Contacts of the strand formed by residues 26 - 34 (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 GLU 26 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18I ILE* 4.4 18.0 - - + +
19I VAL 3.4 9.9 - - - +
20I ARG* 2.8 46.9 + - - +
24I GLY 3.8 2.0 - - - +
25I ARG* 1.3 79.0 - - - +
27I PHE* 1.3 67.4 + - - +
28I ARG* 6.0 0.2 - - + -
47I GLU* 3.5 7.1 - - - +
48I ILE* 2.8 54.7 + - + +
69I PHE* 5.0 0.3 - - - -
55J ARG* 3.5 22.7 + - - -
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Residues in contact with PHE 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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69H PHE* 3.8 38.4 - + - -
17I VAL 3.8 0.7 - - - +
18I ILE* 3.5 5.4 - - - +
19I VAL* 2.9 38.9 + - + +
21I LEU* 3.8 29.8 - - + -
25I ARG* 5.7 1.6 - - + -
26I GLU* 1.3 78.2 - - - +
28I ARG* 1.3 62.5 + - - +
29I GLY 4.2 0.2 - - - -
42I LEU* 3.8 15.0 - - + +
45I ALA* 4.2 12.6 - - + -
46I GLU 3.3 13.9 - - - -
47I GLU* 4.1 26.0 - - + -
55I ARG* 6.5 0.2 - - - -
57I VAL* 4.5 8.7 - - + -
60I VAL* 4.0 26.9 - - + -
62I ILE* 4.0 11.7 - - + -
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Residues in contact with ARG 28 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17I VAL 3.6 4.0 - - - -
18I ILE* 3.8 37.3 - - + +
26I GLU* 6.0 0.4 - - + -
27I PHE* 1.3 77.0 - - - +
29I GLY* 1.3 58.8 + - - +
42I LEU* 4.5 0.9 - - - -
44I ASP 4.2 0.2 - - - +
45I ALA* 2.9 7.2 - - - +
46I GLU* 2.9 48.3 + - - +
48I ILE* 3.3 36.2 - - + +
73I ALA* 4.9 6.4 - - - +
55J ARG* 5.3 5.7 - - - +
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Residues in contact with GLY 29 (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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16I PRO* 3.4 4.8 - - - +
17I VAL* 2.8 38.7 + - - +
27I PHE 4.2 0.2 - - - -
28I ARG* 1.3 76.1 - - - +
30I THR* 1.3 63.0 + - - -
42I LEU* 4.3 6.3 - - - +
44I ASP 3.9 13.0 - - - -
45I ALA* 3.9 7.9 - - - -
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Residues in contact with THR 30 (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 LYS* 3.5 37.0 - - - +
15I SER 3.5 7.2 - - - +
16I PRO* 4.9 4.5 - - - +
29I GLY* 1.3 73.5 - - - -
31I LEU* 1.3 62.3 + - - +
32I ASP* 2.9 11.9 + - - +
42I LEU* 3.2 4.7 - - - -
43I LEU* 3.0 44.5 + - + +
44I ASP* 5.0 3.3 + - - +
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Residues in contact with LEU 31 (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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9I LEU* 3.2 44.9 - - + +
12I SER* 3.9 24.9 - - - +
13I LEU* 3.6 11.5 - - + +
14I LYS 3.0 22.9 + - - -
15I SER 3.2 7.7 + - - +
17I VAL* 4.0 19.0 - - + +
19I VAL* 6.3 0.2 - - + -
29I GLY 3.8 2.0 + - - -
30I THR* 1.3 68.9 - - - +
32I ASP* 1.3 58.7 + - - +
33I GLY 3.5 23.3 - - - +
34I TYR* 4.6 3.6 - - + -
40I LEU* 4.3 20.4 - - + -
41I VAL 3.6 5.8 - - - +
42I LEU* 3.8 11.3 - - + +
70I VAL* 5.4 2.5 - - + -
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Residues in contact with ASP 32 (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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3H PRO* 4.3 28.6 - - - +
8H VAL* 4.8 0.3 - - - +
11H ARG* 4.6 10.9 + - - -
13I LEU* 3.2 16.2 - - - +
14I LYS* 5.1 8.6 + - - +
30I THR* 2.9 4.1 + - - -
31I LEU* 1.3 72.8 - - - +
33I GLY* 1.3 57.9 + - - +
41I VAL* 2.7 28.3 + - + +
43I LEU* 3.4 42.1 - - + +
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Residues in contact with GLY 33 (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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3H PRO* 4.2 16.2 - - - -
13I LEU* 4.3 3.6 - - - -
31I LEU* 3.5 10.1 - - - +
32I ASP* 1.3 82.3 - - - +
34I TYR* 1.3 69.9 + - - +
40I LEU* 3.6 0.2 - - - -
41I VAL* 3.0 37.7 + - - +
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Residues in contact with TYR 34 (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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3H PRO 4.4 7.8 + - - +
4H ARG* 4.9 0.7 - - - -
5H PRO* 3.4 15.3 - - - +
6I LEU* 3.5 28.4 + - + +
9I LEU* 4.2 12.8 - - + -
10I ASN* 2.9 52.9 + - + +
13I LEU* 3.9 23.1 - - + -
31I LEU* 4.6 4.9 - - + -
33I GLY* 1.3 78.6 - - - +
35I ASP* 1.3 74.2 + - - +
38I MET 5.5 0.2 - - - -
39I ASN 3.2 17.7 - - - +
40I LEU* 3.7 13.0 - - + -
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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