Contacts of the helix formed by residues 18 - 28 (chain C) in PDB entry 5LSW
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 GLU 18 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17C LEU* 1.3 76.1 - - - +
19C ARG* 1.3 62.7 + - - +
21C LYS* 3.1 8.4 + - + +
22C ILE* 3.0 43.6 + - + +
25C TRP* 6.6 0.2 - - + -
45C LYS* 4.6 13.7 - - + +
48C SER* 4.7 8.6 - - - +
49C VAL* 4.0 12.1 - - - +
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Residues in contact with ARG 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C LEU* 3.3 5.2 - - + +
18C GLU* 1.3 78.3 - - - +
20C GLU* 1.3 68.8 + - + +
22C ILE* 3.4 10.1 + - + +
23C TYR* 3.1 49.9 + - + -
51C ASP* 5.5 5.2 - - - +
55C MET* 4.2 10.1 - - + -
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Residues in contact with GLU 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C MET* 3.2 26.1 - - + +
17C LEU* 3.1 44.0 + - + +
18C GLU 3.3 0.2 - - - -
19C ARG* 1.3 87.6 + - + +
21C LYS* 1.3 56.0 + - - +
23C TYR* 3.4 8.0 + - - +
24C GLN* 2.9 27.9 + - - +
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Residues in contact with LYS 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C PRO 5.5 3.2 + - - -
16C MET* 3.7 38.4 - - + +
17C LEU 3.1 11.8 + - - +
18C GLU* 3.1 12.8 + - + +
20C GLU* 1.3 75.9 - - - +
22C ILE* 1.3 62.5 + - + +
24C GLN* 3.3 13.7 + - - +
25C TRP* 3.0 52.1 + - + -
304C TRS 3.2 30.9 + - - -
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Residues in contact with ILE 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C GLU* 3.0 36.9 + - + +
19C ARG* 3.8 8.7 - - + +
21C LYS* 1.3 77.2 - - - +
23C TYR* 1.3 56.8 + - - +
25C TRP* 3.2 21.7 + - + +
26C ILE* 2.9 29.1 + - + +
42C LEU* 3.8 17.5 - - + -
45C LYS* 5.1 4.9 - - + -
49C VAL* 3.5 36.6 - - + -
52C LEU* 4.0 16.2 - - + -
55C MET* 3.8 20.2 - - + -
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Residues in contact with TYR 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C ARG* 3.1 44.8 + - + +
20C GLU* 3.8 6.7 - - - +
22C ILE* 1.3 76.3 - - - +
24C GLN* 1.3 56.9 + - - +
26C ILE* 3.3 13.8 + - + +
27C ASN* 2.8 44.6 + - - +
55C MET* 3.5 53.7 - - + +
59C SER* 5.9 2.7 - - - -
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Residues in contact with GLN 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C MET* 3.3 26.2 - - - +
20C GLU 2.9 15.3 + - - +
21C LYS* 3.4 25.9 + - - +
22C ILE 3.2 0.2 - - - -
23C TYR* 1.3 76.1 - - - +
25C TRP* 1.3 59.5 + - + +
27C ASN* 3.2 11.0 + - - +
28C GLU* 2.8 51.6 + - + +
304C TRS 3.2 22.8 + - - -
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Residues in contact with TRP 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C GLU* 6.6 0.2 - - + -
21C LYS* 3.0 40.0 + - + -
22C ILE* 3.2 17.2 + - + +
24C GLN* 1.3 76.4 - - + +
26C ILE* 1.3 62.0 + - - +
28C GLU* 2.9 32.4 + - - -
29C LEU* 3.1 10.6 + - - +
37C ASN* 4.7 0.4 - - - -
38C ALA* 3.2 18.2 - - + +
41C GLU* 3.5 48.1 - - + +
42C LEU* 3.6 24.9 - - + -
45C LYS* 4.2 28.7 - - + -
304C TRS 3.2 42.6 - - - -
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Residues in contact with ILE 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C ILE* 2.9 31.2 + - + +
23C TYR* 3.5 20.0 - - + +
25C TRP* 1.3 76.4 - - - +
27C ASN* 1.3 64.6 + - - +
29C LEU* 3.0 21.2 + - - +
30C SER* 4.2 1.9 + - - -
42C LEU* 3.9 13.9 - - + -
52C LEU* 4.2 2.5 - - + -
55C MET* 3.8 32.1 - - + +
56C LEU* 3.8 22.0 - - + -
59C SER* 3.5 30.3 - - - +
62C THR* 3.7 18.6 + - + +
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Residues in contact with ASN 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C TYR* 2.8 33.7 + - - +
24C GLN* 3.5 9.2 - - - +
26C ILE* 1.3 74.4 - - - +
28C GLU* 1.3 62.4 + - + +
29C LEU 3.1 1.3 + - - -
30C SER* 3.3 22.3 + - - -
31C SER* 4.6 0.7 + - - -
59C SER* 4.5 10.4 + - - -
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Residues in contact with GLU 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C GLN* 2.8 37.6 + - + +
25C TRP* 2.9 22.9 + - - +
27C ASN* 1.3 73.4 - - + +
29C LEU* 1.3 62.1 + - - +
30C SER 3.2 1.0 + - - -
31C SER* 3.5 2.8 + - - +
34C THR* 2.8 53.5 + - + +
35C ARG* 3.5 0.9 - - - -
37C ASN* 4.5 3.5 - - - +
38C ALA* 3.8 10.6 - - + +
304C TRS 3.0 29.4 + - - -
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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