Contacts of the helix formed by residues 15 - 29 (chain A) in PDB entry 3IHL
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 GLY 15 (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 3.4 1.2 + - - -
14A ILE* 1.3 80.5 - - - +
16A LYS* 1.3 67.9 + - - +
17A GLY 3.2 2.9 - - - -
18A ILE* 3.2 2.4 + - - +
19A ILE* 3.0 31.3 + - - +
180A VAL* 4.5 2.7 - - - -
217A ARG* 4.4 2.0 - - - -
300A ADP 3.2 37.5 + - - -
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Residues in contact with LYS 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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6A VAL* 3.9 14.1 - - + +
7A THR* 3.8 7.0 - - - +
8A GLY* 3.3 38.1 - - - +
11A ILE 5.1 0.2 + - - -
12A SER* 4.9 2.8 - - - +
13A GLY 4.7 1.4 - - - +
14A ILE* 3.9 11.2 - - + +
15A GLY* 1.3 75.8 - - - +
17A GLY* 1.3 57.5 + - - +
19A ILE* 3.4 1.7 + - - +
20A ALA* 2.8 32.4 + - - +
146A GLU* 4.4 10.3 - - + -
147A LEU 3.3 21.3 - - - +
148A GLY* 3.8 6.3 - - - -
149A GLY 3.3 10.7 + - - +
150A THR* 5.1 0.6 + - - -
180A VAL* 4.6 4.7 - - + -
300A ADP 2.7 33.6 + - - +
301A PO4 2.8 37.2 + - - -
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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
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16A LYS* 1.3 76.7 - - - +
18A ILE* 1.3 57.0 + - - +
20A ALA* 3.3 1.9 + - - +
21A SER* 2.8 32.0 + - - -
146A GLU* 3.5 24.0 + - - +
300A ADP 2.8 19.6 + - - -
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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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15A GLY 3.2 5.3 + - - +
17A GLY* 1.3 75.5 - - - +
19A ILE* 1.3 53.9 + - + +
21A SER* 3.3 7.9 + - - -
22A SER* 2.7 52.2 + - - +
250A THR* 4.2 26.9 - - + +
253A VAL* 3.8 29.2 - - + -
300A ADP 3.0 52.5 + - + +
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Residues in contact with ILE 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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6A VAL* 4.5 5.8 - - + -
15A GLY* 3.0 20.6 + - - +
16A LYS 3.8 2.5 - - - +
18A ILE* 1.3 75.0 - - + +
20A ALA* 1.3 66.5 + - - +
22A SER* 3.1 3.8 + - - +
23A ILE* 2.9 46.1 + - + +
178A ILE* 4.6 7.9 - - + -
180A VAL* 4.0 32.1 - - + -
215A VAL* 3.9 23.1 - - + -
217A ARG* 5.3 3.4 - - - -
244A ILE* 4.2 12.8 - - + -
253A VAL* 4.0 21.5 - - + -
257A LEU* 4.4 9.4 - - + -
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Residues in contact with ALA 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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6A VAL* 4.0 19.9 - - + +
16A LYS 2.8 18.3 + - - +
17A GLY 3.7 3.6 - - - +
19A ILE* 1.3 76.4 - - - +
21A SER* 1.3 62.8 + - - +
23A ILE* 4.0 0.8 - - - +
24A GLY* 3.3 16.1 + - - -
144A VAL* 3.7 21.0 - - + +
146A GLU* 4.0 31.2 - - + +
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Residues in contact with SER 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 2.8 18.8 + - - -
18A ILE* 3.5 11.3 - - - +
20A ALA* 1.3 79.6 - - - +
22A SER* 1.3 58.0 + - - +
24A GLY* 3.3 2.5 + - - -
25A THR* 2.9 31.2 + - - -
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Residues in contact with SER 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 ILE* 2.7 30.4 + - - +
