Contacts of the helix formed by residues 15 - 28 (chain F) in PDB entry 1ZMD
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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13F GLY 3.6 1.4 + - - -
14F SER* 1.3 78.8 - - - +
16F PRO* 1.4 70.6 - - - +
17F GLY 3.1 3.8 + - - -
18F GLY 3.2 1.5 + - - +
19F TYR* 2.8 29.3 + - - -
42F GLY 3.5 10.3 - - - -
480F FAD 3.2 28.5 + - - -
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Residues in contact with PRO 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452E HIS* 5.7 0.2 - - - +
15F GLY* 1.4 82.0 - - - +
17F GLY* 1.3 59.6 + - - +
19F TYR* 3.9 11.8 - - + -
20F VAL* 3.1 28.2 - - - +
42F GLY 3.7 8.9 - - - +
45F CYS* 3.3 32.1 - - + -
46F LEU* 4.8 4.7 - - + -
328F ALA* 3.8 14.8 - - + +
331F ALA* 4.5 0.4 - - + -
332F GLU* 3.2 29.1 - - + +
480F FAD 3.3 32.5 - - - +
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Residues in contact with GLY 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F PRO* 1.3 79.5 - - - +
18F GLY* 1.3 56.0 + - - -
20F VAL* 4.0 0.7 - - - +
21F ALA* 3.0 30.0 + - - +
318F ILE* 3.5 26.7 - - - +
331F ALA* 3.5 19.3 - - - +
335F GLY* 4.1 2.6 - - - -
480F FAD 2.9 14.2 + - - -
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Residues in contact with GLY 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F VAL* 3.4 19.0 - - - +
13F GLY 3.4 24.5 - - - -
15F GLY 3.2 5.0 + - - +
17F GLY* 1.3 73.8 - - - +
19F TYR* 1.3 59.3 + - - +
21F ALA* 4.3 1.1 - - - -
22F ALA* 2.9 31.1 + - - +
34F CYS* 4.8 0.2 - - - -
147F ALA* 3.7 12.7 - - - +
480F FAD 4.1 1.2 + - - -
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Residues in contact with TYR 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392E SER* 5.7 0.7 + - - -
452E HIS* 6.1 0.5 - - - -
472E ILE* 4.7 0.4 - - + -
473E ASN* 2.7 33.9 + - - -
14F SER* 3.6 15.1 - - - +
15F GLY 2.8 31.4 + - - -
16F PRO* 3.9 9.4 - - + -
18F GLY* 1.3 72.3 - - - -
20F VAL* 1.3 77.8 + - + +
23F ILE* 3.1 48.1 + - + +
42F GLY* 4.9 0.2 - - - -
46F LEU* 4.6 10.5 - - + +
103F ILE* 3.7 43.8 - - + +
106F LEU* 4.7 1.8 - - + -
107F PHE* 3.6 26.5 - - + -
332F GLU* 4.7 6.9 + - - -
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Residues in contact with VAL 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472E ILE* 4.1 20.9 - - + +
473E ASN* 5.4 0.4 - - - +
16F PRO 3.1 22.8 + - - +
17F GLY 4.0 1.1 - - - +
18F GLY 3.2 0.2 - - - -
19F TYR* 1.3 103.5 - - + +
21F ALA* 1.3 59.3 + - - +
23F ILE* 3.2 2.4 + - - +
24F LYS* 2.9 29.3 + - - +
332F GLU* 3.7 31.9 - - + +
336F ILE* 3.5 35.2 - - + -
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Residues in contact with ALA 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F VAL* 4.7 1.6 - - + -
17F GLY 3.0 20.1 + - - +
18F GLY 3.7 4.9 - - - +
20F VAL* 1.3 76.7 - - - +
22F ALA* 1.3 54.1 + - - +
24F LYS* 3.7 2.8 - - - +
25F ALA* 2.8 37.5 + - - +
145F LEU* 3.4 33.2 - - + -
335F GLY* 3.7 25.3 - - - +
339F VAL* 3.8 4.2 - - + +
