Contacts of the helix formed by residues 16 - 26 (chain H) in PDB entry 3I6A
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 MET 16 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7H LEU* 3.8 26.5 - - + -
8H HIS 3.3 35.7 - - - +
9H TYR* 3.6 21.0 - - + -
13H ARG 3.1 1.6 + - - -
15H ARG* 1.3 78.1 - - - +
17H GLU* 1.3 64.0 + - - +
18H SER 3.3 3.1 - - - -
19H THR* 3.1 21.8 + - - -
20H ARG* 3.1 42.8 + - - +
56H PRO* 3.6 20.0 - - + -
57H MET 3.7 14.1 - - - +
58H VAL* 4.0 8.1 - - + -
71H ILE* 5.3 0.2 - - - -
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Residues in contact with GLU 17 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13H ARG* 3.1 33.1 + - + +
14H GLY 4.0 4.2 + - - +
15H ARG 3.7 0.8 - - - -
16H MET* 1.3 76.6 - - - +
18H SER* 1.3 57.7 + - - +
20H ARG* 2.7 43.5 + - - +
21H TRP* 2.9 40.8 + - + -
162H GLU* 3.7 5.4 - - - +
166H TYR* 3.1 25.3 - - + +
204H ARG* 3.7 14.2 - - - +
205H LYS* 2.8 35.7 + - - +
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Residues in contact with SER 18 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14H GLY 5.4 0.2 + - - -
15H ARG 4.5 3.9 + - - -
16H MET 3.3 0.2 - - - -
17H GLU* 1.3 77.3 - - - +
19H THR* 1.3 57.6 + - - +
21H TRP* 3.6 1.7 - - - +
22H LEU* 2.9 29.6 + - - +
68H THR* 4.1 10.7 - - - +
72H LEU* 3.6 26.1 - - - +
159H HIS* 4.4 11.5 - - - -
162H GLU* 3.3 25.7 + - - -
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Residues in contact with THR 19 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7H LEU* 4.5 1.3 - - + -
15H ARG 4.8 0.2 + - - -
16H MET* 3.1 29.9 + - - -
18H SER* 1.3 77.2 + - - +
20H ARG* 1.3 64.7 + - - +
22H LEU* 4.2 0.8 - - - +
23H LEU* 3.0 35.1 + - + +
56H PRO* 5.9 0.2 - - - +
58H VAL* 4.3 4.7 - - + -
68H THR* 4.8 6.4 - - - +
71H ILE* 3.6 33.4 - - + +
72H LEU* 3.6 20.3 - - - +
75H ILE* 3.8 14.4 - - + -
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Residues in contact with ARG 20 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7H LEU* 3.7 16.8 - - + -
9H TYR* 4.0 4.0 - - - +
10H PHE 3.3 17.0 + - - -
12H GLY 2.8 28.4 + - - -
13H ARG 3.3 3.0 + - - -
16H MET* 3.1 29.9 + - - +
17H GLU* 2.7 55.1 + - - +
19H THR* 1.3 76.9 - - - +
21H TRP* 1.3 55.1 + - - +
24H ALA* 3.1 31.0 + - - +
30H PHE* 3.8 20.6 - - + -
32H GLU* 2.8 29.6 + - - -
34H PHE* 4.5 0.4 - - - -
197H PHE* 3.8 14.7 - - + -
203H PRO* 3.7 17.0 - - - -
205H LYS* 3.7 9.0 - - - +
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Residues in contact with TRP 21 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17H GLU* 2.9 33.5 + - + +
18H SER 3.6 5.2 - - - +
20H ARG* 1.3 78.8 - - - +
22H LEU* 1.3 56.8 + - - +
24H ALA* 3.9 1.2 - - - +
25H ALA* 3.0 29.6 + - - +
158H ILE* 4.0 21.6 - - + +
159H HIS* 6.1 0.2 - - - +
161H VAL* 4.5 6.7 - - + -
162H GLU* 3.7 59.4 - - + +
165H TYR* 3.9 27.6 - + + -
166H TYR* 3.8 9.9 + + - -
188H ILE* 5.8 1.3 - - + -
194H VAL* 4.3 23.7 - - + +
197H PHE* 3.4 35.4 - + - -
198H LEU* 3.9 15.5 - - + -
204H ARG* 4.0 23.0 - - - +
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Residues in contact with LEU 22 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18H SER 2.9 18.8 + - - +
19H THR* 4.2 2.0 - - - +
20H ARG 3.4 0.2 - - - -
21H TRP* 1.3 77.3 - - - +
23H LEU* 1.3 63.1 + - - +
25H ALA* 3.4 2.3 + - - +
26H ALA* 3.0 21.8 + - - +
72H LEU* 3.7 36.6 - - + +
75H ILE* 3.6 24.5 - - + -
76H ALA* 3.9 10.8 - - + +
81H LEU* 3.9 22.9 - - + -
155H ARG* 3.9 24.5 - - + -
158H ILE* 4.1 17.6 - - + +
159H HIS* 4.4 10.8 - - + +
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Residues in contact with LEU 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5H PRO* 4.5 13.2 - - + -
7H LEU* 3.9 20.9 - - + -
19H THR* 3.0 37.0 + - + +
22H LEU* 1.3 73.0 - - - +
24H ALA* 1.3 65.6 + - - +
26H ALA* 3.2 5.8 + - - +
27H GLY 3.1 3.3 + - - -
28H VAL* 2.8 55.7 + - + +
30H PHE* 3.8 29.4 - - + -
58H VAL* 5.7 0.7 - - + -
60H ILE* 5.0 1.1 - - + -
75H ILE* 3.8 33.0 - - + -
79H TYR* 4.8 2.9 - - + -
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Residues in contact with ALA 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20H ARG 3.1 19.2 + - - +
21H TRP 3.9 1.3 - - - +
23H LEU* 1.3 75.5 - - - +
25H ALA* 1.3 59.2 + - - +
27H GLY* 2.7 20.8 + - - -
28H VAL 4.5 6.1 - - - +
30H PHE* 4.3 5.8 - - + -
193H THR* 3.2 16.4 - - - +
197H PHE* 3.3 38.1 - - + -
203H PRO* 6.0 0.2 - - + -
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Residues in contact with ALA 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H TRP 3.0 19.0 + - - +
22H LEU* 3.7 5.2 - - + +
23H LEU 3.3 0.2 - - - -
24H ALA* 1.3 75.1 - - - +
26H ALA* 1.3 60.6 + - - +
81H LEU* 5.2 3.6 - - + -
153H LEU* 5.1 9.5 - - + +
158H ILE* 3.4 37.7 - - + -
193H THR* 2.6 26.1 + - - +
194H VAL* 3.8 14.0 - - + +
197H PHE* 5.6 0.2 - - - +
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Residues in contact with ALA 26 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22H LEU 3.0 16.3 + - - +
23H LEU* 3.5 7.4 - - - +
24H ALA 3.1 0.4 - - - -
25H ALA* 1.3 74.3 - - - +
27H GLY* 1.3 62.0 + - - +
28H VAL* 3.5 17.4 + - + +
75H ILE* 5.2 2.0 - - + -
79H TYR* 4.0 30.4 - - + +
81H LEU* 4.2 13.6 - - + +
193H THR* 4.7 1.1 - - - -
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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