Contacts of the strand formed by residues 73 - 84 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45C ASP* 3.5 29.4 + - - +
47C GLY* 3.8 13.2 - - - +
70C GLN* 3.9 34.2 + - + +
71C LYS 3.1 19.8 + - - +
72C ALA* 1.3 103.7 + - - +
74C PHE* 1.3 59.8 + - - +
75C TYR* 3.4 23.3 - - + -
319C TRP* 3.3 9.5 - - - -
320C GLN 3.0 29.4 + - - -
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Residues in contact with PHE 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C LYS* 4.5 26.0 - - + -
45C ASP* 5.2 1.6 + - - -
46C PHE* 3.3 27.5 - - + -
47C GLY 2.8 31.2 + - - -
73C ARG* 1.3 74.9 - - - +
75C TYR* 1.3 58.1 + - - +
317C ASP* 6.1 0.7 - - - -
318C LEU* 3.3 8.1 - - - -
319C TRP* 3.7 44.9 - + + -
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Residues in contact with TYR 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C PHE* 4.3 3.5 - - - -
47C GLY* 3.5 33.0 - - - -
48C LYS 3.6 12.6 - - - -
49C PHE* 3.7 31.0 - + + -
68C THR* 3.5 30.4 - - + -
69C SER 3.4 2.4 + - - -
70C GLN* 2.5 42.2 + - - -
73C ARG* 3.4 25.6 - - + -
74C PHE* 1.3 77.2 - - - +
76C ALA* 1.3 65.7 + - - +
316C LEU 3.8 2.2 - - - +
317C ASP* 3.3 4.9 - - - +
318C LEU* 2.8 45.7 + - + +
320C GLN* 4.1 9.4 - - + -
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Residues in contact with ALA 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C GLU* 3.8 4.7 - - - +
40C SER* 3.1 41.8 + - - +
46C PHE* 3.7 27.3 - - + +
47C GLY 5.2 1.6 + - - -
49C PHE* 4.6 1.6 - - - -
75C TYR* 1.3 80.2 - - - +
77C LEU* 1.3 60.5 + - - +
122C MET* 3.4 19.3 - - + +
123C HIS* 5.2 0.7 - - - -
316C LEU 3.3 5.4 - - - -
317C ASP* 5.0 3.6 - - + -
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Residues in contact with LEU 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C TRP* 4.1 17.0 - - + -
37C TRP* 3.8 32.5 - - + -
38C ILE 3.5 18.8 - - - +
39C GLU* 3.5 30.3 - - + +
49C PHE* 3.8 36.1 - - + -
66C LEU* 3.8 17.3 - - + -
76C ALA* 1.3 75.3 - - - +
78C SER* 1.3 63.1 + - - +
122C MET* 3.2 2.3 - - - +
316C LEU* 2.8 33.8 + - + +
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Residues in contact with SER 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C TRP* 3.2 9.5 - - - -
38C ILE 2.8 34.4 + - - -
77C LEU* 1.3 77.0 - - - +
79C ALA* 1.3 60.0 + - - +
119C GLN* 3.0 41.1 + - - +
122C MET* 3.9 12.4 - - - +
313C VAL* 3.4 13.9 - - - +
314C LEU 3.3 13.0 - - - -
315C GLY* 3.8 7.6 - - - -
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Residues in contact with ALA 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C PHE* 3.6 23.8 - - + -
36C ARG* 3.6 17.0 - - + +
37C TRP* 3.6 28.5 - - + +
78C SER* 1.3 75.1 - - - +
80C SER* 1.3 61.7 + - - +
81C PHE* 3.9 4.3 - - - -
119C GLN* 3.9 0.2 - - - +
313C VAL* 3.3 5.1 - - - -
314C LEU* 2.9 38.9 + - - +
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Residues in contact with SER 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C PHE* 4.4 8.3 - - - -
36C ARG 4.2 6.2 + - - +
79C ALA* 1.3 75.9 - - - +
81C PHE* 1.3 66.4 + - - +
115C ASN* 5.2 5.2 - - - -
119C GLN* 3.6 25.6 + - - +
312C GLY 3.2 12.3 - - - -
313C VAL* 4.3 2.7 - - - +
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Residues in contact with PHE 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C TYR* 3.4 23.1 - - + +
23C PHE* 4.0 24.9 - + + -
79C ALA 3.9 4.3 - - - -
80C SER* 1.3 80.1 - - - +
82C GLU* 1.3 77.8 + - - +
83C PRO* 3.1 9.9 - - - +
84C PHE* 3.7 20.2 - + - -
112C LEU* 5.4 3.1 - - + -
115C ASN* 4.6 1.7 - - - +
311C PHE* 3.4 30.5 - - + -
312C GLY* 2.9 23.5 + - - +
313C VAL* 3.6 7.9 - - - -
314C LEU* 3.5 29.8 - - + -
332C ILE* 4.4 15.0 - - + -
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Residues in contact with GLU 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C TYR* 4.8 6.6 + - - +
81C PHE* 1.3 82.0 - - - +
83C PRO* 1.3 82.9 - - + +
84C PHE* 3.7 4.9 + - - +
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Residues in contact with PRO 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C PHE 3.1 7.8 - - - +
82C GLU* 1.3 99.4 - - + +
84C PHE* 1.3 61.1 + - - +
115C ASN* 3.5 31.6 - - - +
310C ASN* 3.9 20.4 - - - +
311C PHE 3.0 15.9 - - - +
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Residues in contact with PHE 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C TYR* 3.5 69.3 - + + -
81C PHE* 3.7 21.1 - + - -
82C GLU 4.3 1.3 - - - -
83C PRO* 1.3 77.3 - - - +
85C SER* 1.3 76.1 + - - +
86C ASN* 4.2 3.4 - - - -
89C GLN* 5.8 0.2 - - - -
91C LEU* 3.6 26.7 - - + -
112C LEU* 5.6 0.7 - - + -
309C ASP 4.3 2.5 - - - -
310C ASN* 3.4 3.0 - - - -
311C PHE* 2.7 66.1 + + + +
332C ILE* 3.9 7.2 - - + -
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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