Contacts of the helix formed by residues 16 - 29 (chain A) in PDB entry 1W4Z
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 SER 16 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A GLY 4.2 2.6 - - - +
14A ALA 3.3 1.6 + - - -
15A THR* 1.3 84.8 - - - +
17A GLY* 1.3 76.3 + - - +
18A ILE 3.4 1.7 + - - -
19A GLY* 3.5 4.5 + - - -
20A LEU* 3.2 20.5 + - - +
193A PRO* 3.2 18.2 - - - +
1262A NAP 2.9 40.8 + - - +
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Residues in contact with GLY 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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16A SER* 1.3 76.7 + - - +
18A ILE* 1.3 63.8 + - - -
20A LEU* 3.4 6.4 + - - +
21A GLU* 3.1 22.9 + - - +
24A ARG* 5.4 1.0 + - - -
192A THR* 4.0 16.8 - - - -
193A PRO* 4.2 4.3 - - - +
229A PRO* 4.3 7.4 - - - +
1262A NAP 3.6 11.9 - - - -
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Residues in contact with ILE 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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17A GLY* 1.3 69.3 - - - -
19A GLY* 1.3 59.2 + - - +
21A GLU* 3.1 4.3 + - - +
22A ILE* 2.8 44.1 + - + +
90A ASN* 3.4 17.9 - - - +
142A ILE* 4.8 3.6 - - + -
187A PRO* 4.4 5.2 - - + -
190A VAL* 3.8 37.9 - - + -
192A THR* 4.1 2.0 - - + -
229A PRO* 4.4 10.8 - - + +
232A VAL* 3.9 25.1 - - + -
1262A NAP 2.9 54.8 + - + +
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Residues in contact with GLY 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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11A VAL* 4.0 7.4 - - - +
13A GLY 3.6 6.1 - - - -
14A ALA* 3.5 18.0 - - - +
16A SER 3.5 3.0 + - - -
18A ILE* 1.3 77.1 - - - +
20A LEU* 1.3 62.1 + - - +
22A ILE* 3.2 4.3 + - - +
23A ALA 2.9 19.6 + - - -
90A ASN* 3.2 32.2 - - - +
1262A NAP 4.4 0.2 + - - -
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Residues in contact with LEU 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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14A ALA* 3.5 18.0 - - - +
15A THR 4.0 15.9 - - - +
16A SER* 3.2 22.9 + - - +
17A GLY 3.5 10.3 - - - +
18A ILE 3.2 0.6 - - - -
19A GLY* 1.3 75.2 - - - +
21A GLU* 1.3 58.9 + - - +
23A ALA* 3.2 4.8 + - + +
24A ARG* 2.9 57.4 + - + +
46A THR* 3.9 19.1 - - + -
49A GLU* 4.1 19.3 - - - +
50A LEU* 4.8 9.4 - - + -
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Residues in contact with GLU 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 GLY 3.1 10.2 + - - +
18A ILE 3.1 7.9 + - - +
20A LEU* 1.3 76.0 - - - +
22A ILE* 1.3 65.0 + - - +
24A ARG* 2.7 44.8 + - - +
25A ARG* 3.0 24.9 + - - +
229A PRO* 3.7 15.4 - - + +
230A SER* 3.6 43.2 - - - +
233A ALA* 3.8 4.3 - - + +
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Residues in contact with ILE 22 (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 VAL* 4.3 8.1 - - + -
18A ILE* 2.8 42.0 + - + +
19A GLY* 3.2 6.7 + - - +
21A GLU* 1.3 76.7 - - - +
23A ALA* 1.3 65.8 + - - +
25A ARG* 3.0 3.4 + - + +
26A LEU* 2.8 45.6 + - + +
88A VAL* 4.2 21.3 - - + -
90A ASN* 4.5 2.0 - - - +
142A ILE* 4.0 13.5 - - + -
232A VAL* 4.5 1.6 - - + -
233A ALA* 4.0 24.5 - - + -
236A VAL* 3.9 26.2 - - + -
