Contacts of the strand formed by residues 26 - 34 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55H ARG* 3.3 30.3 + - - -
18N ILE* 3.8 14.8 - - + +
19N VAL 2.9 21.3 - - - +
20N ARG* 2.9 39.7 + - - +
21N LEU* 4.7 1.8 - - - +
24N GLY 4.2 1.0 - - - +
25N ARG* 1.3 78.4 - - - +
27N PHE* 1.3 67.9 + - - +
28N ARG* 5.6 4.2 + - + -
46N GLU 3.8 0.3 - - - +
47N GLU* 4.6 0.2 - - - -
48N ILE* 2.9 57.7 + - + +
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Residues in contact with PHE 27 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69M PHE* 3.6 39.3 - + + -
18N ILE* 3.5 4.3 - - - +
19N VAL* 3.2 29.3 + - + +
21N LEU* 3.9 27.4 - - + -
25N ARG* 6.0 0.2 - - + -
26N GLU* 1.3 79.8 - - - +
28N ARG* 1.3 66.9 + - - +
42N LEU* 3.7 21.3 - - + -
45N ALA* 4.2 12.8 - - + -
46N GLU 3.1 17.7 - - - -
47N GLU* 4.2 24.9 - - + -
57N VAL* 4.5 8.1 - - + -
60N VAL* 4.1 24.7 - - + -
62N ILE* 4.2 15.3 - - + -
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Residues in contact with ARG 28 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17N VAL 3.6 11.9 - - - +
18N ILE* 4.2 29.1 - - + +
26N GLU* 5.0 4.7 + - + +
27N PHE* 1.3 82.2 - - - +
29N GLY* 1.3 58.1 + - - +
44N ASP 3.9 1.0 - - - +
45N ALA* 2.8 25.3 - - - -
46N GLU* 3.0 24.3 + - - +
48N ILE* 3.9 27.8 - - + +
73N ALA* 5.9 3.4 - - - +
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Residues in contact with GLY 29 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16N PRO* 3.4 6.8 - - - +
17N VAL* 2.9 35.0 + - - +
28N ARG* 1.3 74.6 - - - +
30N THR* 1.3 63.6 + - - -
31N LEU 3.6 0.7 + - - -
42N LEU* 4.4 8.5 - - - +
43N LEU 3.7 8.5 - - - -
44N ASP 3.8 7.6 - - - -
45N ALA* 3.9 5.8 - - - -
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Residues in contact with THR 30 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14N LYS* 3.5 38.2 + - - +
15N SER 3.7 7.7 - - - +
16N PRO* 4.6 4.7 - - - +
29N GLY* 1.3 72.2 - - - -
31N LEU* 1.3 62.0 + - - +
32N ASP* 2.9 13.2 + - - +
42N LEU* 3.2 4.6 - - - -
43N LEU* 3.0 49.4 + - + +
44N ASP* 5.4 2.8 + - - +
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Residues in contact with LEU 31 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9N LEU* 3.6 42.2 - - + +
12N SER* 3.8 25.1 - - - +
13N LEU* 3.6 8.1 - - + +
14N LYS* 2.9 26.5 + - - -
15N SER 3.2 10.3 + - - +
17N VAL* 4.2 16.2 - - + -
29N GLY 3.6 3.6 + - - -
30N THR* 1.3 69.1 - - - +
32N ASP* 1.3 58.9 + - - +
33N GLY 3.3 26.9 - - - +
34N TYR* 4.9 2.9 - - + -
40N LEU* 4.5 19.1 - - + -
41N VAL 3.7 5.8 - - - +
42N LEU* 3.8 12.3 - - + +
70N VAL* 5.3 2.7 - - + -
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Residues in contact with ASP 32 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2M PRO* 3.2 29.8 - - - +
3M PRO* 3.2 33.7 - - - +
8M VAL* 5.3 0.2 - - - +
11M ARG* 5.1 0.7 + - - -
13N LEU* 3.5 4.6 - - - +
14N LYS* 5.0 10.1 - - - +
30N THR* 2.9 3.9 + - + +
31N LEU* 1.3 74.1 - - - +
33N GLY* 1.3 55.0 + - - +
41N VAL* 2.7 29.3 + - + +
43N LEU* 3.5 40.6 - - + +
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Residues in contact with GLY 33 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2M PRO* 5.1 1.3 - - - -
3M PRO 3.8 14.4 - - - -
5M PRO* 4.6 0.7 - - - -
13N LEU* 3.8 10.5 - - - +
31N LEU* 3.3 17.3 - - - +
32N ASP* 1.3 80.3 - - - +
34N TYR* 1.3 70.2 + - - +
40N LEU* 3.8 0.7 - - - -
41N VAL* 3.5 21.1 + - - +
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Residues in contact with TYR 34 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3M PRO 4.7 0.4 + - - -
4M ARG* 4.1 18.6 + - - +
5M PRO* 3.4 14.7 - - - +
6N LEU* 4.2 21.4 + - + +
9N LEU* 4.3 23.6 - - + -
10N ASN* 2.8 55.8 + - + +
13N LEU* 4.4 15.3 - - + -
31N LEU* 4.9 4.3 - - + -
33N GLY* 1.3 82.0 - - - +
35N ASP* 1.3 75.6 + - - +
38N MET* 5.3 0.7 - - - -
39N ASN 3.0 16.6 - - - +
40N LEU* 3.9 14.4 - - + -
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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