Contacts of the helix formed by residues 15 - 29 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G GLY 3.6 1.8 + - - -
14G SER* 1.3 83.8 - - - +
16G PRO* 1.3 78.3 - - - +
17G GLY 3.2 2.8 + - - -
18G GLY 3.2 1.6 + - - +
19G TYR* 2.9 17.3 + - - -
42G GLY 3.5 10.5 - - - -
480G FAD 3.3 29.3 + - - -
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Residues in contact with PRO 16 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G GLY* 1.3 83.0 - - - +
17G GLY* 1.3 61.0 + - - +
19G TYR* 3.9 12.1 - - + -
20G VAL* 3.2 28.8 + - - +
42G GLY 3.7 8.9 - - - +
45G CYS* 3.6 26.2 - - + -
328G ALA* 3.8 18.4 - - + +
332G GLU* 3.3 25.4 - - + +
480G FAD 3.1 35.7 - - - +
452H HIS* 5.6 0.7 - - + +
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Residues in contact with GLY 17 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16G PRO* 1.3 76.0 - - - +
18G GLY* 1.3 55.1 + - - -
20G VAL* 4.0 0.3 - - - +
21G ALA* 2.9 31.5 + - - +
318G ILE* 3.6 15.7 - - - +
331G ALA* 3.4 29.1 - - - +
332G GLU* 4.0 0.4 - - - -
335G GLY* 4.0 2.6 - - - -
480G FAD 2.9 17.6 + - - -
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Residues in contact with GLY 18 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G VAL* 3.5 11.0 - - - +
13G GLY 3.2 24.9 - - - -
15G GLY 3.2 5.3 + - - +
17G GLY* 1.3 75.6 - - - +
19G TYR* 1.3 56.3 + - - +
21G ALA* 3.5 0.8 + - - -
22G ALA* 3.0 29.1 + - - +
34G CYS* 4.8 0.7 - - - -
147G ALA* 3.6 21.0 - - - +
480G FAD 4.1 1.4 + - - -
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Residues in contact with TYR 19 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G SER* 3.6 16.7 - - - +
15G GLY 2.9 26.0 + - - -
16G PRO* 3.8 12.3 - - + -
18G GLY* 1.3 70.1 - - - -
20G VAL* 1.3 85.3 + - + +
22G ALA* 3.8 1.4 - - - +
23G ILE* 3.2 42.9 + - + +
42G GLY* 5.3 1.3 - - - -
103G ILE* 3.8 43.7 - - + +
106G LEU* 4.8 2.2 - - + -
107G PHE* 3.8 23.2 - + + -
332G GLU* 4.3 8.1 + - - -
392H SER* 5.7 1.0 + - - -
452H HIS* 6.0 1.6 - - - -
473H ASN* 2.5 35.4 + - - -
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Residues in contact with VAL 20 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16G PRO 3.2 20.3 + - - +
17G GLY 4.0 1.3 - - - +
19G TYR* 1.3 96.6 - - + +
21G ALA* 1.3 59.0 + - - +
23G ILE* 3.2 2.8 + - - +
24G LYS* 2.9 29.0 + - - +
332G GLU* 3.6 35.0 - - + +
336G ILE* 3.3 38.1 - - + -
472H ILE* 4.2 20.6 - - + +
473H ASN* 5.4 1.6 - - - +
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Residues in contact with ALA 21 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G VAL* 4.6 2.5 - - + -
17G GLY 2.9 20.7 + - - +
18G GLY* 3.5 5.8 - - - +
20G VAL* 1.3 77.9 - - - +
22G ALA* 1.3 57.9 + - - +
24G LYS* 3.8 1.9 - - - +
25G ALA* 2.8 32.8 + - - +
145G LEU* 3.4 32.1 - - + -
335G GLY* 3.9 24.4 - - - +
336G ILE 4.6 0.2 - - - +
339G VAL* 3.6 4.9 - - + +
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Residues in contact with ALA 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G VAL* 4.1 7.1 - - + +
18G GLY 3.0 17.7 + - - +
19G TYR 3.8 5.2 - - - +
21G ALA* 1.3 76.6 - - - +
