Contacts of the helix formed by residues 19 - 31 (chain A) in PDB entry 5U5S
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 SER 19 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A LYS* 2.6 40.3 + - - +
16A GLU* 2.9 19.9 + - - +
18A LEU* 1.3 78.2 - - - +
20A LYS* 1.3 55.2 + - - +
21A LYS* 2.9 15.0 - - - -
22A HIS* 2.8 26.9 + - - +
23A ALA 3.1 6.9 + - - -
30A TYR* 3.2 2.5 + - - -
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Residues in contact with LYS 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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18A LEU 3.7 2.0 + - - -
19A SER* 1.3 71.5 - - - +
21A LYS* 1.3 60.6 + - - +
22A HIS 3.1 1.3 + - - -
23A ALA* 3.4 30.2 + - + +
24A ALA* 4.2 6.1 + - - +
30A TYR* 4.5 0.2 - - - -
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Residues in contact with LYS 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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16A GLU* 4.9 7.4 - - + +
19A SER* 4.1 10.0 - - - +
20A LYS* 1.3 79.1 - - - +
22A HIS* 1.3 88.7 + - + +
24A ALA* 4.9 2.9 + - - +
25A TYR* 3.7 13.4 + - - +
106A ARG* 5.3 6.1 - - - +
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Residues in contact with HIS 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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16A GLU* 2.6 57.9 + - + +
17A LEU* 3.9 6.1 - - - +
19A SER 2.8 6.1 + - - +
21A LYS* 1.3 98.5 - - + +
23A ALA* 1.3 52.8 + - - +
24A ALA 3.0 3.8 - - - -
25A TYR* 2.7 66.1 + - + -
26A ALA* 2.8 23.8 + - + -
99A LEU* 3.9 9.9 - - + +
102A VAL* 3.5 20.2 - - + -
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Residues in contact with ALA 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 SER 3.1 3.8 + - - -
20A LYS* 3.4 42.0 + - + +
22A HIS* 1.3 75.8 - - - +
24A ALA* 1.3 61.9 + - - +
25A TYR 2.9 1.6 + - - -
26A ALA* 3.5 4.0 - - - -
27A TRP* 3.1 28.4 + - + +
30A TYR* 3.1 33.2 + - + +
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Residues in contact with ALA 24 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A LYS* 4.2 7.2 + - - +
21A LYS 5.2 2.5 - - - +
22A HIS 2.9 0.8 + - - -
23A ALA* 1.3 76.6 - - - +
25A TYR* 1.3 74.3 + - + +
27A TRP* 3.7 14.8 + - - -
95A MET* 4.7 1.9 - - - +
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Residues in contact with TYR 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 LYS* 3.7 12.8 + - - +
22A HIS* 2.7 52.4 + + - -
24A ALA* 1.3 87.5 - - + +
26A ALA* 1.3 58.6 + - - +
27A TRP* 3.7 1.6 - - - -
28A PRO* 4.1 4.0 - - - -
29A PHE* 3.4 16.6 - - - -
95A MET* 3.6 32.9 - - + +
98A LYS* 3.5 43.5 - - + -
99A LEU* 3.5 20.4 - - + +
102A VAL* 5.5 0.7 - - + -
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Residues in contact with ALA 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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17A LEU 3.2 26.5 - - - +
22A HIS* 2.8 20.3 + - + +
23A ALA 3.1 0.2 + - - -
25A TYR* 1.3 78.1 - - - +
27A TRP* 1.3 66.4 + - - +
28A PRO* 3.2 3.8 - - - -
29A PHE* 2.9 18.3 + - - +
30A TYR* 3.0 19.6 + - + -
53A LEU* 5.1 0.6 - - + +
99A LEU* 3.4 22.2 - - + -
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Residues in contact with TRP 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 ALA* 3.1 27.8 + - + +
24A ALA* 3.7 18.3 + - - -
26A ALA* 1.3 77.3 - - - +
28A PRO* 1.4 82.1 - - + +
29A PHE 3.0 1.8 + - - -
30A TYR* 3.1 31.6 + - + +
31A LYS 4.2 3.5 + - - +
95A MET* 4.1 19.8 - - + -
289B PHE* 3.5 42.4 - + + -
292B SER* 3.6 42.5 + - - -
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Residues in contact with PRO 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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26A ALA* 3.2 2.7 - - - -
27A TRP* 1.4 117.5 - - + +
29A PHE* 1.3 81.3 + - + +
31A LYS 3.6 13.7 - - - +
33A VAL* 4.8 11.4 - - - +
92A VAL* 3.5 25.8 - - + -
95A MET* 3.6 27.1 - - + -
287B ALY 4.8 5.0 - - - +
289B PHE* 3.9 11.8 - - + -
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Residues in contact with PHE 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 TYR 3.4 21.3 - - - -
26A ALA 2.9 16.5 + - - +
28A PRO* 1.3 98.9 - - + +
30A TYR* 1.3 63.5 + - - +
31A LYS 3.3 2.7 - - - -
52A ASP* 3.4 6.1 - - - +
53A LEU* 2.9 33.7 + - + +
78A MET* 3.4 39.7 - - + -
79A PHE* 4.2 2.5 - + - -
82A CYS* 3.8 23.6 - - - -
92A VAL* 4.2 4.0 - - + -
95A MET* 3.6 2.5 - - + -
96A ALA* 3.5 35.7 - - + -
99A LEU* 3.3 30.5 - - + -
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Residues in contact with TYR 30 (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 LEU 3.3 18.9 + - - -
18A LEU* 2.7 53.1 + - + -
19A SER 3.2 1.6 + - - -
23A ALA* 3.1 36.3 - - + +
26A ALA* 3.0 28.3 - - + -
27A TRP* 3.1 18.1 + - + +
29A PHE* 1.3 80.5 - - - +
31A LYS* 1.3 76.3 + - - +
52A ASP* 3.1 9.0 - - - +
53A LEU* 4.8 1.3 - - + -
54A SER* 2.6 29.0 + - - +
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Residues in contact with LYS 31 (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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27A TRP 4.2 2.5 + - - +
28A PRO 3.6 17.0 - - - +
29A PHE 4.4 0.3 - - - -
30A TYR* 1.3 102.1 - - - +
32A PRO* 1.3 81.6 - - + +
33A VAL* 3.6 2.1 + - - -
52A ASP* 3.9 6.0 - - - +
54A SER* 3.9 12.3 - - - +
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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