Contacts of the helix formed by residues 14 - 25 (chain A) in PDB entry 4L5L
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 ALA 14 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A LEU* 4.7 9.9 - - + -
7A TYR* 3.3 39.7 - - + -
11A ARG 3.1 2.2 + - - -
13A LEU* 1.3 78.4 - - - +
15A GLN* 1.3 67.2 + - - +
16A PRO 3.3 1.3 - - - -
17A ILE* 2.9 23.2 + - + +
18A ARG* 3.0 28.2 + - + +
56A PRO* 4.8 5.6 - - + -
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Residues in contact with GLN 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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11A ARG* 3.0 28.7 + - - +
12A GLY 4.1 0.2 - - - +
14A ALA* 1.3 77.1 - - - +
16A PRO* 1.4 64.3 - - + +
18A ARG* 2.9 36.1 + - - +
19A LEU* 2.8 44.1 + - + +
157A GLU* 3.4 34.4 + - + +
192A PHE* 5.0 1.5 - - - -
198A PHE* 3.2 28.6 - - - -
199A ILE* 3.1 26.0 + - - +
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Residues in contact with PRO 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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12A GLY 4.1 5.2 - - - +
13A LEU* 3.5 16.2 - - - +
14A ALA 3.4 4.0 - - - -
15A GLN* 1.4 92.8 - - + +
17A ILE* 1.3 55.2 + - - +
19A LEU* 3.8 10.7 - - + +
20A LEU* 2.9 30.0 + - - +
72A LEU* 3.7 11.3 - - + +
153A PHE* 3.9 7.0 - - + +
154A MET* 3.8 44.6 - - + +
157A GLU* 4.2 10.5 - - + -
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Residues in contact with ILE 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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5A LEU* 3.8 31.9 - - + -
13A LEU 4.1 16.8 - - - +
14A ALA* 2.9 12.6 + - - +
16A PRO* 1.3 72.8 - - - +
18A ARG* 1.3 66.7 + - - +
20A LEU* 3.3 2.8 + - - +
21A LEU* 3.0 29.7 + - + +
56A PRO* 4.4 6.7 - - + -
68A SER* 3.9 21.3 - - - +
71A ILE* 4.0 14.4 - - + -
72A LEU* 3.7 30.1 - - + +
75A ILE* 3.8 24.9 - - + -
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Residues in contact with ARG 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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5A LEU* 4.0 11.7 - - + -
7A TYR* 3.7 11.5 - - - +
8A TRP 3.3 17.4 + - - -
10A ILE 2.9 29.4 + - - -
11A ARG 3.4 11.9 + - - -
14A ALA* 3.0 20.3 + - - +
15A GLN* 2.9 36.5 + - - +
17A ILE* 1.3 75.7 - - - +
19A LEU* 1.3 62.9 + - - +
21A LEU* 3.4 6.5 + - - +
22A GLU* 3.1 28.8 + - - +
28A TYR* 4.5 7.9 - - + +
30A GLU* 2.9 37.6 + - - +
32A SER* 5.1 1.8 + - - -
192A PHE* 4.1 20.9 - - + -
197A ARG 5.7 0.9 - - - -
199A ILE* 3.5 20.4 - - - +
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Residues in contact with LEU 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 GLN* 2.8 42.5 + - + +
16A PRO* 3.8 4.5 - - + +
18A ARG* 1.3 73.8 - - - +
20A LEU* 1.3 57.1 + - - +
22A GLU* 3.5 0.4 + - - -
23A TYR* 2.9 24.4 + - - +
153A PHE* 3.8 31.0 - - + +
156A TYR* 3.9 26.9 - - + -
157A GLU* 4.4 2.2 - - + +
183A ILE* 5.9 0.2 - - + -
189A ILE* 3.2 25.8 - - + +
192A PHE* 3.8 26.0 - - + -
193A MET* 4.1 21.8 - - + -
198A PHE* 4.9 2.5 - - + -
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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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16A PRO 2.9 17.2 + - - +
17A ILE 3.7 3.1 - - - +
19A LEU* 1.3 76.6 - - - +
21A LEU* 1.3 57.8 + - - +
23A TYR* 3.2 2.3 + - - +
24A VAL* 2.9 33.1 + - + +
72A LEU* 3.8 34.5 - - + +
75A ILE* 3.7 28.7 - - + -
76A ALA* 4.1 4.7 - - - +
79A HIS* 6.0 0.2 - - - +
81A MET* 3.9 30.3 - - + -
150A HIS* 3.9 11.2 - - + +
153A PHE* 3.9 30.4 - - + -
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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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5A LEU* 4.5 6.1 - - + -
17A ILE* 3.0 38.3 + - + +
18A ARG 3.9 1.3 - - - +
20A LEU* 1.3 75.5 - - - +
22A GLU* 1.3 53.2 + - - +
24A VAL* 3.4 4.1 + - - +
25A GLY* 2.8 29.6 + - - -
26A ASP* 3.0 33.3 + - + +
27A SER 5.3 0.7 - - - +
28A TYR* 3.9 48.7 - - + -
58A TYR* 5.1 12.6 - - + +
75A ILE* 3.9 34.5 - - + -
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Residues in contact with GLU 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 ARG 3.1 18.0 + - - +
19A LEU 3.8 2.9 - - - +
21A LEU* 1.3 73.2 - - - +
23A TYR* 1.3 67.5 + - - +
25A GLY* 3.1 8.5 + - - +
28A TYR* 2.4 33.4 + - - +
188A ASN* 3.1 27.2 + - - +
189A ILE* 4.6 1.8 - - + -
192A PHE* 3.4 41.4 - - + +
197A ARG* 2.7 38.1 + - - -
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Residues in contact with TYR 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 LEU 2.9 14.6 + - - +
20A LEU* 3.2 3.8 + - + +
22A GLU* 1.3 77.6 - - - +
24A VAL* 1.3 73.0 + - + +
81A MET* 4.4 6.5 - - + -
147A THR* 4.7 4.2 - - - +
148A PRO* 3.4 49.5 + - + +
153A PHE* 3.4 35.4 - + + -
186A LEU* 4.1 11.0 - - + -
188A ASN* 3.0 20.8 + - - -
189A ILE* 3.8 8.4 - - + +
303A MES 3.3 68.8 + - + +
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Residues in contact with VAL 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 LEU* 2.9 29.8 + - + +
21A LEU* 3.6 7.6 - - - +
23A TYR* 1.3 88.8 - - + +
25A GLY* 1.3 62.0 + - - +
26A ASP* 3.5 19.6 + - - +
75A ILE* 4.7 3.8 - - + -
79A HIS* 3.5 41.3 - - + +
81A MET* 3.7 22.4 - - + -
302A ZN 3.9 3.1 - - - -
303A MES 3.4 28.5 - - - +
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Residues in contact with GLY 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 2.8 9.9 + - - -
22A GLU* 3.1 12.7 + - - -
23A TYR 3.2 0.2 - - - -
24A VAL* 1.3 79.9 - - - +
26A ASP* 1.3 63.1 + - - +
27A SER 3.9 0.2 + - - -
188A ASN* 4.3 7.6 - - - -
303A MES 5.4 0.4 - - - -
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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