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Residues in contact with ALA 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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11A VAL* 4.7 4.7 - - + +
14A ALA* 4.3 4.3 - - + +
19A GLY 2.9 12.5 + - - +
20A LEU* 3.4 10.1 - - - +
22A ILE* 1.3 78.6 - - - +
24A ARG* 1.3 61.9 + - - +
26A LEU* 4.6 1.1 - - - +
27A GLY* 2.9 22.3 + - - -
33A VAL* 4.0 17.9 - - + +
35A VAL* 4.0 26.9 - - + -
50A LEU* 4.1 18.1 - - + +
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Residues in contact with ARG 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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17A GLY 5.4 0.8 + - - -
20A LEU* 2.9 43.6 + - + +
21A GLU* 2.7 45.8 + - - +
22A ILE 3.2 0.4 - - - -
23A ALA* 1.3 75.2 - - - +
25A ARG* 1.3 59.1 + - - +
27A GLY* 3.6 1.4 - - - -
28A LYS* 2.8 29.9 + - - +
49A GLU* 2.2 38.4 + - + +
50A LEU* 3.9 20.2 - - + +
55A VAL* 4.5 5.3 - - + +
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Residues in contact with ARG 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 GLU* 3.0 16.7 + - - +
22A ILE* 3.0 7.9 + - + +
24A ARG* 1.3 75.3 - - - +
26A LEU* 1.3 65.3 + - + +
28A LYS* 3.1 14.8 + - - +
29A GLU* 2.3 68.5 + - - +
230A SER* 5.6 1.1 - - - +
233A ALA* 4.0 25.6 - - + +
234A GLU* 2.7 45.6 + - - +
237A ALA* 3.5 20.9 - - + +
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Residues in contact with LEU 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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9A ALA* 3.7 24.2 - - + -
11A VAL* 4.0 11.0 - - + -
22A ILE* 2.8 41.4 + - + +
23A ALA* 4.2 2.9 - - - +
25A ARG* 1.3 74.6 - - + +
27A GLY* 1.3 63.8 + - - +
29A GLU* 2.9 17.6 + - + +
30A GLY 3.1 8.8 + - - -
31A LEU* 3.1 19.7 + - + +
33A VAL* 4.2 11.7 - - + -
86A VAL* 4.3 13.0 - - + -
88A VAL* 4.3 3.1 - - + -
233A ALA 6.1 0.2 - - - +
236A VAL* 4.8 8.3 - - + -
237A ALA* 5.1 8.3 - - + -
240A ILE* 3.7 31.2 - - + -
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Residues in contact with GLY 27 (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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23A ALA 2.9 17.8 + - - -
24A ARG 3.6 1.3 - - - -
26A LEU* 1.3 78.8 - - - +
28A LYS* 1.3 61.7 + - - +
30A GLY* 3.1 14.2 + - - -
31A LEU 4.0 4.7 - - - +
33A VAL* 3.8 7.7 - - - +
55A VAL* 3.8 34.9 - - - +
56A GLU 5.6 0.2 + - - -
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Residues in contact with LYS 28 (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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24A ARG 2.8 20.3 + - - +
25A ARG* 3.1 16.8 + - - +
27A GLY* 1.3 73.5 - - - +
29A GLU* 1.3 68.7 + - - +
30A GLY* 3.1 1.8 + - - -
55A VAL* 4.3 2.4 - - - +
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Residues in contact with GLU 29 (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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25A ARG* 2.3 50.1 + - - +
26A LEU* 2.9 16.1 + - + +
28A LYS* 1.3 82.7 - - - +
30A GLY* 1.3 57.2 + - - +
31A LEU* 3.6 13.7 - - + +
237A ALA* 5.1 5.3 - - + +
240A ILE* 5.5 7.2 - - + -
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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