Contacts of the strand formed by residues 34 - 38 (chain B) in PDB entry 5MKV
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 ASP 34 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18B LEU* 4.2 7.3 - - + +
19B ILE 3.4 9.0 - - - +
20B LYS* 3.3 27.7 - - - +
21B GLY* 2.7 29.5 + - - -
33B ALA* 1.3 76.2 - - - +
35B ILE* 1.3 61.8 + - - +
45B ILE* 3.3 7.4 - - - +
46B GLY 2.8 40.7 + - - +
47B GLU* 4.8 5.8 - - - +
48B ASN* 4.5 11.1 + - - -
49B LEU* 3.7 17.0 + - + +
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Residues in contact with ILE 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B LEU 3.7 1.2 - - - +
18B LEU* 3.4 7.3 - - - +
19B ILE* 2.9 46.9 + - + +
24B ILE* 3.8 30.3 - - + -
33B ALA 4.4 2.9 - - - +
34B ASP* 1.3 79.2 - - - +
36B TYR* 1.3 61.8 + - - +
37B MET* 4.4 12.6 - - + +
42B ILE* 3.8 26.2 - - + -
44B GLN 3.5 3.8 - - - +
45B ILE* 4.5 2.2 - - + -
65B VAL* 3.8 22.7 - - + -
401B ILE* 4.0 4.7 - - + -
409B LEU* 3.8 32.1 - - + -
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Residues in contact with TYR 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ARG* 3.1 42.7 + - + +
17B LEU 3.5 14.1 - - - -
18B LEU* 4.4 4.7 - - + -
35B ILE* 1.3 73.6 - - - +
37B MET* 1.3 68.9 + - - +
38B GLU* 3.3 20.3 + - - -
42B ILE* 3.7 2.4 - - - -
43B LYS* 2.8 44.0 + - + -
44B GLN* 2.9 44.7 + - + +
49B LEU* 4.1 10.0 - - + +
50B ILE 5.0 0.4 - - - -
51B VAL* 3.6 26.9 - - + -
52B PRO* 3.6 15.8 - - + +
55B VAL* 4.2 9.6 - - + -
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Residues in contact with MET 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ASP 4.5 0.7 - - - +
16B ARG* 3.4 1.0 - - - -
17B LEU* 2.8 70.0 + - + +
19B ILE* 4.3 15.5 - - - -
35B ILE* 4.4 8.7 - - + -
36B TYR* 1.3 83.9 - - - +
38B GLU* 1.3 64.7 + - - +
41B LEU 3.2 9.9 - - - +
42B ILE* 4.1 10.8 - - + -
407B ALA* 3.7 16.6 - - + -
409B LEU* 3.5 19.5 - - - -
447B ILE* 3.4 24.0 - - + -
450B GLY* 3.5 16.4 - - - +
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Residues in contact with GLU 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ASP 3.9 7.9 - - - +
16B ARG* 3.6 32.4 + - + +
36B TYR* 3.3 26.2 + - + +
37B MET* 1.3 76.9 - - - +
39B ASP* 1.3 84.8 + - - +
40B GLY 3.1 2.9 - - - -
41B LEU* 3.0 21.7 + - - +
43B LYS* 4.0 28.3 + - + +
450B GLY* 6.4 0.4 - - - -
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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