Contacts of the helix formed by residues 6 - 22 (chain D) in PDB entry 4ZM0
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 PHE 6 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5D ASN* 1.3 71.2 - - - +
7D ARG* 1.3 55.6 + - - +
9D ALA* 3.0 8.1 + - - +
10D ARG* 2.8 37.0 + - - +
28D ILE* 5.6 2.5 - - - -
29D THR 2.8 18.7 + - - +
30D ARG* 3.9 14.6 - - + +
5E G 3.0 31.0 + - + +
6E T 4.9 3.6 - - + +
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Residues in contact with ARG 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D ASN* 3.3 11.7 - - - +
6D PHE* 1.3 70.3 - - - +
8D THR* 1.4 58.4 + - - +
10D ARG* 3.6 2.7 + - - +
11D GLY* 3.1 24.9 + - - -
4E T 3.3 40.6 + - + +
5E G 2.7 64.1 + - + +
6E T 3.8 21.6 + - + +
9F C 4.0 13.5 - - - +
10F A 3.8 16.4 + - - +
11F C 5.1 0.4 - - - +
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Residues in contact with THR 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D ILE* 4.4 18.2 - - + -
5D ASN* 2.7 34.3 + - - +
6D PHE 3.2 0.4 - - - -
7D ARG* 1.4 73.0 - - - +
9D ALA* 1.3 60.2 + - - +
11D GLY* 3.4 1.0 + - - -
12D ASN* 2.9 47.5 + - + +
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Residues in contact with ALA 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D ILE* 3.5 25.9 - - + +
5D ASN 2.8 14.9 + - - +
6D PHE* 3.3 12.6 - - - +
8D THR* 1.3 73.9 - - - +
10D ARG* 1.3 54.2 + - - +
12D ASN 2.9 3.3 + - - -
13D LEU* 2.6 38.3 + - - -
16D VAL* 4.5 8.3 - - + -
28D ILE* 4.4 12.6 - - + -
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Residues in contact with ARG 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C ARG* 3.3 40.1 - - + +
13C LEU* 4.7 20.0 - - + -
6D PHE 2.8 19.4 + - - +
7D ARG* 4.0 4.9 - - - +
9D ALA* 1.3 72.7 - - - +
11D GLY* 1.3 58.7 + - - +
12D ASN 3.5 0.5 + - - -
13D LEU* 3.9 4.5 + - - -
6E T 5.2 9.4 - - + -
7F T 4.9 0.3 - - - +
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Residues in contact with GLY 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D ARG 3.1 15.3 + - - -
8D THR* 3.8 3.1 - - - -
9D ALA 3.2 0.2 - - - -
10D ARG* 1.3 75.6 - - - +
12D ASN* 1.4 71.8 + - - +
13D LEU 3.8 0.2 - - - -
6F G 5.0 4.9 + - - +
7F T 3.6 27.7 - - - +
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Residues in contact with ASN 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D THR* 2.9 27.7 + - + +
9D ALA 2.9 5.2 + - - -
11D GLY* 1.4 86.5 + - - +
13D LEU* 1.4 52.7 - - - +
14D SER* 3.2 3.1 - - - -
15D GLU* 2.8 52.6 + - + +
16D VAL* 2.9 17.0 + - + +
6F G 5.2 6.5 + - - -
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Residues in contact with LEU 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C PHE* 3.6 23.0 - - + -
10C ARG* 4.2 10.5 - - + +
9D ALA 2.6 19.5 + - - +
10D ARG* 3.9 11.6 + - - +
11D GLY 3.8 1.0 - - - -
12D ASN* 1.4 69.4 - - - +
14D SER* 1.4 55.8 + - - +
16D VAL* 3.6 8.0 - - - +
17D LEU* 2.8 31.9 + - - +
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Residues in contact with SER 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C PHE* 3.0 20.2 - - - -
30C ARG* 3.7 5.1 + - - +
12D ASN 3.0 1.0 + - - -
13D LEU* 1.4 75.0 - - - +