23G ILE* 1.3 62.3 + - - +
25G ALA* 3.3 2.1 + - - +
26G ALA* 3.0 23.9 + - - +
32G THR* 3.8 16.2 - - + +
34G CYS* 4.1 13.2 - - + -
107G PHE* 4.1 5.6 - - + -
112G VAL* 3.7 27.8 - - + +
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Residues in contact with ILE 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19G TYR* 3.2 39.2 + - + +
20G VAL 3.2 6.5 + - - +
22G ALA* 1.3 73.4 - - - +
24G LYS* 1.3 67.7 + - - +
26G ALA* 3.1 5.0 + - - +
27G GLN* 2.9 51.6 + - - +
106G LEU* 3.9 19.1 - - + +
107G PHE* 4.1 16.2 - - + -
110G ASN* 3.9 15.5 - - - +
112G VAL* 4.3 7.4 - - + -
472H ILE* 3.7 33.9 - - + +
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Residues in contact with LYS 24 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G VAL 2.9 16.8 + - - +
21G ALA 3.9 0.2 - - - +
23G ILE* 1.3 76.5 - - - +
25G ALA* 1.3 63.8 + - - +
27G GLN* 3.0 17.8 + - - +
28G LEU* 2.9 39.0 + - + +
336G ILE* 4.2 22.9 - - + +
339G VAL* 3.6 23.1 - - + -
340G GLU* 4.0 20.1 + - - -
464H LEU* 4.1 17.4 - - + +
468H PHE* 3.3 50.6 - - + -
472H ILE* 3.9 15.7 - - + -
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Residues in contact with ALA 25 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G VAL* 4.4 8.3 - - + -
21G ALA 2.8 20.5 + - - +
22G ALA 3.6 2.2 - - - +
24G LYS* 1.3 77.3 - - - +
26G ALA* 1.3 61.6 + - - +
28G LEU* 3.0 13.6 + - - +
29G GLY 3.2 0.3 + - - -
30G PHE* 3.1 32.5 + - + +
32G THR* 3.6 19.7 - - + +
339G VAL* 3.8 21.5 - - + +
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Residues in contact with ALA 26 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G ALA 3.0 14.0 + - - +
23G ILE 3.6 7.4 - - - +
25G ALA* 1.3 76.0 - - - +
27G GLN* 1.3 61.8 + - - +
29G GLY* 3.1 14.2 + - - -
30G PHE 3.6 14.2 + - - +
32G THR* 3.5 7.1 + - - +
110G ASN* 3.1 31.4 - - + +
111G LYS* 4.9 11.9 + - + +
112G VAL* 4.0 11.7 - - + +
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Residues in contact with GLN 27 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G ILE* 2.9 32.4 + - - +
24G LYS* 3.0 15.0 + - + +
26G ALA* 1.3 77.6 - - - +
28G LEU* 1.3 60.2 + - - +
29G GLY 3.2 1.1 + - - -
109G GLN* 6.1 0.6 - - - +
110G ASN* 3.3 27.5 + - - +
468H PHE* 3.9 29.4 - - + -
470H LYS* 4.0 33.6 + - + +
471H SER 3.2 24.3 + - - +
472H ILE* 3.8 17.0 + - - +
474H PHE* 5.4 1.2 + - - -
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Residues in contact with LEU 28 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24G LYS* 2.9 18.8 + - + +
25G ALA* 3.0 10.2 + - - +
27G GLN* 1.3 78.5 - - - +
29G GLY* 1.3 57.2 + - - +
30G PHE* 3.6 11.7 - - + -
339G VAL* 3.8 25.6 - - + +
340G GLU* 3.7 39.9 - - + +
343G ALA* 4.2 14.6 - - + +
468H PHE* 4.0 26.7 - - + -
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Residues in contact with GLY 29 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G ASP* 4.4 2.4 - - - +
26G ALA 3.1 12.2 + - - -
27G GLN 3.2 2.0 + - - -
28G LEU* 1.3 78.7 - - - +
30G PHE* 1.3 64.8 + - - +
31G LYS 3.8 1.4 + - - -
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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