11.5 - - + -
339A VAL* 3.4 45.1 - - + +
340A GLU* 4.0 15.0 - - + -
343A ALA* 4.4 11.7 - - + -
468B PHE* 4.1 26.0 - - + -
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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