Contacts of the helix formed by residues 15 - 28 (chain I) in PDB entry 5UWC
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 ASN 15 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13I TYR 3.7 3.0 + - - +
14I VAL* 1.3 74.0 - - - +
16I CYS* 1.3 62.1 + - - +
17I SER* 3.4 11.1 + - - -
18I ASN* 3.1 47.1 + - + +
19I MET* 3.3 25.8 + - - +
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Residues in contact with CYS 16 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14I VAL* 3.7 14.5 + - - -
15I ASN* 1.3 69.4 + - - +
17I SER* 1.3 59.6 + - - +
19I MET* 3.3 3.5 + - - +
20I ILE* 2.9 40.5 + - + +
83I PRO* 4.3 5.6 - - - -
84I CYS* 3.1 51.1 - - + -
119I GLU* 5.0 3.1 - - - +
122I GLN* 6.3 2.7 - - + -
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Residues in contact with SER 17 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235G LYS* 2.8 34.9 + - - +
15I ASN* 3.4 9.3 + - - -
16I CYS* 1.3 78.0 - - - +
18I ASN* 1.3 57.6 + - - +
20I ILE* 3.5 2.3 + - - +
21I ASP* 2.8 45.3 + - - +
119I GLU* 3.7 14.9 + - - -
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Residues in contact with ASN 18 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255G ARG* 5.1 6.2 + - - -
15I ASN* 3.1 41.1 + - + +
17I SER* 1.3 80.9 - - - +
19I MET* 1.3 58.8 + - + +
21I ASP* 3.7 9.4 - - - +
22I GLU* 2.9 34.2 + - + +
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Residues in contact with MET 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I VAL* 3.8 34.3 - - - -
15I ASN 3.3 13.0 + - - +
16I CYS* 3.3 6.3 + - - +
18I ASN* 1.3 77.1 - - + +
20I ILE* 1.3 63.4 + - - +
22I GLU* 3.4 5.3 + - - +
23I ILE* 3.1 27.7 + - - +
77I ILE* 3.6 27.9 - - + +
80I ASN* 3.4 45.1 - - + +
81I LEU* 4.1 12.3 - - + -
84I CYS* 4.5 4.9 - - - -
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Residues in contact with ILE 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16I CYS* 2.9 23.2 + - + +
17I SER* 3.9 3.6 - - - +
19I MET* 1.3 71.9 - - - +
21I ASP* 1.3 69.5 + - - +
23I ILE* 3.2 8.9 + - - +
24I ILE* 3.0 30.5 + - + +
81I LEU* 4.3 16.4 - - + -
84I CYS* 4.5 9.6 - - + -
115I LEU* 3.9 38.4 - - + +
118I LEU* 3.8 26.9 - - + -
119I GLU* 3.6 28.0 - - + +
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Residues in contact with ASP 21 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235G LYS* 4.9 7.7 - - - +
255G ARG* 3.5 17.6 + - - +
277G ARG* 2.7 25.6 + - - -
17I SER* 2.8 34.7 + - - +
18I ASN* 3.7 8.6 + - - +
20I ILE* 1.3 76.5 - - - +
22I GLU* 1.3 56.9 + - - +
24I ILE* 3.3 2.4 + - - +
25I THR* 2.9 36.5 + - + +
119I GLU* 5.9 0.7 - - - +
201I CIT 3.0 32.7 - - - +
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Residues in contact with GLU 22 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18I ASN* 2.9 19.5 + - + +
19I MET* 3.6 7.9 - - - +
21I ASP* 1.3 75.3 - - - +
23I ILE* 1.3 61.2 + - - +
25I THR* 2.5 39.5 + - - +
26I HIS* 3.0 35.3 + - - -
73I ALA* 5.7 0.7 - - - +
77I ILE* 3.8 17.9 - - + +
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Residues in contact with ILE 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19I MET 3.1 13.2 + - - +
20I ILE* 3.2 6.0 + - - +
22I GLU* 1.3 74.7 - - - +
24I ILE* 1.3 58.5 + - - +
26I HIS* 3.2 3.5 + - - -
27I LEU* 2.9 39.0 + - + +
74I ILE* 3.6 25.3 - - + +
77I ILE* 3.6 36.6 - - + -
78I LEU* 4.0 26.7 - - + +
81I LEU* 4.2 13.2 - - + -
111I LEU* 3.9 9.4 - - + -
115I LEU* 3.6 24.7 - - + -
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Residues in contact with ILE 24 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278G VAL* 4.3 23.1 - - + -
20I ILE* 3.0 27.9 + - + +
21I ASP 3.7 0.2 - - - +
23I ILE* 1.3 74.1 - - - +
25I THR* 1.3 62.6 + - - +
27I LEU* 3.2 7.2 + - + +
28I LYS* 3.0 45.1 + - + +
112I THR* 4.0 31.4 - - + +
115I LEU* 3.8 30.7 - - + -
116I TRP 4.9 0.9 - - - +
201I CIT 3.4 28.3 - - + +
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Residues in contact with THR 25 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21I ASP* 2.9 18.2 + - + +
22I GLU* 2.5 38.5 + - - +
24I ILE* 1.3 74.6 - - - +
26I HIS* 1.3 65.2 + - - +
28I LYS* 3.3 15.8 + - - +
29I GLN* 3.3 18.3 + - - -
201I CIT 2.8 38.0 - - - +
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Residues in contact with HIS 26 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22I GLU* 3.0 44.8 + - + -
23I ILE* 3.2 3.0 + - - +
25I THR* 1.3 82.2 + - - +
27I LEU* 1.3 63.7 + - - +
28I LYS 3.1 1.6 - - - -
29I GLN* 3.3 31.7 + - + +
70I ASN 6.0 0.4 + - - -
73I ALA* 3.8 31.3 - - + +
74I ILE* 3.4 25.5 - - + +
77I ILE* 5.2 2.9 - - + -
104I TRP* 3.8 11.0 - - + -
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Residues in contact with LEU 27 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23I ILE* 2.9 37.2 + - + +
24I ILE* 3.2 13.0 + - + +
26I HIS* 1.3 73.8 - - - +
28I LYS* 1.3 50.8 + - + +
29I GLN 3.4 1.9 + - - -
35I LEU* 3.8 1.8 - - + +
74I ILE* 3.8 15.7 - - + -
104I TRP* 4.2 10.3 - - + -
107I PHE* 4.0 19.7 - - + -
108I ARG* 2.7 61.5 + - + +
111I LEU* 3.8 21.5 - - + -
112I THR* 3.5 28.0 - - - +
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Residues in contact with LYS 28 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277G ARG 3.3 13.3 + - - -
278G VAL* 2.7 29.6 + - + +
280G GLU* 2.7 27.0 + - - -
24I ILE* 3.0 36.2 + - + +
25I THR 3.3 11.2 + - - +
26I HIS 3.1 0.6 - - - -
27I LEU* 1.3 76.0 - - + +
29I GLN* 1.3 60.9 + - - +
31I PRO* 3.4 15.8 - - + +
34I LEU* 4.6 11.6 - - - +
35I LEU* 3.8 23.1 - - + -
108I ARG* 3.7 5.8 - - - +
201I CIT 3.4 24.2 - - - +
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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