Contacts of the strand formed by residues 73 - 84 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45F ASP* 3.2 42.1 + - - +
46F PHE 4.3 3.0 + - - -
47F GLY* 3.8 14.6 - - - +
70F GLN* 3.2 44.4 - - + +
71F LYS 3.3 14.3 + - - +
72F ALA* 1.3 83.5 + - - +
74F PHE* 1.3 59.5 + - - +
75F TYR* 3.4 20.0 - - + -
319F TRP* 3.3 9.1 - - - -
320F GLN 3.0 28.6 + - - -
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Residues in contact with PHE 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43F LYS* 4.0 25.4 - - + -
45F ASP 5.2 1.4 + - - +
46F PHE* 3.3 27.1 - + + -
47F GLY 2.8 25.8 + - - -
73F ARG* 1.3 74.7 - - - +
75F TYR* 1.3 60.5 + - - +
124F GLY* 6.5 0.7 - - - -
318F LEU 3.3 7.9 - - - +
319F TRP* 3.8 44.0 - + + -
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Residues in contact with TYR 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F PHE* 4.4 2.9 - - - -
47F GLY* 3.5 33.7 - - - -
48F LYS 3.6 12.6 - - - -
49F PHE* 3.7 31.4 - + + -
68F THR* 3.5 29.8 - - + -
69F SER 3.5 2.9 + - - -
70F GLN* 2.5 42.6 + - - +
73F ARG* 3.4 28.5 - - + -
74F PHE* 1.3 74.0 - - - +
76F ALA* 1.3 64.6 + - - +
316F LEU 3.7 2.9 - - - -
317F ASP* 3.3 6.1 - - - +
318F LEU* 2.8 45.3 + - + +
320F GLN* 4.2 8.7 - - + -
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Residues in contact with ALA 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F GLU* 3.8 4.2 - - - +
40F SER* 3.0 43.3 + - - +
46F PHE* 3.8 26.9 - - + +
47F GLY 5.2 1.4 + - - -
49F PHE* 4.4 1.8 - - - -
75F TYR* 1.3 79.4 - - - +
77F LEU* 1.3 60.3 + - - +
122F MET* 3.4 16.8 - - + +
316F LEU 3.3 5.3 + - - -
317F ASP* 3.9 7.2 - - - +
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Residues in contact with LEU 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F TRP* 4.1 17.3 - - + -
37F TRP* 3.7 37.4 - - + +
38F ILE 3.5 15.5 - - - +
39F GLU* 3.5 31.0 - - + -
49F PHE* 3.8 33.9 - - + -
66F LEU* 3.8 20.6 - - + -
76F ALA* 1.3 76.0 - - - +
78F SER* 1.3 63.1 + - - +
122F MET* 3.2 1.8 - - - +
316F LEU* 2.8 32.9 + - + +
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Residues in contact with SER 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F TRP* 3.1 8.3 - - - -
38F ILE 2.8 37.1 + - - -
77F LEU* 1.3 77.9 - - - +
79F ALA* 1.3 60.6 + - - +
117F LEU* 4.9 0.2 - - - +
119F GLN* 3.0 37.6 + - - +
122F MET* 3.9 12.0 - - - +
313F VAL* 3.4 19.5 - - - -
314F LEU 3.3 7.9 - - - -
315F GLY* 3.8 6.7 - - - -
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Residues in contact with ALA 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F PHE* 3.6 31.6 - - + -
36F ARG* 3.6 16.4 - - + +
37F TRP* 3.6 20.6 - - + +
78F SER* 1.3 75.5 - - - +
80F SER* 1.3 61.8 - - - +
81F PHE* 3.8 4.2 - - - -
119F GLN* 3.8 2.9 - - - +
313F VAL* 3.3 2.1 - - - -
314F LEU* 2.9 36.2 + - - +
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Residues in contact with SER 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F PHE* 4.3 8.7 - - - -
36F ARG 4.2 5.4 + - - +
79F ALA* 1.3 76.1 - - - +
81F PHE* 1.3 64.6 + - - +
115F ASN* 5.2 4.3 - - - -
119F GLN* 3.6 25.6 + - - +
312F GLY 3.2 12.1 - - - -
313F VAL* 4.1 5.2 - - - -
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Residues in contact with PHE 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F TYR* 3.4 23.1 - - + +
23F PHE* 4.0 23.3 - + + -
79F ALA 3.8 4.7 - - - -
80F SER* 1.3 80.2 - - - +
82F GLU* 1.3 78.5 + - - +
83F PRO* 3.0 9.6 - - - +
84F PHE* 3.7 20.2 - + - -
112F LEU* 5.4 2.9 - - + -
115F ASN* 4.6 1.7 - - - +
311F PHE* 3.4 29.8 - - + -
312F GLY* 2.9 23.2 + - - +
313F VAL 3.6 8.3 - - - -
314F LEU* 3.5 30.3 - - + -
332F ILE* 4.4 15.0 - - + -
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Residues in contact with GLU 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F TYR* 4.8 6.9 - - - +
81F PHE* 1.3 83.1 - - - +
83F PRO* 1.3 90.1 - - - +
84F PHE* 3.7 5.0 + - - +
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Residues in contact with PRO 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81F PHE 3.0 7.6 - - - +
82F GLU* 1.3 107.2 - - - +
84F PHE* 1.3 62.0 + - - +
115F ASN* 3.5 33.2 - - + +
310F ASN* 4.0 15.0 - - + +
311F PHE 3.0 14.8 - - - +
312F GLY* 4.7 0.2 - - - -
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Residues in contact with PHE 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F TYR* 3.5 68.4 - + + -
81F PHE* 3.7 20.6 - + - -
82F GLU 4.2 1.3 - - - +
83F PRO* 1.3 77.1 - - - +
85F SER* 1.3 76.0 - - - +
86F ASN* 4.2 4.3 - - + -
89F GLN* 5.8 0.2 - - - +
91F LEU* 3.6 25.8 - - + -
112F LEU* 5.6 0.4 - - + -
309F ASP 4.2 0.9 - - - -
310F ASN* 3.2 6.0 - - - -
311F PHE* 2.7 67.8 + + + +
332F ILE* 3.9 8.1 - - + -
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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