Contacts of the strand formed by residues 38 - 45 (chain I) 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 LEU 38 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7I PHE* 4.3 20.6 - - + -
17I VAL* 4.0 23.1 - - + -
29I LEU* 4.1 18.6 - - + -
31I SER 3.9 1.1 - - - -
32I VAL* 3.7 23.6 - - + -
36I LEU* 4.0 9.0 - - + +
37I ASN* 1.3 74.9 - - - +
39I LYS* 1.3 60.6 + - - +
40I LEU* 5.0 5.8 - - + -
61I PHE* 3.1 4.3 - - - +
62I ILE* 2.5 52.8 + - + +
67I VAL* 4.5 12.8 - - + -
70I VAL* 4.0 27.8 - - + -
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Residues in contact with LYS 39 (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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44H ALA 4.8 1.8 + - - -
45H ALA* 2.9 41.6 + - + +
48H SER* 3.8 13.5 + - - -
29I LEU* 3.7 2.1 - - - +
30I GLN* 2.9 47.6 + - + +
31I SER* 3.2 27.2 + - - +
38I LEU* 1.3 73.2 - - - +
40I LEU* 1.3 79.9 + - - +
59I ASN* 4.1 24.4 - - - +
60I ILE 3.2 14.6 - - - +
61I PHE* 4.0 13.7 - - + +
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Residues in contact with LEU 40 (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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15I VAL* 4.4 7.4 - - + +
17I VAL* 4.3 25.1 - - + -
25I ILE* 4.4 15.9 - - + -
27I GLY* 4.2 24.0 - - - +
28I THR 3.7 4.3 - - - +
29I LEU* 3.5 34.3 - - + +
30I GLN* 4.9 1.6 - - - +
38I LEU* 5.0 7.9 - - + +
39I LYS* 1.3 92.9 - - - +
41I ASP* 1.3 62.2 + - - +
43I ILE* 4.4 10.5 - - + -
59I ASN* 3.1 9.0 - - - +
60I ILE* 2.7 39.8 + - + +
62I ILE* 5.2 7.4 - - + -
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Residues in contact with ASP 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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27I GLY* 3.5 0.5 - - - -
28I THR* 2.8 41.1 + - - +
30I GLN* 2.5 35.2 + - + +
40I LEU* 1.3 76.1 - - - +
42I ASN* 1.3 92.4 + - - +
43I ILE 3.3 2.0 - - - +
58I ARG* 3.1 15.3 - - - +
59I ASN* 3.9 9.8 + - - +
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Residues in contact with ASN 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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26I LYS* 3.8 3.1 + - - +
27I GLY* 4.2 1.6 - - - -
28I THR* 4.3 12.1 + - - +
41I ASP* 1.3 96.4 + - - +
43I ILE* 1.3 68.9 + - - +
44I SER* 3.3 9.2 + - - -
57I VAL 5.9 0.7 - - - -
58I ARG 3.7 8.8 + - - -
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Residues in contact with ILE 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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25I ILE* 4.4 10.8 - - + -
26I LYS 3.2 9.2 - - - +
40I LEU* 4.4 17.5 - - + +
41I ASP 4.3 0.4 - - - -
42I ASN* 1.3 80.1 - - - +
44I SER* 1.3 62.5 + - - +
45I SER* 4.5 4.7 - - - +
54I LEU* 3.7 37.5 - - + +
55I GLY 5.2 4.5 - - - +
57I VAL* 4.0 24.2 + - + +
58I ARG 4.9 0.4 + - - -
59I ASN* 4.6 2.9 - - - -
60I ILE* 3.9 41.3 - - + +
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Residues in contact with SER 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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24I GLU 4.7 0.2 - - - +
25I ILE* 4.1 0.3 - - - +
26I LYS* 2.7 61.4 + - - +
42I ASN 3.7 5.6 + - - -
43I ILE* 1.3 75.1 - - - +
45I SER* 1.3 60.6 + - - +
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Residues in contact with SER 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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23I ILE* 4.6 7.3 - - - +
24I GLU 4.0 14.5 + - - -
25I ILE* 4.2 14.9 - - - +
43I ILE* 4.2 4.9 - - - +
44I SER* 1.3 75.2 - - - +
46I THR* 1.3 67.1 + - - +
47I ASP* 3.5 9.6 + - - -
51I TYR* 6.0 0.9 - - - -
54I LEU* 4.1 31.4 - - - +
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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