Contacts of the strand formed by residues 19 - 25 (chain M) in PDB entry 5EEZ
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 VAL 19 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12M ILE* 4.7 0.2 - - + -
14M ALA* 3.8 14.6 - - + -
16M GLU* 3.4 21.5 - - + +
18M GLY* 1.3 76.6 - - - +
20M ASN* 1.3 70.2 + - - +
21M VAL* 4.5 1.6 - - + -
36M GLU 3.5 0.5 - - - +
37M LYS* 3.2 4.9 - - - -
38M LEU* 2.8 45.1 + - + +
57M VAL* 4.2 14.4 - - + -
58M ARG 3.4 11.2 - - - +
59M GLY* 4.0 1.8 - - - -
60M LYS 3.2 38.1 - - - +
61M ALA* 4.4 8.1 - - + -
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Residues in contact with ASN 20 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18M GLY* 2.8 29.3 + - - -
19M VAL* 1.3 73.7 + - - +
21M VAL* 1.3 63.6 + - - +
22M ILE* 3.8 11.8 - - + +
35M SER* 3.0 22.1 + - - +
36M GLU 3.4 2.5 - - - -
37M LYS* 3.0 29.3 + - - +
56M LYS 3.6 1.2 - - - +
57M VAL* 3.5 7.4 - - - +
58M ARG* 2.9 49.2 + - + +
109W U 4.2 4.3 + - - +
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Residues in contact with VAL 21 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12M ILE* 3.5 50.3 - - + -
19M VAL* 4.5 2.5 - - + -
20M ASN* 1.3 74.6 - - - +
22M ILE* 1.3 63.3 + - - +
23M GLY 4.1 0.2 + - - -
34M HIS 3.9 1.2 - - - +
35M SER* 3.6 0.7 - - - -
36M GLU* 2.8 35.3 + - - +
38M LEU* 4.0 13.2 - - + -
44M LEU* 3.8 27.8 - - + -
46M ALA* 5.4 0.7 - - + -
55M ILE* 3.8 16.8 - - + -
56M LYS 3.8 2.0 - - - -
57M VAL* 4.6 3.6 - - + +
101N TRP* 4.3 14.0 - - + -
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Residues in contact with ILE 22 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20M ASN* 4.1 11.7 - - + +
21M VAL* 1.3 76.8 - - - +
23M GLY* 1.3 61.1 + - - +
24M LEU* 3.7 3.0 + - + -
32M PHE* 3.4 52.0 - - + -
34M HIS 3.4 10.1 - - - +
35M SER* 4.0 15.0 - - - +
55M ILE* 3.3 8.1 - - - +
56M LYS* 2.8 51.0 + - + +
58M ARG* 3.6 42.8 - - + +
101N TRP* 4.1 2.0 - - - -
109W U 4.5 4.5 - - - +
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Residues in contact with GLY 23 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22M ILE* 1.3 70.3 - - - +
24M LEU* 1.3 63.7 + - - -
32M PHE* 3.5 3.8 - - - -
33M HIS* 2.9 37.0 + - - -
34M HIS 2.9 13.9 + - - -
52M THR* 3.8 11.4 - - - -
54M ALA 3.8 0.2 - - - -
55M ILE* 4.9 0.2 - - - -
101N TRP* 3.6 24.6 - - - -
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Residues in contact with LEU 24 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34L HIS* 5.2 0.4 - - + +
36L GLU* 4.0 17.7 - - + +
44L LEU* 4.0 23.1 - - + -
22M ILE* 3.8 15.7 - - + +
23M GLY* 1.3 79.0 - - - -
25M THR* 1.3 66.5 + - - +
30M THR* 3.9 27.6 - - + -
31M ARG 3.5 5.4 - - - +
32M PHE* 3.9 28.7 - - + -
33M HIS* 4.0 1.3 - - - -
52M THR* 3.2 6.9 - - - -
53M SER 3.2 21.8 + - - -
54M ALA* 2.7 29.5 + - + +
56M LYS* 4.0 14.1 - - + +
101M TRP* 5.3 2.0 - - + -
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Residues in contact with THR 25 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24M LEU* 1.3 74.4 - - - +
26M ARG* 1.3 59.5 - - - +
29M ASP 2.8 24.6 + - - -
30M THR* 4.2 1.2 - - - -
31M ARG* 2.9 65.3 + - + +
33M HIS* 3.8 25.6 - - + -
51M HIS 3.4 6.5 - - - +
53M SER* 4.0 0.4 - - - -
101M TRP* 2.8 34.1 + - - +
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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