Contacts of the helix formed by residues 43 - 48 (chain E) in PDB entry 1S9C
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 ASP 43 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35E GLY 4.7 0.5 - - - +
36E ALA* 3.4 14.3 - - + -
37E SER* 3.0 47.3 + - - +
40E ASP* 2.8 20.6 + - - +
42E LYS* 1.3 75.2 - - - +
44E LEU* 1.3 61.3 + - - +
45E LYS 2.8 6.7 - - - -
46E PHE* 2.8 32.2 + - - +
47E ILE* 3.3 15.3 + - + +
225E ARG* 4.5 10.7 + - - +
229E GLN* 4.4 8.9 + - - -
234E ASN* 4.4 4.5 + - - +
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Residues in contact with LEU 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E ILE* 4.2 25.0 - - + +
40E ASP 3.9 1.4 + - - -
41E PRO* 3.0 21.4 + - + +
43E ASP* 1.3 78.4 - - - +
45E LYS* 1.3 58.2 - - - +
47E ILE* 4.4 4.9 - - - +
48E TYR* 2.9 61.2 + - + +
51E SER* 4.0 8.0 - - - +
199F ILE* 4.4 16.8 - - + +
200F ASP* 6.1 0.4 - - - +
201F PRO* 5.1 15.5 - - + -
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Residues in contact with LYS 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E PRO 4.5 0.2 + - - -
42E LYS 3.4 17.2 + - - +
44E LEU* 1.3 79.3 - - - +
46E PHE* 1.3 69.7 + - + +
51E SER* 4.0 12.5 + - - -
53E ASP* 3.5 42.4 + - + +
54E PHE* 3.2 10.7 - - - -
55E SER* 3.1 51.4 + - - +
233E ASP 5.1 0.6 + - - -
234E ASN* 2.6 37.4 + - + +
235E ASP* 4.2 7.1 + - - +
236E VAL* 4.2 6.6 - - - +
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Residues in contact with PHE 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E ALA 5.1 0.5 - - - -
28E ILE* 3.9 13.0 - - - +
31E ALA* 3.5 29.6 - - + +
36E ALA* 4.6 6.5 - - + -
42E LYS 4.5 4.9 - - - -
43E ASP* 2.8 29.5 + - - +
45E LYS* 1.3 93.9 - - + +
47E ILE* 1.3 59.9 + - - +
48E TYR 3.8 0.4 - - - -
54E PHE* 4.1 5.6 - - - -
55E SER* 3.7 21.1 - - - +
57E LEU* 3.5 35.9 - - + +
225E ARG* 5.4 4.9 - - + -
228E LEU* 3.8 15.0 - - + -
234E ASN* 4.0 30.1 - - - -
236E VAL* 3.8 22.7 - - + -
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Residues in contact with ILE 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E ILE* 3.2 35.8 - - + +
31E ALA* 5.1 0.7 - - + -
32E LEU* 4.1 11.0 - - + -
36E ALA* 3.9 14.4 - - + +
37E SER* 3.6 19.1 - - - +
38E ILE* 3.5 42.4 - - + +
43E ASP 3.3 15.7 - - - +
44E LEU* 3.2 3.7 + - - +
46E PHE* 1.3 83.2 - - - +
48E TYR* 1.3 59.4 + - + +
183F ASN* 4.0 2.7 - - - +
186F ALA* 3.8 28.3 - - + +
189F ARG* 4.2 7.1 + - - -
199F ILE* 4.2 3.8 - - + +
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Residues in contact with TYR 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E LEU* 2.9 33.5 + - + +
46E PHE 3.8 0.2 - - - -
47E ILE* 1.3 76.3 - - - +
49E GLU* 1.3 80.2 + - - +
50E GLY* 3.4 28.9 - - - -
51E SER* 3.0 32.9 + - - -
54E PHE* 3.0 14.5 - - - -
189F ARG* 4.0 1.8 - - - -
196F PRO* 3.6 18.9 - - + +
199F ILE* 3.5 39.5 - - + -
200F ASP* 3.4 41.7 + - + +
203F PHE* 4.2 5.4 - - - -
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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