Contacts of the strand formed by residues 73 - 84 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A ASP* 3.5 34.1 + - - +
46A PHE 4.7 3.0 + - - -
47A GLY* 3.8 10.8 - - - +
70A GLN* 2.8 44.2 + - + +
71A LYS 3.3 13.9 + - - +
72A ALA* 1.3 82.8 + - - +
74A PHE* 1.3 60.1 + - - +
75A TYR* 3.4 24.2 - - + -
319A TRP* 3.3 10.0 - - - -
320A GLN 3.0 28.3 + - - -
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Residues in contact with PHE 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LYS* 3.4 26.0 - - + +
45A ASP 5.2 1.4 + - - -
46A PHE* 3.3 27.9 - + + -
47A GLY 2.8 29.1 + - - -
73A ARG* 1.3 75.5 - - - +
75A TYR* 1.3 57.9 + - - +
317A ASP* 6.2 0.7 - - - -
318A LEU 3.3 8.1 - - - +
319A TRP* 3.7 43.7 - + + -
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Residues in contact with TYR 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A PHE* 4.4 3.1 - - - -
47A GLY* 3.5 34.1 - - - -
48A LYS 3.7 12.6 - - - -
49A PHE* 3.7 31.0 - + + -
68A THR* 3.5 30.1 - - + -
69A SER 3.4 2.6 + - - -
70A GLN* 2.5 41.9 + - - +
73A ARG* 3.4 24.7 - - + -
74A PHE* 1.3 78.2 - - - +
76A ALA* 1.3 64.4 + - - +
316A LEU 3.7 2.7 - - - +
317A ASP* 3.3 5.4 - - - -
318A LEU* 2.7 47.3 + - + +
320A GLN* 4.1 10.1 - - + -
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Residues in contact with ALA 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A GLU* 3.8 5.0 - - - +
40A SER* 3.1 43.2 + - - +
46A PHE* 3.7 27.0 - - + +
47A GLY 5.2 1.2 + - - -
49A PHE* 4.5 1.6 - - - -
75A TYR* 1.3 78.2 - - - +
77A LEU* 1.3 61.5 + - - +
122A MET* 4.0 11.4 - - + +
316A LEU 3.3 5.4 - - - -
317A ASP* 4.4 10.3 - - - +
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Residues in contact with LEU 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A TRP* 4.1 17.0 - - + -
37A TRP* 3.8 34.9 - - + -
38A ILE 3.5 20.0 - - - +
39A GLU* 3.5 30.7 - - + +
49A PHE* 3.8 36.3 - - + -
66A LEU* 3.8 16.6 - - + -
76A ALA* 1.3 74.8 - - - +
78A SER* 1.3 63.5 + - - +
122A MET* 4.5 1.3 - - - +
315A GLY* 3.5 0.2 - - - -
316A LEU* 2.8 33.4 + - + +
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Residues in contact with SER 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A TRP* 3.2 8.7 - - - -
38A ILE 2.8 33.8 + - - -
77A LEU* 1.3 73.9 - - - +
79A ALA* 1.3 61.2 + - - +
119A GLN* 3.0 33.5 + - - +
122A MET* 3.2 35.5 - - - +
313A VAL* 3.4 6.3 - - - -
314A LEU 3.3 11.4 - - - -
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Residues in contact with ALA 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A PHE* 3.6 29.2 - - + -
36A ARG* 3.6 13.2 - - + +
37A TRP* 3.6 26.2 - - + +
78A SER* 1.3 75.1 - - - +
80A SER* 1.3 60.9 + - - +
81A PHE* 3.9 3.6 - - - -
119A GLN* 3.9 2.7 - - - +
313A VAL* 3.3 2.7 - - - -
314A LEU* 2.9 38.6 + - - +
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Residues in contact with SER 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A PHE* 4.3 8.3 - - - -
36A ARG 4.2 5.3 + - - +
79A ALA* 1.3 74.9 - - - +
81A PHE* 1.3 67.0 + - - +
115A ASN* 5.2 3.0 + - - -
119A GLN* 2.8 30.3 + - - +
312A GLY 3.3 8.9 + - - -
313A VAL* 4.0 6.8 - - - +
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Residues in contact with PHE 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A TYR* 3.4 23.6 - - + +
23A PHE* 3.9 23.1 - + + -
79A ALA 3.9 4.3 - - - -
80A SER* 1.3 81.8 - - - +
82A GLU* 1.3 77.0 + - - +
83A PRO* 3.1 9.5 - - - +
84A PHE* 3.6 20.0 - + - -
112A LEU* 5.4 2.9 - - + -
115A ASN* 4.6 1.7 - - - +
311A PHE* 3.4 30.3 - - + -
312A GLY* 3.0 22.9 + - - +
313A VAL 3.6 7.2 - - - -
314A LEU* 3.5 30.5 - - + -
332A ILE* 4.4 15.3 - - + -
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Residues in contact with GLU 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A TYR* 4.8 6.6 - - - +
81A PHE* 1.3 82.5 - - - +
83A PRO* 1.3 88.0 - - - +
84A PHE* 3.6 5.4 + - - +
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Residues in contact with PRO 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A PHE 3.1 7.2 - - - +
82A GLU* 1.3 108.4 - - - +
84A PHE* 1.3 60.4 + - - +
115A ASN* 3.5 34.3 - - + +
310A ASN* 4.0 13.9 - - + +
311A PHE 3.0 15.9 - - - +
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Residues in contact with PHE 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A TYR* 3.5 67.1 - + + -
81A PHE* 3.6 22.0 - + - -
82A GLU 4.3 1.8 - - - +
83A PRO* 1.3 77.9 - - - +
85A SER* 1.3 74.8 - - - +
86A ASN* 4.3 4.3 - - + -
91A LEU* 3.6 22.9 - - + -
112A LEU* 5.6 0.9 - - + -
309A ASP 4.3 0.9 - - - -
310A ASN* 3.1 5.6 - - - -
311A PHE* 2.8 68.2 + + + +
332A ILE* 3.9 7.4 - - + -
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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