Contacts of the helix formed by residues 14 - 28 (chain A) in PDB entry 4L8E
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 THR 14 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ALA* 2.9 15.4 + - + -
13A PRO* 1.3 80.5 - - + +
15A PRO* 1.3 77.2 - - - +
17A GLY 3.3 10.7 + - - -
18A TYR* 3.0 25.8 + - - -
38A ILE* 4.0 26.7 - - + -
57A ILE* 3.5 3.8 - - - +
301A GSH 3.9 6.1 - - - -
302A GSH 3.2 24.1 - - - -
303A GSH 4.0 10.3 - - - -
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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
----------------------------------------------------------
14A THR* 1.3 87.9 - - - +
16A ASN* 1.3 61.6 + - - +
18A TYR* 3.4 1.2 + - + -
19A LYS* 3.2 15.6 + - - +
173A PRO* 3.2 44.4 - - + +
174A TRP* 3.6 38.1 - - + +
177A CYS* 4.2 3.4 - - - -
301A GSH 4.2 6.1 - - - -
303A GSH 3.6 45.1 - - - +
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Residues in contact with ASN 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A THR* 3.2 1.6 + - - -
15A PRO* 1.3 73.6 - - - +
17A GLY* 1.3 65.7 + - - +
19A LYS* 2.9 45.5 + - - +
20A ILE* 4.0 0.9 - - - +
57A ILE 4.3 0.2 - - - +
58A PRO* 3.4 34.0 - - + +
77A SER* 4.7 0.7 - - - +
174A TRP* 3.0 16.6 + - - -
301A GSH 2.8 26.1 + - - +
302A GSH 3.3 47.2 + - + +
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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
----------------------------------------------------------
11A TYR* 3.7 21.5 - - - -
12A ALA 3.6 15.9 - - - -
14A THR* 3.1 13.0 + - - -
16A ASN* 1.3 76.5 - - - +
18A TYR* 1.3 61.5 + - - +
20A ILE* 3.1 15.2 + - - +
21A THR 3.3 8.7 + - - -
57A ILE* 4.0 9.6 - - - +
58A PRO* 4.6 7.2 - - - -
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Residues in contact with TYR 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A TYR* 3.3 23.0 + - - -
13A PRO* 3.6 23.0 - - + +
14A THR 3.0 25.7 + - - +
15A PRO 3.4 4.5 + - - +
17A GLY* 1.3 73.4 - - - +
19A LYS* 1.3 66.9 + - - +
21A THR* 3.5 7.6 - - - -
22A LEU* 2.8 28.4 + - - +
173A PRO* 4.1 1.8 - - + -
207A ALA* 3.4 25.6 - - + -
208A TYR* 3.4 61.5 + + + +
303A GSH 3.7 28.3 - - + +
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Residues in contact with LYS 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A PRO 3.2 12.2 + - - +
16A ASN* 2.9 32.0 + - - +
17A GLY 3.2 0.6 - - - -
18A TYR* 1.3 78.4 - - - +
20A ILE* 1.3 68.7 + - + +
22A LEU* 4.5 0.2 - - - -
23A PHE* 3.3 9.4 + - - +
77A SER* 2.9 33.0 + - - +
81A LEU* 3.8 9.3 - - + +
109A GLN* 2.8 29.9 + - - +
110A VAL* 4.2 3.0 - - - +
169A ILE* 3.1 41.9 - - - +
170A ALA* 3.2 28.9 - - + +
173A PRO* 3.9 6.5 - - + +
174A TRP* 3.9 5.4 - - - -
301A GSH 5.2 0.8 + - - -
302A GSH 3.9 4.2 + - - -
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Residues in contact with ILE 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 3.8 24.5 - - + -
16A ASN 4.0 2.7 - - - +
17A GLY 3.1 5.3 + - - +
18A TYR 3.1 0.6 - - - -
19A LYS* 1.3 76.8 - - - +
21A THR* 1.3 60.4 + - - +
23A PHE* 3.2 4.9 + - + +
24A LEU* 2.9 42.5 + - + +
58A PRO* 3.6 28.9 - - + -
60A ILE* 4.5 1.6 - - + -
77A SER* 3.8 26.7 - - - +
80A ILE* 3.7 33.4 - - + -
81A LEU* 3.9 16.6 - - + -
84A LEU* 4.3 6.5 - - + -
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Residues in contact with THR 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 3.6 25.1 - - + -
11A TYR* 3.7 21.1 - - + -
