Contacts of the helix formed by residues 12 - 26 (chain A) in PDB entry 4WNC
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 12 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A GLY 3.2 7.5 + - - -
11A PHE* 1.3 75.6 - - - +
13A ARG* 1.3 68.2 + - - +
14A ILE 3.2 2.7 - - - -
15A GLY 3.9 2.2 - - - +
16A ARG* 2.8 36.0 + - - +
35A ASP* 5.3 0.2 - - - -
38A ILE* 5.5 0.7 - - - -
98A SER 5.3 3.1 + - - -
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Residues in contact with ARG 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLY* 1.3 70.1 - - - +
14A ILE* 1.3 63.2 + - + +
16A ARG* 3.2 28.3 - - - +
17A LEU* 3.0 41.0 + - - +
50A ASP* 2.7 44.6 + - - +
51A SER 5.5 0.8 - - - +
52A THR* 3.7 10.3 + - - -
53A HIS* 3.6 5.3 - - - -
183A ALA* 5.2 16.2 - - + +
317A GLU* 2.9 50.7 + - + +
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Residues in contact with ILE 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A GLY 3.2 0.4 - - - -
13A ARG* 1.3 81.2 - - + +
15A GLY* 1.3 61.7 + - - +
18A VAL* 2.7 51.7 + - + +
98A SER* 4.2 11.4 - - - +
122A SER* 4.0 28.0 - - - +
316A ASN 4.5 3.4 - - - +
317A GLU* 4.1 22.0 - - + +
320A TYR* 4.3 22.0 - - + -
321A SER* 3.8 15.0 + - - +
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Residues in contact with GLY 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A VAL* 3.7 10.3 - - - +
10A GLY 3.3 24.3 + - - -
11A PHE* 4.1 6.3 - - - -
12A GLY* 3.4 5.2 + - - +
14A ILE* 1.3 78.5 - - - +
16A ARG* 1.3 60.9 + - - +
18A VAL* 3.7 4.3 - - - +
19A THR* 3.0 27.4 + - - -
98A SER* 3.6 12.6 + - - -
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Residues in contact with ARG 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A PHE* 2.8 72.3 + - + +
12A GLY* 2.8 37.9 + - - +
13A ARG* 3.2 37.5 - - - +
15A GLY* 1.3 72.1 - - - -
17A LEU* 1.3 62.9 + - + +
19A THR* 3.3 4.2 + - - -
20A ARG* 2.9 24.6 + - - +
38A ILE* 4.6 0.8 - - - +
46A MET* 3.3 59.8 + - - +
47A PHE* 3.6 12.6 - - + +
50A ASP* 4.7 3.7 + - - +
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Residues in contact with LEU 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ARG* 3.0 27.0 + - - +
14A ILE* 5.4 0.2 - - - -
16A ARG* 1.3 79.0 - - + +
18A VAL* 1.3 59.4 + - - +
20A ARG* 3.3 27.8 + - - +
21A ALA* 2.8 29.8 + - - +
50A ASP* 4.4 9.4 - - - +
53A HIS* 3.7 22.9 - - + +
317A GLU* 3.5 46.9 - - + +
318A PHE* 4.3 15.1 - - + -
321A SER* 3.3 20.9 - - - +
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Residues in contact with VAL 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A VAL* 4.6 9.9 - - + -
14A ILE* 2.7 45.4 + - + +
15A GLY* 3.7 6.5 - - - +
17A LEU* 1.3 72.5 - - - +
19A THR* 1.3 59.9 + - - +
21A ALA* 3.2 2.4 + - - +
22A ALA* 2.9 28.2 + - - +
30A ILE* 4.8 4.3 - - + -
96A VAL* 4.3 26.2 - - + -
321A SER* 3.9 25.4 - - - +
324A VAL* 4.1 15.3 - - + -
325A VAL* 3.7 14.3 - - + +
328A MET* 4.6 3.1 - - + -
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Residues in contact with THR 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A VAL* 4.0 14.7 - - - +
11A PHE* 3.8 14.7 - - + -
15A GLY 3.0 14.5 + - - -