15D GLU* 1.3 58.7 + - - +
17D LEU* 3.2 2.4 + - - -
18D ASN* 2.9 37.2 + - - -
5F T 2.9 51.4 + - - +
6F G 3.7 19.2 + - - -
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Residues in contact with GLU 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D ASN* 2.8 37.4 + - + +
14D SER* 1.3 73.1 - - - +
16D VAL* 1.3 60.0 - - + +
18D ASN* 3.5 10.5 + - + +
19D ASN* 3.0 42.6 + - - +
6F G 5.1 5.9 + - - +
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Residues in contact with VAL 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D GLN* 5.7 3.1 - - - +
4D ILE* 4.4 19.7 - - + -
9D ALA* 4.3 10.1 - - + +
12D ASN* 2.9 28.7 + - + +
13D LEU* 3.6 10.8 - - - +
15D GLU* 1.3 75.9 - - + +
17D LEU* 1.4 53.6 + - - +
19D ASN* 3.1 10.7 + - - +
20D VAL* 2.8 41.5 + - + +
26D VAL* 3.9 30.1 - - + -
38D ILE* 4.7 10.8 - - + -
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Residues in contact with LEU 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C PHE* 5.4 3.4 - - + -
28C ILE* 6.4 1.6 - - + -
30C ARG* 3.6 31.8 + - + +
36C ALA* 5.3 10.2 - - + +
13D LEU 2.8 21.0 + - - +
14D SER 3.8 0.4 - - - +
16D VAL* 1.4 72.0 - - - +
18D ASN* 1.4 57.0 + - - +
20D VAL* 3.5 11.1 + - - +
21D GLU* 3.0 29.1 + - - +
38D ILE* 6.3 0.7 - - - -
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Residues in contact with ASN 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C ARG* 2.8 25.1 + - - +
33C ARG* 3.1 25.3 + - - +
14D SER* 2.9 28.2 + - - +
15D GLU* 3.7 10.6 - - + +
16D VAL 3.2 0.2 - - - -
17D LEU* 1.4 75.1 - - - +
19D ASN* 1.4 63.1 + - - +
21D GLU* 3.3 7.3 + - - +
22D ALA* 3.1 22.1 + - - +
5F T 4.8 3.7 + - - -
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Residues in contact with ASN 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D GLN* 3.6 33.0 + - - +
15D GLU* 3.0 32.8 + - - +
16D VAL* 3.3 11.4 - - - +
18D ASN* 1.4 73.6 - - - +
20D VAL* 1.3 63.9 + - - +
22D ALA* 3.1 19.7 + - - +
24D GLU* 3.2 24.7 + - + +
26D VAL* 4.5 3.8 - - + -
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Residues in contact with VAL 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C ALA* 3.9 15.9 - - + -
16D VAL* 2.8 24.1 + - + +
17D LEU* 3.6 7.4 - - - +
19D ASN* 1.3 72.3 - - - +
21D GLU* 1.4 56.7 + - - +
23D GLY* 2.9 20.6 + - - -
24D GLU 3.2 16.1 - - - +
26D VAL* 3.8 14.4 - - + -
38D ILE* 3.3 32.5 - - + +
39D VAL* 3.4 9.4 - - - +
40D SER* 3.2 38.6 + - - +
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Residues in contact with GLU 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C ARG* 3.8 5.6 + - - +
33C ARG* 3.0 37.7 + - - +
34C GLU* 3.5 46.7 + - + +
17D LEU 3.0 17.1 + - - +
18D ASN 3.3 6.3 + - - +
20D VAL* 1.4 75.2 - - - +
22D ALA* 1.3 57.2 + - - +
23D GLY* 3.1 4.4 + - - -
40D SER* 4.4 13.0 + - - -
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Residues in contact with ALA 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D ASN 3.1 11.2 + - - +
19D ASN* 3.1 16.4 + - - +
21D GLU* 1.3 74.9 - - - +
23D GLY* 1.3 57.6 + - - +
24D GLU* 3.6 1.5 + - + +
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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