Contacts of the strand formed by residues 40 - 49 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5H PRO* 4.3 0.7 - - - -
9I LEU* 4.8 8.3 - - + -
19I VAL* 4.0 19.5 - - + -
31I LEU* 4.3 16.4 - - + -
33I GLY 3.6 3.8 - - - +
34I TYR* 3.7 16.4 - - + -
38I MET* 3.6 21.1 - - + +
39I ASN* 1.3 91.1 - - - +
41I VAL* 1.3 64.2 + - - +
42I LEU* 5.0 3.4 - - + -
60I VAL 3.3 0.9 - - - +
61I VAL* 3.2 8.1 - - - +
62I ILE* 2.9 45.0 + - + +
67I VAL* 4.0 18.4 - - + -
70I VAL* 3.8 27.4 - - + -
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Residues in contact with VAL 41 (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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4H ARG 4.5 0.2 - - - -
5H PRO* 3.4 39.9 - - + -
8H VAL* 3.5 33.2 - - + -
31I LEU* 3.6 1.0 - - - -
32I ASP* 2.7 46.3 + - + +
33I GLY* 3.0 22.6 + - - +
40I LEU* 1.3 78.2 - - - +
42I LEU* 1.3 66.0 + - - +
43I LEU* 4.7 8.7 - - + -
59I SER* 5.1 1.3 - - - -
60I VAL 3.3 8.1 - - - +
61I VAL* 4.7 2.9 - - + -
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Residues in contact with LEU 42 (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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17I VAL* 4.1 12.6 - - + -
19I VAL* 4.2 17.0 - - + -
27I PHE* 3.8 30.5 - - + +
29I GLY* 4.3 17.0 - - - +
30I THR 3.2 14.1 - - - +
31I LEU* 3.8 17.7 - - + +
40I LEU* 5.0 3.1 - - + -
41I VAL* 1.3 86.9 - - - +
43I LEU* 1.3 65.2 + - - +
45I ALA* 4.1 10.7 - - + +
59I SER* 2.8 27.4 - - - -
60I VAL* 2.9 25.6 + - + +
62I ILE* 4.5 10.8 - - + -
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Residues in contact with LEU 43 (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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8H VAL* 6.2 0.4 - - + -
11H ARG* 5.8 5.4 - - - +
29I GLY* 3.9 0.3 - - - -
30I THR* 3.0 35.8 + - + +
32I ASP* 3.4 42.8 - - + +
41I VAL* 4.7 4.7 - - + -
42I LEU* 1.3 73.8 - - - +
44I ASP* 1.3 84.9 + - - +
45I ALA 3.3 2.2 + - - -
58I GLY 3.1 3.1 - - - +
59I SER* 3.3 24.9 - - - -
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Residues in contact with ASP 44 (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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28I ARG 4.2 0.3 - - - +
29I GLY* 3.9 7.4 - - - -
30I THR* 5.0 3.6 + - - +
43I LEU* 1.3 88.7 - - - +
45I ALA* 1.3 57.6 + - - +
46I GLU* 5.6 1.7 - - - +
57I VAL 3.4 8.3 - - - -
58I GLY* 2.5 21.1 + - - +
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Residues in contact with ALA 45 (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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27I PHE* 4.2 15.5 - - + -
28I ARG 2.9 18.6 - - - +
29I GLY* 3.9 7.2 - - - -
42I LEU* 4.1 19.7 - - + -
43I LEU 4.2 0.9 - - - +
44I ASP* 1.3 77.5 - - - +
46I GLU* 1.3 62.3 + - - +
56I LYS* 3.4 4.2 - - - +
57I VAL* 2.9 43.8 + - + +
60I VAL* 4.6 1.6 - - + -
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Residues in contact with GLU 46 (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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27I PHE* 3.3 9.4 - - - -
28I ARG* 2.9 48.4 + - + +
44I ASP 5.6 1.3 - - - +
45I ALA* 1.3 78.6 - - - +
47I GLU* 1.3 60.6 + - - +
48I ILE* 3.8 7.1 + - + +
53I VAL* 3.9 24.6 - - + +
55I ARG 3.5 6.5 - - - +
56I LYS* 2.6 42.0 + - + +
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Residues in contact with GLU 47 (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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20H ARG* 3.9 9.9 + - - -
69H PHE* 4.3 11.9 - - - -
25I ARG* 3.1 39.3 + - + +
26I GLU 3.5 9.4 - - - +
27I PHE* 4.1 25.1 - - + -
46I GLU* 1.3 70.9 - - - +
48I ILE* 1.3 61.7 + - - +
53I VAL* 3.6 2.1 - - - -
54I VAL* 3.1 44.1 + - + +
55I ARG* 2.9 44.5 + - + +
57I VAL* 6.1 0.2 - - - +
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Residues in contact with ILE 48 (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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24I GLY 4.8 0.5 - - - +
25I ARG* 3.8 1.8 - - - -
26I GLU* 2.8 57.4 + - + +
28I ARG* 3.3 48.5 - - + +
46I GLU* 4.4 13.5 - - + +
47I GLU* 1.3 75.2 - - - +
49I GLN* 1.3 60.6 + - - +
50I ASN 4.2 0.7 + - - +
51I GLY* 3.7 35.2 - - - +
52I GLU 3.6 5.6 - - - +
53I VAL* 4.9 8.3 - - + -
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Residues in contact with GLN 49 (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 GLY 5.6 0.2 - - - +
24I GLY* 4.4 5.8 - - - -
25I ARG* 3.4 59.5 + - + +
47I GLU 3.7 1.2 + - - -
48I ILE* 1.3 70.4 - - - +
50I ASN* 1.3 91.4 + - + +
52I GLU* 3.0 18.0 + - - +
54I VAL* 4.3 11.9 - - + -
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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