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Residues in contact with ALA 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F VAL* 4.1 11.2 - - + +
18F GLY 2.9 18.4 + - - +
19F TYR 3.7 4.7 - - - +
21F ALA* 1.3 75.2 - - - +
23F ILE* 1.3 64.3 + - - +
25F ALA 3.5 0.2 + - - -
26F ALA 3.1 17.8 + - - -
32F THR* 3.6 23.9 - - + +
34F CYS* 4.1 13.7 - - + -
107F PHE* 4.1 15.0 - - + -
112F VAL* 3.5 13.7 - - + +
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Residues in contact with ILE 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472E ILE* 3.8 33.9 - - + +
19F TYR* 3.1 47.4 + - + +
20F VAL 3.2 3.8 + - - +
22F ALA* 1.3 74.2 - - - +
24F LYS* 1.3 59.6 + - - +
26F ALA* 3.2 5.0 + - - +
27F GLN* 2.8 52.8 + - - +
106F LEU* 3.8 20.6 - - + +
107F PHE* 4.0 16.8 - - + -
110F ASN* 3.9 16.9 - - - +
112F VAL* 4.2 6.5 - - + -
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Residues in contact with LYS 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464E LEU* 4.3 16.4 - - - +
468E PHE* 3.5 46.5 - - - -
472E ILE* 4.1 14.4 - - + -
20F VAL 2.9 16.5 + - - +
21F ALA 3.7 0.7 - - - +
23F ILE* 1.3 78.8 - - - +
25F ALA* 1.3 56.9 + - - +
27F GLN* 3.1 15.1 + - - +
28F LEU* 2.9 51.7 + - + +
336F ILE* 4.2 22.3 - - + +
339F VAL* 3.4 25.6 - - + -
340F GLU* 4.0 18.2 + - - -
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Residues in contact with ALA 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F VAL* 4.4 9.6 - - + -
21F ALA 2.8 21.6 + - - +
22F ALA 3.8 2.7 - - - +
23F ILE 3.3 0.2 - - - -
24F LYS* 1.3 73.1 - - - +
26F ALA* 1.3 60.6 + - - +
28F LEU* 3.2 7.5 + - - -
29F GLY 3.3 0.2 + - - -
30F PHE* 2.9 45.7 + - + +
32F THR* 3.6 20.0 - - + +
339F VAL* 4.0 17.4 - - + +
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Residues in contact with ALA 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F ALA 3.1 13.6 + - - +
23F ILE 3.2 7.2 + - - +
25F ALA* 1.3 75.8 - - - +
27F GLN* 1.3 57.8 + - - +
29F GLY* 2.9 21.3 + - - -
30F PHE 3.5 14.1 - - - +
32F THR* 3.5 7.1 + - - +
110F ASN* 3.1 30.5 - - + +
111F LYS* 4.9 2.2 - - + +
112F VAL* 3.9 12.8 - - + +
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Residues in contact with GLN 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468E PHE* 3.6 32.8 - - + -
470E LYS* 3.9 36.9 + - + +
471E SER 3.0 26.6 + - - +
472E ILE* 4.0 6.0 + - - +
474E PHE 5.5 0.6 + - - -
23F ILE* 2.8 28.0 + - - +
24F LYS* 3.1 20.4 + - - +
26F ALA* 1.3 78.2 - - - +
28F LEU* 1.3 58.4 + - - +
29F GLY* 3.3 1.0 + - - -
109F GLN* 6.1 0.8 - - - +
110F ASN* 3.3 28.0 + - - +
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Residues in contact with LEU 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468E PHE* 4.1 16.4 - - + -
24F LYS* 2.9 40.6 + - + +
25F ALA* 3.2 6.5 + - - +
27F GLN* 1.3 75.8 - - - +
29F GLY* 1.3 58.4 + - - +
30F PHE* 3.6 13.0 - - + -
339F VAL* 3.7 41.7 - - + +
340F GLU* 3.9 14.6 - - + +
343F ALA* 4.4 15.6 - - + +
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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