Contacts of the strand formed by residues 31 - 39 (chain J) in PDB entry 5UK7
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 LYS 31 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23J SER* 3.4 21.5 + - - -
24J ILE 3.9 3.4 - - - +
25J TYR* 3.3 48.2 + - + +
29J GLY 3.3 3.4 + - - +
30J ILE* 1.3 76.0 - - - +
32J LEU* 1.3 71.9 + - - +
33J GLN* 3.2 40.0 + - + +
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Residues in contact with LEU 32 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61F THR* 3.8 28.9 - - + -
22J VAL 3.6 1.2 - - - +
23J SER* 3.6 0.7 - - - -
24J ILE* 2.8 48.8 + - + +
26J LEU* 4.0 21.5 - - + -
30J ILE* 3.7 16.8 - - + -
31J LYS* 1.3 82.9 - - - +
33J GLN* 1.3 61.4 + - - +
46J LEU* 3.8 15.3 - - + +
48J ASN* 6.3 0.2 - - - +
52J GLN* 4.0 15.9 - - - +
54J VAL* 3.8 17.3 - - + -
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Residues in contact with GLN 33 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22J VAL 3.3 5.4 - - - +
23J SER* 3.7 12.9 + - - +
31J LYS* 3.2 43.9 + - + +
32J LEU* 1.3 76.1 - - - +
34J GLY* 1.3 58.7 + - - +
46J LEU* 4.1 5.4 - - - +
48J ASN* 3.7 24.5 + - - +
65J SER* 4.2 9.4 + - - +
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Residues in contact with GLY 34 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21J PRO* 3.5 4.9 - - - +
22J VAL* 2.8 35.4 + - - +
33J GLN* 1.3 76.7 - - - +
35J GLN* 1.3 65.3 + - - -
46J LEU* 3.6 13.5 - - - +
47J LYS 4.9 0.2 - - - -
48J ASN* 4.5 11.4 - - - -
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Residues in contact with GLN 35 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19J ARG* 3.8 41.2 + - + +
20J VAL 4.3 4.9 - - - +
21J PRO* 4.3 15.2 - - + +
34J GLY* 1.3 77.1 - - - +
36J ILE* 1.3 70.5 + - - +
37J GLU 2.9 0.9 + - - -
46J LEU* 3.7 4.1 - - - +
47J LYS* 2.8 50.9 + - + +
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Residues in contact with ILE 36 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12J LEU* 3.6 36.6 - - + +
15J LEU* 3.8 35.8 + - + +
16J ARG* 4.1 18.4 - - + +
19J ARG* 5.6 3.6 - - - +
20J VAL 4.7 3.2 + - - -
22J VAL* 3.8 21.9 - - + +
24J ILE* 4.7 4.0 - - + -
34J GLY 4.3 0.2 + - - -
35J GLN* 1.3 73.8 - - - +
37J GLU* 1.3 61.7 + - - +
38J SER* 3.5 28.0 - - - +
39J PHE* 4.3 13.7 - - + -
44J ILE* 3.8 17.5 - - + -
45J LEU 3.9 3.8 - - - -
46J LEU* 4.8 2.2 - - + -
62J VAL* 4.6 3.6 - - + -
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Residues in contact with GLU 37 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16J ARG* 3.7 17.6 + - - +
35J GLN* 2.9 1.7 + - - -
36J ILE* 1.3 74.6 - - - +
38J SER* 1.3 68.3 + - - +
45J LEU* 2.8 40.5 + - + +
47J LYS* 4.1 30.3 + - + +
51J SER* 5.8 2.5 - - - -
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Residues in contact with SER 38 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2F ALA* 5.5 1.0 - - - +
7F LEU* 3.3 19.8 - - - +
16J ARG* 4.7 5.6 - - - +
36J ILE* 3.5 4.8 - - - +
37J GLU* 1.3 95.9 - - - +
39J PHE* 1.3 77.2 + - - +
44J ILE* 3.4 6.1 - - - +
45J LEU* 2.7 36.8 + - - +
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Residues in contact with PHE 39 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2F ALA* 3.3 40.1 - - + +
6F SER* 5.4 0.2 + - - -
7F LEU* 3.5 10.3 - - - +
9J ASP* 3.6 43.7 - - + -
12J LEU* 3.7 37.2 - - + -
13J ASN* 3.8 26.0 - - - -
16J ARG* 4.7 7.2 - - - -
36J ILE* 4.3 6.5 - - + -
38J SER* 1.3 88.1 + - - +
40J ASP* 1.3 74.9 + - - +
43J VAL 3.2 15.0 - - - +
44J ILE* 3.8 17.3 - - + -
56J LYS* 4.3 1.6 - - - -
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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