19A ILE 3.1 1.3 + - - -
21A SER* 1.3 69.5 - - - +
23A ILE* 1.3 61.5 + - - +
25A THR* 3.2 7.6 + - - -
26A ILE* 2.8 36.4 + - - +
250A THR 4.8 0.3 + - - -
253A VAL* 3.4 17.3 - - - +
254A PRO* 3.5 20.3 - - - +
257A LEU* 3.7 22.0 - - - -
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Residues in contact with ILE 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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4A ILE* 4.0 16.4 - - + -
6A VAL* 4.5 8.1 - - + -
19A ILE* 2.9 37.6 + - + +
20A ALA 4.0 3.4 - - - +
22A SER* 1.3 75.7 - - - +
24A GLY* 1.3 62.5 + - - +
26A ILE* 3.2 8.2 + - - +
27A LEU* 2.9 45.5 + - + +
144A VAL* 4.4 9.0 - - + -
178A ILE* 3.1 36.3 - - + -
257A LEU* 4.6 4.7 - - + -
262A ILE* 4.4 13.0 - - + -
266A PHE* 4.1 14.4 - - + -
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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 ALA 3.3 13.0 + - - -
21A SER* 3.3 4.2 + - - -
22A SER 3.2 0.4 - - - -
23A ILE* 1.3 80.7 - - - +
25A THR* 1.3 61.6 + - - +
27A LEU* 3.3 2.0 + - - +
28A LYS* 3.1 35.8 + - - +
34A VAL* 4.0 21.6 - - - +
144A VAL* 4.5 4.7 - - - +
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Residues in contact with THR 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 SER* 2.9 19.3 + - - -
22A SER* 3.2 10.5 + - - +
24A GLY* 1.3 75.2 - - - +
26A ILE* 1.3 66.3 + - + +
28A LYS* 3.5 10.4 + - - +
29A SER* 3.3 20.6 + - - -
254A PRO* 5.2 12.8 - - + -
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Residues in contact with ILE 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 SER 2.8 24.8 + - - +
23A ILE* 3.6 7.4 - - - +
25A THR* 1.3 73.4 - - + +
27A LEU* 1.3 69.0 + - + +
29A SER* 2.6 24.8 + - - +
30A CYS* 3.6 7.6 + - - +
254A PRO* 3.9 24.9 - - + +
257A LEU* 3.9 34.1 - - + -
258A GLU* 3.9 25.1 - - + +
262A ILE* 4.3 8.5 - - + -
263A VAL* 3.5 31.4 - - + -
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Residues in contact with LEU 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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4A ILE* 3.8 22.9 - - + -
23A ILE* 2.9 28.3 + - + +
26A ILE* 1.3 84.8 - - + +
28A LYS* 1.3 61.1 + - - +
30A CYS* 3.1 17.6 + - + +
32A LEU* 3.5 33.5 + - + +
34A VAL* 3.8 17.7 - - + -
142A ILE* 3.5 28.9 - - + -
144A VAL* 5.2 1.8 - - + -
263A VAL* 5.3 13.0 - - + -
266A PHE* 4.6 15.5 - - + -
272A LEU* 4.3 12.6 - - + -
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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 GLY* 3.1 26.6 + - - +
25A THR* 3.9 7.9 - - - +
26A ILE 3.3 0.4 - - - -
27A LEU* 1.3 75.9 - - - +
29A SER* 1.3 57.5 + - - +
30A CYS 3.1 0.2 - - - -
31A GLY* 3.1 18.7 + - - -
32A LEU 3.7 13.2 + - - +
34A VAL* 3.7 31.9 + - + +
134A ASP* 3.3 36.0 + - - +
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Residues in contact with SER 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 THR* 3.3 9.7 + - - -
26A ILE* 2.6 24.9 + - - +
28A LYS* 1.3 78.4 - - - +
30A CYS* 1.3 61.3 + - - +
31A GLY 3.3 2.2 + - - -
258A GLU* 4.8 6.2 + - - -
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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