Contacts of the strand formed by residues 73 - 84 (chain J) in PDB entry 5LK5
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 ARG 73 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45J ASP* 3.5 28.9 + - - +
47J GLY* 3.8 13.2 - - - +
70J GLN* 3.9 35.5 + - + +
71J LYS 3.1 20.7 + - - +
72J ALA* 1.3 103.4 + - - +
74J PHE* 1.3 60.0 + - - +
75J TYR* 3.4 24.1 - - + -
319J TRP* 3.3 9.1 - - - -
320J GLN 3.0 28.8 + - - -
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Residues in contact with PHE 74 (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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45J ASP 5.2 1.4 + - - +
46J PHE* 3.3 28.3 - + + -
47J GLY 2.8 29.8 + - - -
73J ARG* 1.3 74.5 - - - +
75J TYR* 1.3 57.5 + - - +
124J GLY* 6.5 0.9 - - - -
317J ASP* 6.1 0.7 - - - -
318J LEU 3.4 7.6 - - - +
319J TRP* 3.7 43.5 - + + -
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Residues in contact with TYR 75 (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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46J PHE* 4.4 3.5 - - - -
47J GLY* 3.5 34.3 - - - -
48J LYS 3.6 12.8 - - - -
49J PHE* 3.7 30.7 - + + -
68J THR* 3.5 29.6 - - + -
69J SER 3.4 2.8 + - - -
70J GLN* 2.5 41.9 + - - +
73J ARG* 3.4 28.3 - - + -
74J PHE* 1.3 74.0 - - - +
76J ALA* 1.3 65.2 + - - +
316J LEU 3.7 2.2 - - - -
317J ASP* 3.3 5.2 - - - -
318J LEU* 2.8 45.4 + - + +
320J GLN* 4.2 9.0 - - + -
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Residues in contact with ALA 76 (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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39J GLU* 3.8 4.2 - - - +
40J SER* 3.0 44.0 + - - +
46J PHE* 3.8 27.1 - - + +
47J GLY 5.2 1.2 + - - -
49J PHE* 4.5 1.8 - - - -
75J TYR* 1.3 78.7 - - - +
77J LEU* 1.3 60.7 + - - +
122J MET* 4.0 11.0 - - + +
316J LEU 3.3 5.6 - - - -
317J ASP* 4.4 9.6 - - - +
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Residues in contact with LEU 77 (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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33J TRP* 4.2 16.8 - - + -
37J TRP* 3.7 34.7 - - + -
38J ILE 3.5 18.8 - - - +
39J GLU* 3.5 31.0 - - + -
49J PHE* 3.7 32.8 - - + -
66J LEU* 3.8 21.5 - - + -
76J ALA* 1.3 76.2 - - - +
78J SER* 1.3 63.1 + - - +
122J MET* 4.7 1.3 - - - -
315J GLY* 3.6 0.3 - - - -
316J LEU* 2.8 33.6 + - + +
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Residues in contact with SER 78 (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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37J TRP* 3.2 8.6 - - - -
38J ILE 2.8 37.3 + - - -
77J LEU* 1.3 74.2 - - - +
79J ALA* 1.3 60.3 + - - +
119J GLN* 3.0 33.6 + - - +
122J MET* 3.2 35.9 - - - +
313J VAL* 3.4 10.8 - - - -
314J LEU 3.3 7.4 - - - -
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Residues in contact with ALA 79 (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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23J PHE* 3.6 30.1 - - + -
36J ARG 3.6 12.8 - - - +
37J TRP* 3.6 26.4 - - + +
78J SER* 1.3 75.7 - - - +
80J SER* 1.3 60.2 + - - +
81J PHE* 3.8 4.4 - - - -
119J GLN* 3.8 2.9 - - - +
313J VAL* 3.3 2.1 - - - -
314J LEU* 2.9 38.1 + - - +
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Residues in contact with SER 80 (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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23J PHE* 4.3 8.7 - - - -
36J ARG 4.2 5.4 + - - +
79J ALA* 1.3 75.2 - - - +
81J PHE* 1.3 65.3 + - - +
115J ASN* 5.2 4.3 - - - -
119J GLN* 3.6 25.8 + - - +
312J GLY 3.2 11.7 - - - -
313J VAL* 4.1 5.2 - - - -
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Residues in contact with PHE 81 (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 TYR* 3.4 23.1 - - + +
23J PHE* 4.0 22.7 - + + -
79J ALA 3.8 4.9 - - - -
80J SER* 1.3 79.8 - - - +
82J GLU* 1.3 78.5 + - - +
83J PRO* 3.0 9.4 - - - +
84J PHE* 3.7 20.4 - + - -
112J LEU* 4.8 2.9 - - + -
115J ASN* 4.7 1.6 - - - +
311J PHE* 3.4 29.4 - - + -
312J GLY* 3.0 23.2 + - - +
313J VAL 3.6 8.1 - - - -
314J LEU* 3.5 29.4 - - + -
332J ILE* 4.4 15.0 - - + -
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Residues in contact with GLU 82 (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 TYR* 4.8 7.2 - - - +
81J PHE* 1.3 82.4 - - - +
83J PRO* 1.3 89.8 - - - +
84J PHE* 3.6 5.0 + - - +
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Residues in contact with PRO 83 (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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81J PHE 3.0 7.8 - - - +
82J GLU* 1.3 107.4 - - - +
84J PHE* 1.3 61.8 + - - +
115J ASN* 3.5 32.5 - - - +
310J ASN* 4.0 20.6 - - - +
311J PHE 3.0 14.8 - - - +
312J GLY* 4.6 0.2 - - - -
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Residues in contact with PHE 84 (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 TYR* 3.6 67.3 - + + -
81J PHE* 3.7 21.1 - + - -
82J GLU 4.2 1.8 - - - +
83J PRO* 1.3 77.3 - - - +
85J SER* 1.3 75.6 + - - +
86J ASN* 4.3 4.5 - - + -
89J GLN* 5.8 0.2 - - - +
91J LEU* 3.6 25.8 - - + -
112J LEU* 5.7 0.7 - - + -
309J ASP 4.3 2.7 - - - -
310J ASN* 3.4 3.8 - - - -
311J PHE* 2.8 67.6 + + + +
332J ILE* 3.9 8.5 - - + -
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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