Contacts of the strand formed by residues 26 - 34 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18F ILE* 4.0 11.8 - - + +
19F VAL 3.2 7.4 - - - +
20F ARG* 3.4 35.7 + - + +
24F GLY 3.0 4.6 + - - +
25F ARG* 1.3 73.2 - - - +
27F PHE* 1.3 61.5 + - - +
28F ARG* 5.8 1.2 - - - -
47F GLU* 3.4 2.8 - - - +
48F ILE* 2.5 63.5 + - + +
49F GLN 5.1 5.3 - - - +
51F GLY* 5.5 2.9 - - - -
69F PHE* 5.3 3.8 - - - -
47G GLU* 5.6 1.4 - - - +
55G ARG* 3.6 36.8 + - - -
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Residues in contact with PHE 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69E PHE* 3.8 33.4 - + - -
17F VAL 4.3 0.4 - - - -
18F ILE* 3.2 8.1 - - - +
19F VAL* 2.9 35.0 + - + +
21F LEU* 3.7 35.4 - - + -
25F ARG* 4.7 1.8 - - + -
26F GLU* 1.3 78.8 - - - +
28F ARG* 1.3 65.7 + - - +
29F GLY 4.2 0.2 - - - -
42F LEU* 4.1 17.0 - - + -
45F ALA* 4.5 7.0 - - + -
46F GLU 3.3 15.5 - - - -
47F GLU* 4.2 27.1 - - + -
57F VAL* 4.4 17.3 - - + -
60F VAL* 4.4 24.0 - - + -
62F ILE* 4.8 6.3 - - + -
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Residues in contact with ARG 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F PRO* 6.3 0.8 - - - +
17F VAL 3.3 4.3 - - - +
18F ILE* 3.8 26.0 - - + +
26F GLU* 5.8 2.5 - - - +
27F PHE* 1.3 80.7 - - - +
29F GLY* 1.3 58.2 + - - +
44F ASP 4.0 0.5 - - - +
45F ALA* 3.2 6.0 - - - -
46F GLU* 3.1 44.5 + - - +
48F ILE* 3.0 31.0 - - + +
73F ALA* 3.7 26.5 - - - +
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Residues in contact with GLY 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F PRO* 3.3 6.6 - - - +
17F VAL* 2.7 46.7 + - - +
27F PHE 4.2 0.4 - - - -
28F ARG* 1.3 74.0 - - - +
30F THR* 1.3 59.1 + - - -
42F LEU* 4.6 6.2 - - - +
43F LEU 3.8 0.2 - - - -
44F ASP 3.7 13.2 - - - -
45F ALA* 3.8 8.9 - - - +
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Residues in contact with THR 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F LYS* 3.0 42.0 - - - +
15F SER 3.8 5.2 - - - +
16F PRO* 4.2 5.6 - - + +
29F GLY* 1.3 71.3 - - - -
31F LEU* 1.3 61.4 + - - +
32F ASP* 3.0 6.0 + - - -
42F LEU* 3.2 5.0 - - - -
43F LEU* 3.0 46.0 + - + +
44F ASP* 4.3 4.5 + - - +
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Residues in contact with LEU 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F LEU* 3.9 46.4 - - + +
12F SER* 4.0 17.9 - - - +
13F LEU* 3.6 14.3 - - + -
14F LYS 3.0 22.7 + - - -
15F SER 3.3 10.0 + - - +
17F VAL* 3.9 18.4 - - + -
29F GLY 3.7 2.4 + - - -
30F THR* 1.3 69.0 - - - +
32F ASP* 1.3 58.6 + - - +
33F GLY 3.5 16.8 - - - +
34F TYR* 5.0 2.2 - - + -
40F LEU* 4.4 14.4 - - + -
41F VAL 3.3 17.3 - - - +
42F LEU* 3.8 13.5 - - + -
70F VAL* 5.3 2.5 - - + -
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Residues in contact with ASP 32 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3E PRO* 3.6 32.4 - - - +
8E VAL* 4.4 7.8 - - - +
11E ARG* 4.8 4.0 + - - -
13F LEU* 3.5 12.1 - - - +
14F LYS* 5.2 2.5 - - - +
30F THR* 3.0 5.4 + - - +
31F LEU* 1.3 73.4 - - - +
33F GLY* 1.3 60.0 + - - +
41F VAL* 3.0 30.3 + - + +
43F LEU* 3.4 38.9 - - + +
52I GLU* 5.3 3.8 - - - +
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Residues in contact with GLY 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E PRO* 4.5 14.1 - - - -
13F LEU* 3.9 9.6 - - - -
31F LEU* 3.5 10.0 - - - +
32F ASP* 1.3 83.9 - - - +
34F TYR* 1.3 66.5 + - - +
40F LEU* 3.5 0.5 - - - -
41F VAL* 3.0 36.2 + - - +
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Residues in contact with TYR 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E PRO 3.7 12.2 + - - +
4E ARG* 4.1 2.8 - - - -
5E PRO* 3.3 16.3 - - - +
6F LEU* 3.3 42.4 + - + +
9F LEU* 4.0 21.3 - - + -
10F ASN* 3.4 39.7 + - + +
13F LEU* 4.0 17.9 - - + -
31F LEU* 5.0 2.7 - - + -
33F GLY* 1.3 79.0 - - - +
35F ASP* 1.3 84.3 + - - +
38F MET* 5.3 0.7 - - - -
39F ASN 3.3 15.9 - - - +
40F LEU* 3.8 13.2 - - + -
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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