Contacts of the helix formed by residues 15 - 27 (chain A) in PDB entry 1U1H
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 ARG 15 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A MSE 3.1 27.4 - - + -
12A GLY 3.1 8.4 + - - +
13A PRO 3.6 0.6 - - - +
14A LYS* 1.3 79.4 + - - +
16A GLU* 1.3 65.8 + - - +
17A LEU 3.3 0.7 - - - -
18A LYS* 3.2 36.9 + - + +
19A PHE* 3.3 35.8 - - + -
514A TRP* 3.4 74.1 - - + +
521A ARG* 4.0 10.5 - - - +
522A CYS* 4.2 10.3 - - - -
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Residues in contact with GLU 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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11A MSE 2.9 2.7 + - - +
12A GLY* 3.3 8.8 - - - -
13A PRO* 3.5 19.7 - - - +
14A LYS* 2.9 34.4 + - + +
15A ARG* 1.3 72.2 + - - +
17A LEU* 1.3 62.6 + - - +
19A PHE* 3.3 8.3 + - - +
20A ALA* 3.0 22.2 + - - +
37A VAL* 4.3 15.4 - - + +
41A LEU* 4.5 11.0 - - + +
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Residues in contact with LEU 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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10A ARG* 3.3 26.0 - - + +
11A MSE 3.1 32.5 + - + +
16A GLU* 1.3 76.2 - - - +
18A LYS* 1.3 60.7 + - - +
20A ALA* 4.2 2.7 - - - -
21A LEU* 2.8 47.5 + - + +
34A LEU* 4.3 9.0 - - + -
37A VAL* 4.5 9.0 - - + -
38A SER* 3.9 22.0 - - - +
41A LEU* 4.2 5.0 - - + +
62A PHE* 4.0 14.8 - - + -
63A ALA 3.6 23.3 - - - +
64A HIS* 4.5 2.9 - - + -
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Residues in contact with LYS 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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11A MSE 4.2 15.6 - - + +
15A ARG* 3.2 37.9 + - + +
17A LEU* 1.3 78.5 - - - +
19A PHE* 1.3 80.8 + - + +
21A LEU* 3.8 2.3 - - - +
22A GLU* 2.9 61.2 + - - +
520A SER* 3.3 26.9 + - - +
521A ARG* 2.8 39.3 - - - +
522A CYS* 4.9 0.9 - - - -
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Residues in contact with PHE 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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14A LYS 3.8 13.9 - - - -
15A ARG* 3.3 49.3 + - + -
16A GLU* 3.3 7.3 + - - +
17A LEU 3.3 0.4 - - - -
18A LYS* 1.3 94.4 - - + +
20A ALA* 1.3 61.1 + - - +
22A GLU* 3.7 9.8 - - + +
23A SER* 2.8 31.9 + - - -
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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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16A GLU 3.0 17.0 + - - +
17A LEU* 3.7 4.7 - - - +
19A PHE* 1.3 78.1 - - - +
21A LEU* 1.3 57.1 + - - +
23A SER* 3.3 5.5 + - - -
24A PHE* 2.9 30.0 + - - +
29A SER* 4.2 1.7 + - - -
34A LEU* 4.1 18.9 - - + +
37A VAL* 3.7 33.9 - - + -
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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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11A MSE 4.4 8.5 - - + -
17A LEU* 2.8 43.2 + - + +
18A LYS 3.8 2.7 - - - +
20A ALA* 1.3 77.7 - - - +
22A GLU* 1.3 52.4 + - - +
24A PHE* 3.3 4.4 + - - +
25A TRP* 2.8 61.2 + - + -
34A LEU* 4.2 14.4 - - + -
64A HIS* 3.3 29.8 - - + +
95A PHE* 3.4 35.4 - - + -
519A GLY 4.7 2.2 - - - +
520A SER* 4.7 7.0 - - - -
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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 LYS* 2.9 50.3 + - - +
19A PHE* 3.9 12.6 - - + +
21A LEU* 1.3 74.6 - - - +
23A SER* 1.3 64.4 + - - +
25A TRP* 4.0 16.4 - - + +
26A ASP* 2.9 38.1 + - - +
520A SER* 2.7 28.4 + - - -
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Residues in contact with SER 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 PHE 2.8 24.1 + - - -
20A ALA* 3.6 5.6 - - - -
22A GLU* 1.3 72.8 - - - +
24A PHE* 1.3 64.3 + - - +
26A ASP* 3.2 3.3 + - - +
27A GLY 3.1 4.0 + - - -
28A LYS* 3.0 49.1 + - - +
29A SER* 2.9 27.1 + - - -
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Residues in contact with PHE 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 2.9 18.1 + - - +
21A LEU 3.6 2.5 - - - +
23A SER* 1.3 76.6 - - - +
25A TRP* 1.3 73.2 + + - +
27A GLY* 2.8 20.6 + - - -
29A SER* 3.0 16.6 + - - +
30A THR* 3.7 20.0 - - - -
31A ALA* 3.7 25.8 - - + -
34A LEU* 3.9 17.3 - - + -
91A LEU* 3.8 17.5 - - + -
92A ASP* 6.0 2.2 - - - -
95A PHE* 3.5 33.0 - + - -
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Residues in contact with TRP 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 40.4 + - + +
22A GLU* 4.0 17.0 - - + +
24A PHE* 1.3 88.9 - + - +
26A ASP* 1.3 65.3 + - - +
27A GLY 3.4 0.5 + - - -
65A TYR* 3.8 37.0 - + - -
95A PHE* 3.5 40.2 - + + -
99A ARG* 3.3 51.0 + - - +
520A SER* 3.3 39.7 - - - -
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Residues in contact with ASP 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 GLU* 2.9 27.2 + - - +
23A SER 3.7 4.0 - - - +
24A PHE 3.1 0.4 - - - -
25A TRP* 1.3 81.1 - - - +
27A GLY* 1.3 62.5 + - - +
28A LYS* 3.6 28.0 + - + +
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Residues in contact with GLY 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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23A SER 3.1 0.2 + - - -
24A PHE 2.8 16.4 + - - -
25A TRP 3.2 1.2 - - - -
26A ASP* 1.3 79.3 - - - +
28A LYS* 1.3 57.7 + - - +
29A SER 3.3 9.7 + - - -
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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