17A GLY 3.3 1.6 + - - -
18A TYR* 3.4 23.0 + - - -
20A ILE* 1.3 73.9 - - - +
22A LEU* 1.3 66.6 + - - +
24A LEU* 4.4 6.3 - - - +
25A GLU* 2.9 29.5 + - - +
31A TYR* 3.9 22.0 - - + +
33A ILE* 4.6 4.5 - - + -
207A ALA* 3.7 19.5 + - - +
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Residues in contact with LEU 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A TYR 2.8 25.2 + - - +
19A LYS 3.6 3.8 - - - +
21A THR* 1.3 78.2 + - - +
23A PHE* 1.3 61.0 + - - +
25A GLU* 3.8 2.3 - - - +
26A GLU* 2.9 33.5 + - + +
164A TYR* 4.5 10.3 - - - +
169A ILE* 4.0 22.0 - - + +
172A TYR* 4.1 15.0 - - + -
173A PRO* 3.8 24.9 - - + -
203A ALA* 4.1 1.9 - - + +
204A THR* 3.6 43.7 - - + +
207A ALA* 3.7 14.8 - - + -
208A TYR* 4.1 7.6 - - + -
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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 LYS 3.3 2.6 + - - +
20A ILE* 3.2 8.4 + - - +
22A LEU* 1.3 79.0 - - - +
24A LEU* 1.3 71.1 + - + +
26A GLU* 3.2 5.7 + - - +
27A VAL* 3.1 38.2 + - + +
29A LEU* 5.2 0.7 - - + -
81A LEU* 3.8 24.2 - - + -
84A LEU* 3.5 41.7 - - + -
85A ALA* 3.9 4.9 - - - -
88A THR* 3.7 25.8 - - + -
90A ARG 3.9 15.5 - - - -
91A PHE* 4.1 9.2 - + - -
166A ILE* 3.9 26.9 - - + -
169A ILE* 4.2 15.4 - - + +
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Residues in contact with LEU 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ILE* 4.8 10.1 - - + -
9A LEU* 4.1 11.7 - - + -
20A ILE* 2.9 37.4 + - + +
21A THR 4.0 1.3 - - - +
23A PHE* 1.3 78.8 - - + +
25A GLU* 1.3 58.5 + - - +
27A VAL* 5.0 0.4 - - - -
28A GLY* 2.8 26.3 + - - -
29A LEU* 3.3 46.7 + - + +
31A TYR* 3.6 50.2 - - + -
84A LEU* 4.1 16.8 - - + -
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Residues in contact with GLU 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 THR 2.9 22.8 + - - +
22A LEU 3.9 2.7 - - - +
24A LEU* 1.3 74.8 - - - +
26A GLU* 1.3 65.0 + - - +
28A GLY* 3.7 8.4 + - - -
31A TYR* 2.7 33.8 + - - +
203A ALA* 3.8 24.1 - - + +
206A ALA* 3.8 17.9 - - - +
207A ALA* 4.2 17.7 - - - +
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Residues in contact with GLU 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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22A LEU* 2.9 29.8 + - + +
23A PHE* 3.5 6.7 - - - +
25A GLU* 1.3 78.9 - - - +
27A VAL* 1.3 61.3 + - - +
90A ARG* 4.4 8.3 + - - -
91A PHE* 3.5 26.6 - - + -
164A TYR* 3.3 17.9 + - + +
169A ILE* 4.8 2.5 - - + -
201A ARG* 2.8 48.0 + - - +
203A ALA* 3.3 22.4 + - + +
204A THR* 4.5 2.3 + - - -
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Residues in contact with VAL 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A PHE* 3.1 42.1 + - + +
24A LEU 4.2 0.7 - - - +
26A GLU* 1.3 77.7 - - - +
28A GLY* 1.3 59.6 + - - +
29A LEU* 4.1 19.5 - - + +
88A THR* 4.2 21.3 - - + +
90A ARG* 4.0 24.9 + - + +
91A PHE* 3.9 17.5 - - + -
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Residues in contact with GLY 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU 2.8 10.4 + - - -
25A GLU* 3.7 7.2 + - - -
26A GLU 3.5 2.4 - - - -
27A VAL* 1.3 78.8 - - - +
29A LEU* 1.3 62.4 + - - +
30A PRO* 3.6 8.1 - - - +
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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
------------------------------------------------------------
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