Contacts of the helix formed by residues 21 - 32 (chain D) in PDB entry 5LF4
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 LEU 21 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12D VAL 5.3 2.2 - - - +
13D ASN* 4.1 13.5 - - - +
14D THR 3.6 13.9 - - - +
15D PHE* 3.9 22.2 - - + -
20D ARG* 1.3 71.1 - - - +
22D PHE* 1.3 68.1 + - - +
23D GLN 4.5 1.3 - - - +
24D VAL* 3.0 34.5 + - + +
25D GLU* 3.0 16.2 + - - +
121D LEU* 4.2 11.0 - - + -
123D PHE* 4.6 6.3 - - + -
77E LEU* 4.0 15.0 - - + +
126E ARG* 3.6 49.8 - - - +
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Residues in contact with PHE 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D ARG* 3.3 55.9 - - - -
11D GLY 6.0 0.7 - - - +
14D THR* 3.4 26.6 + - + +
15D PHE 3.7 18.6 - - - -
16D SER* 3.5 29.6 - - - -
17D PRO* 4.5 6.7 - - + -
20D ARG 3.5 2.0 + - - -
21D LEU* 1.3 70.0 - - - +
23D GLN* 1.3 67.1 + - + +
25D GLU* 3.1 8.4 + - + +
26D TYR* 2.9 60.9 + + + -
8E ASN* 4.9 0.9 - - - -
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Residues in contact with GLN 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C VAL* 3.7 16.4 - - - +
10C PHE* 2.8 58.4 + - - +
12D VAL* 3.5 41.9 + - + +
21D LEU* 3.2 1.4 - - + +
22D PHE* 1.3 80.9 - - + +
24D VAL* 1.3 57.4 + - - +
26D TYR* 3.8 12.4 - - - +
27D ALA* 2.9 28.8 + - - +
123D PHE* 4.3 4.3 - - + -
135D ARG* 4.1 2.1 - - - +
136D PRO* 3.5 23.3 - - + +
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Residues in contact with VAL 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D LEU* 3.0 24.9 + - + +
23D GLN* 1.3 74.2 - - - +
25D GLU* 1.3 69.9 + - - +
27D ALA* 3.2 8.3 + - - +
28D ILE* 2.9 38.4 + - + +
121D LEU* 3.5 29.8 - - + -
123D PHE* 4.2 13.5 - - + -
136D PRO* 4.3 2.5 - - + -
158D PRO 4.2 5.8 - - - +
159D SER* 3.8 32.1 - - - +
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Residues in contact with GLU 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D ARG* 3.2 45.4 + - + +
21D LEU 3.0 18.3 + - - +
22D PHE* 3.7 8.7 - - + +
24D VAL* 1.3 89.4 - - - +
26D TYR* 1.3 69.1 + - + +
28D ILE* 3.1 21.1 + - - +
29D GLU* 3.1 26.0 + - - +
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Residues in contact with TYR 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C PHE* 3.5 26.9 - - + -
11C SER 3.2 26.5 - - - +
12C PRO* 3.6 43.3 - - + +
14C GLY* 3.4 10.4 - - - -
10D ARG* 4.1 8.6 + - - -
22D PHE* 2.9 55.3 + + + +
23D GLN* 3.9 9.6 - - - +
25D GLU* 1.3 81.3 - - + +
27D ALA* 1.3 62.4 + - - +
29D GLU* 3.1 15.3 + - - +
30D ALA 3.1 16.6 + - - -
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Residues in contact with ALA 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C PHE* 3.9 26.8 - - + -
23D GLN 2.9 18.8 + - - +
24D VAL 3.2 5.1 + - - +
26D TYR* 1.3 76.9 - - - +
28D ILE* 1.3 61.2 + - - +
30D ALA* 3.2 17.2 + - - +
31D ILE* 3.4 14.2 + - - +
136D PRO* 4.0 7.0 - - + -
137D PHE 3.9 9.9 - - - +
138D GLY* 4.2 0.5 - - - -
158D PRO* 3.8 20.9 - - + -
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Residues in contact with ILE 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D VAL* 2.9 33.8 + - + +
25D GLU* 3.1 24.9 + - - +
27D ALA* 1.3 75.3 - - - +
29D GLU* 1.3 64.9 + - + +
31D ILE* 3.2 25.0 + - + +
32D LYS* 4.0 7.1 + - + +
157D ASP* 4.6 17.0 - - + +
158D PRO* 4.0 20.2 - - + -
159D SER* 4.8 4.7 - - - +
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Residues in contact with GLU 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C PRO* 4.1 0.7 - - - +
13C ASP* 2.8 46.1 + - - +
14C GLY* 4.3 1.8 - - - -
25D GLU* 3.1 11.9 + - - +
26D TYR* 3.1 25.1 + - - +
28D ILE* 1.3 79.1 - - + +
30D ALA* 1.3 59.8 + - - +
32D LYS* 3.2 26.5 + - + +
33D LEU* 4.0 5.4 + - - +
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Residues in contact with ALA 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C PHE* 3.8 18.2 - - + -
14C GLY* 3.7 25.0 - - - +
26D TYR 3.1 6.6 + - - +
27D ALA 3.2 10.7 + - - +
29D GLU* 1.3 74.1 - - - +
31D ILE* 1.3 62.7 + - - +
33D LEU* 3.0 27.5 + - + +
34D GLY 3.9 1.9 + - - -
80D GLY* 4.1 6.6 - - - -
81D LEU* 4.3 15.4 - - + +
138D GLY 4.4 5.2 - - - +
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Residues in contact with ILE 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D ALA 3.5 8.5 - - - +
28D ILE* 3.2 21.4 + - + +
30D ALA* 1.3 76.2 - - - +
32D LYS* 1.3 60.8 + - + +
34D GLY* 3.0 17.5 + - - -
79D SER* 3.9 7.2 + - - +
80D GLY* 4.1 4.3 - - - -
138D GLY 3.3 8.3 - - - +
139D VAL* 3.2 44.9 - - - +
140D ALA* 3.5 25.6 - - + +
157D ASP* 5.6 0.9 - - + -
158D PRO* 3.9 8.7 - - + -
170D ILE* 4.8 0.9 - - + -
171D GLY* 3.4 29.1 - - - +
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Residues in contact with LYS 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D ILE* 4.1 9.6 - - + +
29D GLU* 3.2 19.6 + - + +
31D ILE* 1.3 79.5 - - + +
33D LEU* 1.3 57.6 + - + +
34D GLY 3.2 1.6 - - - -
171D GLY* 3.3 19.8 + - - +
172D SER* 3.3 36.4 + - - +
174D SER* 2.9 26.0 + - - +
175D GLU* 4.1 24.1 + - - +
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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
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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