Contacts of the strand formed by residues 73 - 84 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45G ASP* 3.3 40.3 + - - +
46G PHE 4.3 4.2 + - - -
47G GLY* 3.8 10.8 - - - +
70G GLN* 3.2 44.2 + - + +
71G LYS 3.3 13.9 + - - +
72G ALA* 1.3 81.9 + - - +
74G PHE* 1.3 59.5 + - - +
75G TYR* 3.4 24.3 - - + -
319G TRP* 3.3 9.8 - - - -
320G GLN 3.0 29.2 + - - -
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Residues in contact with PHE 74 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43G LYS* 5.1 14.8 - - + -
45G ASP 5.2 1.4 + - - -
46G PHE* 3.3 27.7 - + + -
47G GLY 2.8 31.4 + - - -
73G ARG* 1.3 74.3 - - - +
75G TYR* 1.3 58.6 + - - +
318G LEU* 3.3 8.3 - - - -
319G TRP* 3.7 45.5 - + + -
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Residues in contact with TYR 75 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46G PHE* 4.3 2.9 - - - -
47G GLY* 3.5 33.9 - - - -
48G LYS 3.6 12.8 - - - -
49G PHE* 3.7 31.2 - + + -
68G THR* 3.5 31.0 - - + -
69G SER 3.4 2.4 + - - -
70G GLN* 2.5 42.4 + - - +
73G ARG* 3.4 26.7 - - + -
74G PHE* 1.3 75.3 - - - +
76G ALA* 1.3 65.8 + - - +
316G LEU 3.8 2.2 - - - +
317G ASP* 3.3 6.1 - - - +
318G LEU* 2.8 44.8 + - + +
320G GLN* 4.1 9.4 - - + -
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Residues in contact with ALA 76 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39G GLU* 3.8 4.5 - - - +
40G SER* 3.1 35.6 + - - +
46G PHE* 3.7 36.2 - - + +
47G GLY 5.2 1.6 + - - -
49G PHE* 4.5 1.4 - - - -
75G TYR* 1.3 79.4 - - - +
77G LEU* 1.3 61.5 + - - +
122G MET* 4.0 9.9 - - + +
316G LEU 3.3 5.4 - - - -
317G ASP* 3.9 11.7 - - - +
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Residues in contact with LEU 77 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33G TRP* 4.1 16.8 - - + -
37G TRP* 3.8 33.6 - - + +
38G ILE 3.5 19.7 - - - +
39G GLU* 3.5 30.1 - - + +
49G PHE* 3.8 35.4 - - + -
66G LEU* 3.8 17.3 - - + -
76G ALA* 1.3 74.6 - - - +
78G SER* 1.3 65.1 + - - +
122G MET* 4.5 0.6 - - - +
315G GLY* 3.6 0.2 - - - -
316G LEU* 2.8 33.8 + - + +
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Residues in contact with SER 78 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37G TRP* 3.1 10.2 - - - -
38G ILE 2.8 34.8 + - - -
76G ALA 5.2 0.2 - - - -
77G LEU* 1.3 73.0 - - - +
79G ALA* 1.3 62.3 + - - +
119G GLN* 3.3 23.0 + - - +
122G MET* 2.5 44.5 - - - +
313G VAL* 3.6 7.6 - - - -
314G LEU 3.4 6.5 - - - -
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Residues in contact with ALA 79 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G PHE* 3.6 28.9 - - + -
36G ARG* 3.6 14.4 - - + +
37G TRP* 3.6 26.7 - - + +
78G SER* 1.3 76.4 - - - +
80G SER* 1.3 62.6 + - - +
81G PHE* 3.9 3.8 - - - -
119G GLN* 4.0 3.1 - - - -
313G VAL* 3.3 3.2 - - - -
314G LEU* 2.9 37.6 + - - +
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Residues in contact with SER 80 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G PHE* 4.3 8.5 - - - -
36G ARG 4.2 5.7 + - - +
79G ALA* 1.3 76.3 - - - +
81G PHE* 1.3 66.5 + - - +
115G ASN* 5.2 3.4 + - - -
119G GLN* 2.9 31.4 + - - -
312G GLY 3.3 8.9 + - - -
313G VAL* 4.0 6.7 - - - +
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Residues in contact with PHE 81 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22G TYR* 3.4 23.6 - - + +
23G PHE* 4.0 23.3 - + + -
79G ALA 3.9 3.6 - - - -
80G SER* 1.3 82.7 - - - +
82G GLU* 1.3 78.3 + - - +
83G PRO* 3.1 9.4 - - - +
84G PHE* 3.7 19.7 - + - -
112G LEU* 5.4 3.1 - - + -
115G ASN* 4.7 1.7 - - - +
311G PHE* 3.4 29.8 - - + -
312G GLY* 3.0 24.2 + - - +
313G VAL 3.6 7.4 - - - -
314G LEU* 3.5 30.3 - - + -
332G ILE* 4.4 15.5 - - + -
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Residues in contact with GLU 82 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22G TYR* 4.8 7.0 - - - +
81G PHE* 1.3 81.3 - - - +
83G PRO* 1.3 88.7 - - - +
84G PHE* 3.7 5.2 + - - +
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Residues in contact with PRO 83 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81G PHE 3.3 7.2 - - - +
82G GLU* 1.3 108.3 - - - +
84G PHE* 1.3 59.3 + - - +
115G ASN* 3.5 32.3 - - - +
310G ASN* 3.9 19.3 - - - +
311G PHE 3.0 16.8 - - - +
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Residues in contact with PHE 84 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22G TYR* 3.5 68.9 - + + -
81G PHE* 3.7 20.9 - + - -
82G GLU 4.2 1.8 - - - +
83G PRO* 1.3 76.9 - - - +
85G SER* 1.3 75.1 - - - +
86G ASN* 4.2 3.4 - - + -
89G GLN* 5.8 0.2 - - - -
91G LEU* 3.6 25.8 - - + -
112G LEU* 5.5 1.1 - - + -
309G ASP 4.3 2.0 - - - -
310G ASN* 3.4 3.3 - - - -
311G PHE* 2.7 66.5 + + + +
332G 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