Contacts of the strand formed by residues 24 - 32 (chain N) in PDB entry 4M75
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 ILE 24 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136H TRP* 6.3 2.9 - - + -
16N GLN* 3.5 44.0 - - + +
17N ILE 3.4 7.0 - - - +
18N GLU* 4.4 21.3 - - + +
22N GLY 3.3 15.5 - - - +
23N GLU* 1.3 74.0 - - - +
25N ILE* 1.3 70.8 + - - +
26N GLN* 5.1 3.4 - - + +
45N GLU* 3.3 27.6 + - - +
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Residues in contact with ILE 25 (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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101M SER* 5.7 2.0 - - - -
15N MSE 3.8 1.2 - - - +
16N GLN* 3.3 1.8 - - - -
17N ILE* 2.7 49.2 + - + +
19N LEU* 4.4 18.4 - - + -
23N GLU* 4.8 1.8 - - - +
24N ILE* 1.3 83.8 - - - +
26N GLN* 1.3 65.3 + - - +
27N GLY 4.2 0.2 + - - -
40N LEU* 4.3 15.0 - - + +
43N VAL* 3.5 26.9 - - + -
44N THR 3.6 2.9 - - - +
45N GLU* 3.9 24.2 - - + +
69N ILE* 3.9 17.3 - - + -
71N ILE* 3.8 23.8 - - + -
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Residues in contact with GLN 26 (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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15N MSE 3.5 4.9 - - - +
16N GLN* 3.7 35.6 + - + +
24N ILE* 5.3 3.0 - - + +
25N ILE* 1.3 75.2 - - - +
27N GLY* 1.3 59.0 + - - +
42N ASN 3.3 0.4 - - - +
43N VAL* 3.2 4.7 - - - +
44N THR* 2.8 55.6 + - + +
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Residues in contact with GLY 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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14N GLN* 3.4 6.3 - - - +
15N MSE 3.2 30.4 + - - +
26N GLN* 1.3 72.9 - - - +
28N ILE* 1.3 64.7 + - - -
29N LEU 3.9 0.7 + - - -
40N LEU* 3.9 19.5 - - - +
42N ASN 2.6 18.6 - - - -
43N VAL* 4.3 0.7 - - - -
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Residues in contact with ILE 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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12N GLY* 3.3 28.3 - - - +
13N GLN 3.0 19.1 - - - +
14N GLN* 4.5 10.5 - - + +
27N GLY* 1.3 75.7 - - - +
29N LEU* 1.3 59.7 + - - +
40N LEU* 4.0 2.0 - - - -
41N SER* 2.2 52.6 + - - +
42N ASN* 3.2 34.2 + - + +
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Residues in contact with LEU 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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7N LEU* 3.2 32.8 - - + +
10N ALA* 4.0 21.1 - - + +
11N LYS* 3.8 11.3 - - + -
12N GLY* 2.8 32.6 + - - -
13N GLN 3.2 7.2 + - - +
15N MSE 3.8 23.4 - - - +
27N GLY 3.9 3.8 + - - -
28N ILE* 1.3 69.1 - - - +
30N THR* 1.3 59.7 + - - +
31N ASN 3.5 27.4 - - - +
32N VAL* 4.7 6.5 - - + -
38N LEU* 3.6 27.6 - - + -
39N THR 3.7 5.8 - - - +
40N LEU* 3.9 10.7 - - + +
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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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11N LYS* 4.4 11.2 - - - +
28N ILE 3.1 0.4 + - - -
29N LEU* 1.3 72.4 - - - +
31N ASN* 1.3 65.3 + - + +
39N THR* 2.6 25.5 + - - +
40N LEU 4.4 0.2 - - - -
41N SER* 3.0 35.8 + - - -
68N GLU* 5.0 6.1 + - - +
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Residues in contact with ASN 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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11N LYS* 3.9 28.0 + - - +
29N LEU* 3.5 6.7 - - - +
30N THR* 1.3 85.8 - - + +
32N VAL* 1.3 98.7 + - - +
38N LEU* 3.1 7.9 - - - +
39N THR* 2.9 38.0 + - - +
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Residues in contact with VAL 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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4N LEU* 4.3 4.0 - - + -
7N LEU* 3.9 33.0 - - + +
8N THR* 3.7 41.7 - - + -
11N LYS* 4.6 6.9 + - - +
29N LEU* 4.7 4.5 - - + -
31N ASN* 1.3 97.2 + - - +
33N ASP* 1.3 73.8 + - - +
36N MSE 4.3 5.8 - - - -
37N ASN 3.6 6.7 - - - +
38N LEU* 4.4 9.0 - - + -
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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