Contacts of the helix formed by residues 13 - 24 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F ILE* 4.9 4.1 - - + +
6F ILE 4.3 7.4 - - - +
7F SER* 3.9 23.6 - - - +
9F GLY* 4.6 13.9 - - - +
10F PRO 4.7 2.9 - - - +
11F GLY 3.5 11.6 + - - +
12F ASN* 1.3 73.9 - - - +
14F MET* 1.3 85.6 + - + +
15F ASN 3.3 2.5 - - - -
16F LEU* 3.1 13.4 + - - +
17F TYR* 3.1 19.4 + - - +
34F LEU* 3.8 22.2 - - + -
49F PRO* 3.9 30.7 - - + -
50F GLY* 4.7 6.1 - - - +
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Residues in contact with MET 14 (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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12F ASN* 3.5 8.5 + - - +
13F ILE* 1.3 94.4 - - + +
15F ASN* 1.3 60.6 + - - +
16F LEU 3.1 1.3 - - - -
17F TYR* 3.2 38.6 + - + +
18F ARG* 2.9 61.4 + - - +
34F LEU* 4.2 18.4 - - + -
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Residues in contact with ASN 15 (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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70E ALA* 4.1 13.3 - - - +
73E ILE* 6.0 0.3 - - - +
77E PHE* 5.5 1.2 - - - -
96E GLY 3.6 19.1 + - - +
97E ALA 5.4 0.2 - - - -
98E ASP* 3.6 25.3 + - - +
12F ASN* 3.0 25.1 + - - +
14F MET* 1.3 77.1 - - - +
16F LEU* 1.3 57.4 + - - +
18F ARG* 2.9 22.6 + - - +
19F GLY* 3.0 20.4 + - - -
22F ARG* 5.1 2.8 + - - -
180F GLU* 3.3 32.2 - - + +
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Residues in contact with LEU 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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5F ILE* 4.1 12.1 - - + -
12F ASN 5.2 1.0 + - - +
13F ILE* 3.1 16.4 + - - +
14F MET 3.1 0.4 - - - -
15F ASN* 1.3 77.1 - - - +
17F TYR* 1.3 66.2 + - - +
19F GLY 3.2 0.2 + - - -
20F VAL* 2.9 41.9 + - + +
47F PHE* 4.5 14.6 - - + -
49F PRO* 3.9 32.3 - - + -
83F VAL* 4.6 20.9 - - + -
179F PRO* 5.7 1.8 - - + -
180F GLU* 3.9 27.4 + - + +
190F LEU* 4.8 12.6 - - + -
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Residues in contact with TYR 17 (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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5F ILE* 3.8 15.5 - - + +
13F ILE 3.1 7.7 + - - +
14F MET* 3.2 42.1 + - + +
16F LEU* 1.3 75.8 - - - +
18F ARG* 1.3 68.1 + - + +
20F VAL* 3.7 1.6 - - - +
21F LYS* 2.8 45.9 + - + +
32F ILE* 3.8 47.9 + - + +
33F GLU 5.8 0.2 - - - -
34F LEU* 4.4 23.6 - - + -
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Residues in contact with ARG 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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67E GLU* 5.6 2.2 + - - +
70E ALA* 3.3 30.6 - - - +
71E GLU* 3.7 19.3 - - - +
94E LEU 5.2 2.6 + - - -
95E ARG 4.1 16.0 + - - -
96E GLY* 4.4 6.5 - - - -
12F ASN* 4.7 2.4 + - - +
14F MET* 2.9 42.5 + - + +
15F ASN* 2.9 46.1 + - - +
17F TYR* 1.3 89.1 - - + +
19F GLY* 1.3 56.0 + - - +
21F LYS* 3.8 3.9 - - - +
22F ARG* 2.9 44.9 + - - +
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Residues in contact with GLY 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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15F ASN 3.0 15.4 + - - -
16F LEU 3.2 3.3 + - - -
18F ARG* 1.3 76.4 - - - +
20F VAL* 1.3 57.6 + - - +
22F ARG* 3.3 25.7 + - - +
23F ALA* 3.0 27.2 + - - +
180F GLU* 4.3 9.2 - - - -
187F ARG* 5.3 1.7 - - - +
190F LEU* 3.7 13.7 - - - +
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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
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3F ILE* 4.2 26.9 - - + -
5F ILE* 4.1 10.1 - - + -
16F LEU* 2.9 37.4 + - + +
17F TYR 3.7 2.9 - - - +
19F GLY* 1.3 72.8 - - - +
21F LYS* 1.3 65.8 + - - +
22F ARG 3.1 1.6 - - - -
23F ALA* 3.2 6.2 + - - +
24F SER* 2.9 22.7 + - - -
32F ILE* 3.9 22.0 - - + -
47F PHE* 3.8 24.5 - - + -
190F LEU* 4.6 7.6 - - + -
194F ILE* 4.6 5.8 - - + +
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Residues in contact with LYS 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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17F TYR* 2.8 38.7 + - + +
18F ARG* 3.8 5.2 - - - +
20F VAL* 1.3 72.4 - - - +
22F ARG* 1.3 62.0 + - - +
24F SER* 3.0 21.9 + - - +
25F GLU* 3.5 8.5 + - - +
32F ILE* 3.9 28.4 - - + +
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Residues in contact with ARG 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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70E ALA 3.7 16.6 + - - -
71E GLU 4.0 12.9 + - - +
72E GLN* 3.7 16.9 + - - +
73E ILE 3.3 23.9 + - - -
74E ASP* 4.0 22.0 - - - +
15F ASN* 5.1 2.0 + - - -
18F ARG* 2.9 28.8 + - - +
19F GLY* 3.3 31.3 + - - +
21F LYS* 1.3 79.9 - - - +
23F ALA* 1.3 60.6 + - - +
24F SER 3.4 0.3 + - - -
25F GLU* 3.5 17.7 - - - +
26F ASN* 5.8 0.5 + - - -
180F GLU* 4.3 11.9 + - - +
187F ARG* 4.0 29.8 + - + +
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Residues in contact with ALA 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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19F GLY 3.0 16.1 + - - +
20F VAL* 3.2 5.3 + - - +
22F ARG* 1.3 77.0 - - - +
24F SER* 1.3 60.4 + - - +
25F GLU* 3.2 2.1 + - - +
26F ASN* 4.4 4.3 + - - -
27F PHE* 3.5 19.6 - - - -
187F ARG* 4.1 19.7 - - + +
190F LEU* 3.8 26.7 - - + -
191F GLU* 3.9 19.0 - - + +
194F ILE* 4.2 7.0 - - + -
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Residues in contact with SER 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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3F ILE* 5.0 2.5 - - - -
20F VAL* 2.9 15.1 + - - -
21F LYS* 3.0 21.5 + - - +
22F ARG 3.3 0.2 - - - -
23F ALA* 1.3 76.4 - - - +
25F GLU* 1.3 64.9 + - - +
26F ASN 3.4 0.9 - - - -
27F PHE* 3.1 31.1 + - - +
30F VAL* 3.9 29.4 + - - +
32F ILE* 4.4 8.2 - - - +
194F ILE* 4.0 11.4 - - - +
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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