16A ARG 3.4 9.6 - - - -
18A VAL* 1.3 74.4 - - - +
20A ARG* 1.3 63.7 + - - +
22A ALA* 3.3 1.7 + - - +
23A PHE* 3.1 51.6 + - + -
30A ILE* 4.2 19.5 - - + +
33A ILE* 4.5 2.6 - - + +
47A PHE* 3.6 18.2 - - + -
69A ILE* 3.9 9.6 - - + -
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Residues in contact with ARG 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ARG* 2.9 12.9 + - - +
17A LEU* 3.3 25.8 + - + +
19A THR* 1.3 75.6 - - - +
21A ALA* 1.3 59.2 + - - +
23A PHE* 3.3 4.5 + - - +
24A ASN* 3.0 29.6 + - - +
47A PHE* 3.2 48.4 + - + -
48A GLN 3.8 2.0 + - - -
50A ASP* 3.6 17.9 + - - +
53A HIS* 3.7 19.7 + - - +
54A GLY 2.9 29.7 + - - -
55A LYS 4.1 1.6 + - - -
56A PHE* 3.3 35.8 - - + +
57A HIS 5.3 0.2 - - - +
318A PHE* 5.0 12.2 - - + -
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Residues in contact with ALA 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LEU 2.8 18.0 + - - +
18A VAL 3.6 4.7 - - - +
20A ARG* 1.3 75.6 - - - +
22A ALA* 1.3 57.2 + - - +
24A ASN* 3.8 5.4 - - - +
25A SER* 2.9 35.1 + - - -
318A PHE* 6.2 3.1 - - + -
321A SER 4.1 6.1 - - - +
322A ASN* 3.7 35.3 - - - +
325A VAL* 4.0 14.4 - - + -
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Residues in contact with ALA 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL 2.9 16.1 + - - +
19A THR 3.6 5.8 - - - +
20A ARG 3.2 0.2 - - - -
21A ALA* 1.3 77.8 - - - +
23A PHE* 1.3 58.0 + - + +
25A SER* 3.8 3.3 + - - -
26A GLY* 2.9 28.9 + - - -
27A LYS 4.1 0.2 + - - -
28A VAL* 3.8 30.9 - - + +
30A ILE* 3.6 25.6 - - + -
325A VAL* 3.9 9.8 - - + +
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Residues in contact with PHE 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A THR* 3.1 45.4 + - + +
20A ARG 4.0 3.4 - - - +
22A ALA* 1.3 79.9 - - + +
24A ASN* 1.3 61.6 + - - +
26A GLY* 4.0 5.1 + - - -
29A ASP* 6.0 1.3 - - - -
30A ILE* 4.0 26.0 - - + -
47A PHE* 5.0 0.9 - + - -
56A PHE* 4.7 10.5 - - + -
69A ILE* 3.5 39.9 - - + -
70A ASN* 4.1 22.1 + - - +
72A ASN* 3.4 34.5 - - + -
74A ILE* 4.0 11.2 - - + -
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Residues in contact with ASN 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ARG 3.0 18.3 + - - +
21A ALA* 3.8 6.7 - - - +
22A ALA 3.3 0.2 - - - -
23A PHE* 1.3 80.4 - - - +
25A SER* 1.3 60.6 + - - +
56A PHE* 6.1 0.2 - - - -
322A ASN* 5.7 0.7 - - - +
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Residues in contact with SER 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ALA 2.9 18.3 + - - -
22A ALA 3.8 1.2 + - - -
24A ASN* 1.3 79.1 - - - +
26A GLY* 1.3 64.4 + - - +
27A LYS* 3.1 40.3 + - - +
322A ASN* 5.2 7.9 - - - -
325A VAL* 3.8 9.4 - - - +
326A ASP* 5.9 0.2 - - - -
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Residues in contact with GLY 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A LYS 5.0 4.9 + - - -
22A ALA 2.9 14.8 + - - -
23A PHE* 4.0 4.4 + - - -
24A ASN 3.5 1.8 - - - -
25A SER* 1.3 76.1 - - - +
27A LYS* 1.3 62.0 + - - +
28A VAL* 3.3 8.3 + - - +
29A ASP* 5.3 2.7 - - - +
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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