Contacts of the strand formed by residues 40 - 49 (chain E) in PDB entry 1I5L
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 LEU 40 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9E LEU* 4.5 8.5 - - + -
19E VAL* 3.6 42.6 - - + -
31E LEU* 4.6 12.1 - - + -
33E GLY 3.7 4.0 - - - +
34E TYR* 4.1 13.9 - - + -
38E MET* 3.1 35.9 - - + +
39E ASN* 1.3 78.3 - - - +
41E VAL* 1.3 67.7 + - - +
42E LEU* 4.2 2.9 - - + -
60E VAL 3.8 0.4 - - - +
61E VAL* 3.3 6.2 - - - +
62E ILE* 2.9 42.2 + - + +
67E VAL* 4.2 8.5 - - + -
70E VAL* 3.8 17.9 - - + -
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Residues in contact with VAL 41 (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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3D PRO 5.8 0.2 - - - -
4D ARG 4.2 3.8 - - - -
5D PRO* 3.4 40.2 - - + -
8D VAL* 3.9 23.6 - - + -
31E LEU* 3.8 4.7 - - - +
32E ASP* 2.8 42.6 + - + +
33E GLY* 3.1 19.0 + - - +
40E LEU* 1.3 80.6 - - - +
42E LEU* 1.3 66.8 + - - +
43E LEU* 5.0 5.8 - - + -
59E SER* 5.5 1.3 - - - -
60E VAL 3.2 9.6 - - - +
61E VAL* 4.0 11.0 - - + -
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Residues in contact with LEU 42 (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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17E VAL* 3.9 26.0 - - + -
19E VAL* 4.2 12.1 - - + -
27E PHE* 3.7 34.5 - - + +
28E ARG 5.0 0.4 - - - +
29E GLY 4.4 4.7 - - - +
30E THR 3.3 14.4 - - - +
31E LEU* 4.0 9.9 - - + -
40E LEU* 5.1 2.5 - - + -
41E VAL* 1.3 79.9 - - - +
43E LEU* 1.3 63.7 + - - +
45E ALA* 4.2 11.2 - - + -
59E SER* 2.9 9.5 - - - -
60E VAL* 2.9 46.8 + - + +
62E ILE* 3.9 19.5 - - + -
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Residues in contact with LEU 43 (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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11D ARG* 6.1 3.6 - - - +
29E GLY* 4.0 0.3 - - - -
30E THR* 2.9 39.7 + - + +
32E ASP* 3.9 32.8 - - + +
41E VAL* 5.0 5.2 - - + -
42E LEU* 1.3 77.4 - - - +
44E ASP* 1.3 84.6 + - - +
45E ALA 3.5 0.2 - - - -
58E GLY 3.7 4.0 - - - +
59E SER* 3.3 25.4 - - - -
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Residues in contact with ASP 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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28E ARG 3.8 0.7 - - - +
29E GLY* 3.7 10.9 - - - -
30E THR* 4.4 2.6 + - - +
43E LEU* 1.3 86.9 - - - +
45E ALA* 1.3 59.1 + - - +
46E GLU* 5.4 1.9 - - - +
57E VAL 3.6 7.2 - - - -
58E GLY* 3.1 17.6 + - - +
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Residues in contact with ALA 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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27E PHE* 4.0 20.2 - - + -
28E ARG 3.0 15.7 - - - +
29E GLY* 4.5 0.4 - - - -
42E LEU* 4.2 22.2 - - + +
43E LEU 4.6 0.7 - - - -
44E ASP* 1.3 75.5 - - - +
46E GLU* 1.3 64.9 + - - +
56E LYS* 3.3 3.9 - - - +
57E VAL* 2.7 49.7 + - + +
60E VAL* 4.4 1.8 - - + -
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Residues in contact with GLU 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 PHE* 3.4 7.3 - - - -
28E ARG* 3.1 48.6 + - + +
44E ASP 5.4 1.8 - - - +
45E ALA* 1.3 79.3 - - - +
47E GLU* 1.3 64.2 + - - +
48E ILE* 3.6 9.2 + - + +
53E VAL* 4.3 26.9 - - + +
55E ARG 3.4 7.2 - - - +
56E LYS* 3.3 36.3 - - + -
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Residues in contact with GLU 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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20D ARG* 3.6 14.8 + - - -
69D PHE* 4.2 11.4 - - - -
21E LEU* 6.0 0.3 - - - +
25E ARG* 3.0 38.6 + - + +
26E GLU 3.4 5.6 - - - +
27E PHE* 4.0 31.0 - - + -
46E GLU* 1.3 72.2 - - - +
48E ILE* 1.3 60.7 + - - +
53E VAL* 3.5 5.5 - - - +
54E VAL* 2.9 35.5 + - + +
55E ARG* 2.9 47.3 + - + +
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Residues in contact with ILE 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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24E GLY 4.6 1.0 - - - +
25E ARG* 3.6 7.6 - - - -
26E GLU* 2.6 57.6 + - + +
28E ARG* 3.2 38.4 - - + +
46E GLU* 3.7 14.6 - - + +
47E GLU* 1.3 80.5 - - - +
49E GLN* 1.3 63.0 + - - +
50E ASN 4.2 0.6 + - - -
51E GLY* 3.9 27.6 - - - +
52E GLU 3.5 10.5 - - - +
53E VAL* 4.5 15.0 - - + -
54E VAL* 4.8 0.4 - - - -
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Residues in contact with GLN 49 (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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24E GLY 5.5 2.5 - - - -
25E ARG* 3.1 46.6 + - + +
48E ILE* 1.3 73.2 - - - +
50E ASN* 1.3 88.6 + - + +
51E GLY 3.3 0.9 - - - -
52E GLU* 2.9 24.2 + - - +
54E VAL* 3.7 25.5 - - + +
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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