Contacts of the helix formed by residues 13 - 24 (chain D) in PDB entry 2WJZ
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 ILE 13 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5D ILE* 5.0 4.4 - - + +
6D ILE 4.3 5.4 - - - +
7D SER* 3.9 35.7 - - - +
9D GLY* 4.4 11.2 - - - +
10D PRO 4.4 9.4 - - - +
11D GLY 3.5 9.8 + - - +
12D ASN* 1.3 75.9 - - - +
14D MET* 1.3 85.1 + - + +
15D ASN 3.3 2.9 - - - -
16D LEU* 3.1 14.2 + - - +
17D TYR* 3.1 19.8 + - - +
34D LEU* 4.1 9.4 - - + -
49D PRO* 3.9 32.3 - - + -
50D GLY 4.7 3.4 - - - +
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Residues in contact with MET 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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12D ASN* 3.5 8.1 + - - +
13D ILE* 1.3 93.7 - - + +
15D ASN* 1.3 59.4 + - - +
16D LEU 3.1 1.6 - - - -
17D TYR* 3.6 37.7 - - + +
18D ARG* 2.9 61.1 + - + +
34D LEU* 4.2 18.2 - - + -
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Residues in contact with ASN 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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70C ALA* 3.0 19.4 - - - +
73C ILE* 4.7 6.1 - - - +
77C PHE* 5.7 1.2 - - - -
96C GLY 4.3 15.0 + - - -
98C ASP* 4.8 12.1 + - - -
12D ASN* 3.0 25.9 + - - +
14D MET* 1.3 77.2 - - - +
16D LEU* 1.3 57.5 + - - +
18D ARG* 2.9 25.4 + - - +
19D GLY 3.0 20.8 + - - -
22D ARG* 5.1 3.1 + - - -
180D GLU* 3.3 31.1 - - + +
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Residues in contact with LEU 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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5D ILE* 4.1 11.7 - - + -
12D ASN 5.2 1.3 + - - +
13D ILE* 3.1 15.1 + - - +
15D ASN* 1.3 78.0 - - - +
17D TYR* 1.3 66.9 + - - +
19D GLY 3.1 0.5 + - - -
20D VAL* 2.9 41.7 + - + +
47D PHE* 4.5 14.4 - - + -
49D PRO* 3.9 31.4 - - + -
83D VAL* 4.6 22.0 - - + -
179D PRO* 5.7 1.6 - - + -
180D GLU* 3.9 29.0 + - + +
190D LEU* 4.8 12.8 - - + -
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Residues in contact with TYR 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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5D ILE* 3.7 20.1 - - + +
13D ILE 3.1 8.6 + - - +
14D MET* 3.2 39.9 + - + +
16D LEU* 1.3 74.9 - - - +
18D ARG* 1.3 66.6 + - + +
20D VAL* 3.3 1.2 + - - +
21D LYS* 2.8 61.3 + - + +
32D ILE* 4.2 28.4 + - + +
34D LEU* 3.9 31.9 - - + -
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Residues in contact with ARG 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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67C GLU 5.7 0.6 + - - -
70C ALA* 3.5 16.6 + - - +
71C GLU* 3.4 41.6 - - - +
95C ARG 5.9 1.2 + - - -
12D ASN* 4.7 5.5 + - - +
14D MET* 2.9 40.8 + - + +
15D ASN* 2.9 46.5 + - - +
17D TYR* 1.3 90.2 - - + +
19D GLY* 1.3 56.2 + - - +
21D LYS* 3.4 4.9 + - - +
22D ARG* 2.9 44.5 + - - +
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Residues in contact with GLY 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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15D ASN 3.0 15.1 + - - -
16D LEU 3.1 3.1 + - - -
18D ARG* 1.3 75.8 - - - +
20D VAL* 1.3 56.5 + - - +
22D ARG* 3.3 24.5 + - - +
23D ALA* 3.0 27.4 + - - +
180D GLU* 4.4 5.4 - - - -
187D ARG* 5.3 1.9 - - - +
190D LEU* 3.7 18.2 - - - +
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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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3D ILE* 4.2 21.3 - - + -
5D ILE* 4.1 9.0 - - + -
16D LEU* 2.9 36.3 + - + +
17D TYR 3.7 3.1 - - - +
19D GLY* 1.3 73.1 - - - +
21D LYS* 1.3 63.8 + - - +
22D ARG 3.1 1.6 - - - -
23D ALA* 3.2 5.9 + - - +
24D SER* 2.9 23.4 + - - -
32D ILE* 3.5 28.0 - - + -
47D PHE* 3.8 24.9 - - + -
190D LEU* 4.6 8.5 - - + -
194D ILE* 4.6 5.3 - - + +
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Residues in contact with LYS 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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17D TYR* 2.8 53.0 + - + +
18D ARG* 3.8 5.4 - - - +
20D VAL* 1.3 73.2 - - - +
22D ARG* 1.3 62.2 + - - +
24D SER* 3.0 21.3 + - - +
25D GLU* 3.5 12.2 + - - +
32D ILE* 3.5 14.1 - - + +
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Residues in contact with ARG 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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70C ALA 5.4 0.8 + - - -
71C GLU 4.5 4.9 + - - -
72C GLN* 3.9 22.7 + - - +
73C ILE 4.3 10.5 + - - -
74C ASP* 3.9 28.1 - - - +
15D ASN* 5.1 2.8 + - - -
18D ARG* 2.9 38.1 + - - +
19D GLY* 3.3 31.6 + - - +
20D VAL 3.1 0.2 - - - -
21D LYS* 1.3 77.0 - - - +
23D ALA* 1.3 62.0 + - - +
25D GLU* 3.3 38.6 + - - +
180D GLU* 4.3 9.5 + - - +
187D ARG* 3.6 32.2 - - + +
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Residues in contact with ALA 23 (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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19D GLY 3.0 15.9 + - - +
20D VAL* 3.2 4.5 + - - +
22D ARG* 1.3 76.7 - - - +
24D SER* 1.3 60.0 + - - +
25D GLU 3.2 2.0 + - - -
26D ASN* 4.4 1.0 + - - -
27D PHE* 3.5 19.9 - - - -
187D ARG* 3.7 29.3 + - + +
190D LEU* 3.8 27.1 - - + -
191D GLU* 3.9 12.9 - - + +
194D ILE* 4.2 7.0 - - + -
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Residues in contact with SER 24 (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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3D ILE* 4.9 1.8 - - - -
20D VAL 2.9 15.2 + - - -
21D LYS* 3.0 19.6 + - - +
23D ALA* 1.3 76.4 - - - +
25D GLU* 1.3 65.4 + - - +
26D ASN 3.4 1.1 - - - -
27D PHE* 3.0 30.3 + - - +
30D VAL* 3.7 30.2 - - - +
32D ILE* 3.6 11.9 - - - +
194D ILE* 4.0 13.7 - - - +
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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