Contacts of the helix formed by residues 14 - 25 (chain A) in PDB entry 4WLQ
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 ASP 14 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A GLU* 3.3 16.7 + - + +
13A SER* 1.3 77.2 - - - +
15A PRO* 1.3 75.9 - - - +
16A GLY* 2.8 10.4 + - - -
17A VAL* 2.8 45.4 + - + +
18A PHE* 2.9 36.8 + - - -
221A MET* 4.4 2.0 - - - -
280A TYR* 5.3 1.7 - - - -
283A GLU* 4.5 8.9 - - - +
287A ARG* 4.0 11.4 + - - -
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Residues in contact with PRO 15 (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 ASP* 1.3 94.8 - - - +
16A GLY* 1.3 56.8 + - - +
19A THR* 2.8 38.3 + - - -
32A VAL* 3.3 36.1 - - + +
33A GLU* 4.3 0.4 - - - -
34A GLU* 3.6 42.0 - - + +
221A MET* 4.3 6.3 - - + -
280A TYR* 3.8 14.1 - - + +
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Residues in contact with GLY 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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14A ASP* 2.8 8.2 + - - -
15A PRO* 1.3 77.4 - - - +
17A VAL* 1.3 64.7 + - - +
19A THR* 3.1 1.4 + - - -
20A GLU* 3.0 28.6 + - - +
280A TYR* 3.5 41.9 - - - -
283A GLU* 5.3 0.4 - - - -
284A ASN* 4.7 6.7 - - - -
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Residues in contact with VAL 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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11A MET* 3.9 25.8 - - + -
12A GLU* 3.8 21.5 - - + +
14A ASP* 2.8 32.6 + - + +
16A GLY* 1.3 75.7 - - - +
18A PHE* 1.3 59.8 + - + +
20A GLU* 3.6 0.5 + - - -
21A LEU* 2.9 28.4 + - - +
143A PHE* 4.1 21.2 - - + +
284A ASN* 4.3 8.0 + - - +
287A ARG* 3.2 37.5 - - - +
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Residues in contact with PHE 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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11A MET* 3.7 18.2 - - + -
12A GLU 4.0 2.7 - - - -
13A SER* 3.7 23.3 - - - -
14A ASP 2.9 33.5 + - - +
15A PRO 4.1 0.2 - - - +
16A GLY 3.3 0.2 - - - -
17A VAL* 1.3 76.4 - - + +
19A THR* 1.3 58.3 + - - +
21A LEU* 3.4 12.4 - - + +
22A ILE* 2.8 35.5 + - - +
32A VAL* 4.0 20.9 - - + -
53A ILE* 6.2 3.4 - - + -
89A ALA* 3.6 29.6 - - + -
93A ILE* 3.7 22.4 - - + -
165A PHE* 4.1 11.9 - + - -
221A MET* 3.7 26.9 - - + -
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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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15A PRO 2.8 23.0 + - - -
16A GLY* 3.1 7.3 + - - -
18A PHE* 1.3 75.0 - - - +
20A GLU* 1.3 70.0 + - + +
21A LEU 3.1 0.7 - - - -
22A ILE* 3.1 6.0 + - - +
23A LYS* 2.9 48.6 + - - +
30A ALA 4.9 0.6 - - - +
31A GLN* 3.9 18.3 - - + +
32A VAL* 3.0 29.0 + - - +
277A LEU* 5.8 0.7 - - + -
280A TYR* 4.7 12.5 - - + -
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Residues in contact with GLU 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 GLY 3.0 11.6 + - - +
19A THR* 1.3 78.6 - - + +
21A LEU* 1.3 51.4 + - - +
23A LYS* 2.9 21.0 + - + +
24A GLY* 2.6 33.8 + - - -
143A PHE* 3.5 27.5 - - + -
277A LEU* 4.7 4.8 - - + +
280A TYR* 5.3 7.0 - - + -
281A LYS* 3.0 46.4 + - - +
284A ASN* 3.2 28.2 + - - +
288A LYS* 4.8 3.3 + - - -
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Residues in contact with LEU 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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11A MET* 4.1 16.2 - - + -
17A VAL* 2.9 20.2 + - + +
18A PHE* 3.4 16.2 - - + +
19A THR 3.1 0.2 - - - -
20A GLU* 1.3 76.8 - - - +
22A ILE* 1.3 57.6 + - - +
24A GLY* 2.8 16.5 + - - -
25A PHE* 3.2 42.6 + - + -
90A THR* 4.1 10.5 - - - +
93A ILE* 3.8 28.9 - - + -
139A VAL* 4.1 5.2 - - + -
140A HIS* 4.1 14.1 - - - -
143A PHE* 3.8 29.1 - - + -
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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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18A PHE 2.8 17.0 + - - +
19A THR* 3.1 5.8 + - - +
21A LEU* 1.3 71.9 - - + +
23A LYS* 1.3 66.5 + - - +
24A GLY 3.2 0.5 + - - -
25A PHE* 3.3 12.8 + - + +
27A CYS* 3.1 48.1 + - + +
30A ALA* 4.6 15.7 - - + +
31A GLN 5.2 1.1 - - - +
32A VAL* 3.5 30.7 - - + -
93A ILE* 3.8 32.5 - - + -
97A LEU* 4.2 9.2 - - + -
223A ILE* 4.4 19.3 - - + -
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Residues in contact with LYS 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* 2.9 36.6 + - - +
20A GLU* 2.9 18.1 + - + +
22A ILE* 1.3 76.5 - - - +
24A GLY* 1.3 57.0 + - - +
26A GLY 3.1 7.1 + - - -
27A CYS 3.8 9.9 - - - +
28A ARG* 2.8 37.0 + - - +
30A ALA 5.0 9.9 - - - +
31A GLN* 5.7 1.1 - - - -
226A ASP* 5.9 3.8 - - - -
277A LEU* 3.2 41.2 - - - +
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Residues in contact with GLY 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 GLU 2.6 13.2 + - - -
21A LEU* 2.8 7.9 + - - -
23A LYS* 1.3 74.5 - - - +
25A PHE* 1.3 57.0 + - - +
26A GLY 3.0 8.3 + - - -
139A VAL* 3.8 28.4 - - - +
143A PHE* 5.0 3.4 - - - -
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Residues in contact with PHE 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 LEU* 3.2 39.3 + - + -
22A ILE* 3.3 12.7 + - - +
24A GLY* 1.3 74.9 - - - +
26A GLY* 1.3 59.0 + - - +
27A CYS 4.7 0.4 - - - +
90A THR* 3.9 27.1 - - + -
93A ILE* 4.5 17.7 - - + -
94A VAL* 4.6 4.7 - - + -
97A LEU* 5.1 0.9 - - + -
107A LEU 3.9 7.8 - - - +
110A THR* 3.5 31.5 + - + -
111A LEU* 3.9 34.5 + - + -
135A VAL* 6.3 0.2 - - - -
136A ILE* 3.6 28.5 - - + -
139A VAL* 3.6 31.9 - - + -
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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