Contacts of the strand formed by residues 68 - 80 (chain G) in PDB entry 5K0Y
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 ILE 68 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282A G 3.0 30.8 + - - +
283A A 3.4 4.6 - - - -
40G ILE* 3.8 21.2 - - + +
42G LEU* 5.4 6.3 - - + -
61G PRO* 3.8 29.2 - - + -
66G VAL* 5.3 1.8 - - + -
67G SER* 1.3 71.0 - - - +
69G ARG* 1.3 61.5 + - - +
70G GLY 6.0 0.7 - - - +
72G ILE* 5.7 5.6 - - + -
129G GLY* 4.3 10.8 - - - +
130G GLU 3.4 20.6 - - - +
131G CYS* 4.0 20.9 - - + -
141G ASN* 4.5 8.7 - - + -
143G LEU* 3.9 34.1 - - + -
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Residues in contact with ARG 69 (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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111A A 3.2 34.1 + - - +
112A U 3.7 19.7 + - - +
113A G 3.9 14.6 - - - +
114A G 3.0 54.3 + - - -
282A G 3.9 20.6 - - - +
283A A 4.1 7.0 - - - +
341A G 5.0 10.1 + - - -
42G LEU* 6.0 1.3 - - - -
67G SER* 4.5 6.9 + - - +
68G ILE* 1.3 78.8 - - - +
70G GLY* 1.4 59.9 + - - +
130G GLU* 3.3 36.4 + - - +
131G CYS* 3.6 22.7 + - - +
132G ARG* 3.6 12.3 - - - +
133G PRO* 5.6 0.4 - - - +
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Residues in contact with GLY 70 (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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110A U 5.0 3.4 - - - -
111A A 4.9 14.0 - - - -
282A G 5.2 1.4 + - - +
42G LEU* 5.3 6.0 - - - +
68G ILE* 6.0 0.9 - - - +
69G ARG* 1.4 75.2 - - - +
71G ARG* 1.4 65.5 + - - -
72G ILE* 3.9 9.2 + - - +
130G GLU* 3.9 10.3 - - - -
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Residues in contact with ARG 71 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A U 3.2 43.2 + - - +
110A U 4.3 14.3 + - - +
342A U 3.2 31.3 + - - +
343A C 3.2 36.8 + - - -
850A A 4.1 4.6 + - - -
851A G 3.3 38.9 + - - +
70G GLY* 1.4 72.1 - - - +
72G ILE* 1.4 60.5 + - - +
73G LEU* 4.1 19.3 + - + +
129G GLY* 3.8 0.7 - - - -
130G GLU* 3.0 44.3 + - + +
140G PHE* 4.3 2.5 - - + -
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Residues in contact with ILE 72 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42G LEU* 4.0 35.0 - - + +
44G PHE* 4.3 18.2 - - + -
68G ILE* 5.7 5.2 - - + -
70G GLY 3.9 8.7 + - - +
71G ARG* 1.4 75.9 - - - +
73G LEU* 1.4 66.1 + - - +
127G THR* 3.7 22.7 - - + -
128G VAL 3.4 17.5 - - - +
129G GLY* 4.7 6.7 - - - -
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Residues in contact with LEU 73 (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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342A U 5.1 1.1 - - - +
343A C 3.9 25.1 - - - -
71G ARG* 4.2 19.3 + - + +
72G ILE* 1.4 82.6 - - - +
74G SER* 1.4 69.6 + - - +
90G ARG* 3.9 25.8 - - - +
127G THR* 3.7 4.2 - - - +
128G VAL* 2.9 41.7 + - + +
140G PHE* 3.8 29.6 - - + -
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Residues in contact with SER 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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73G LEU* 1.4 78.2 + - - +
75G GLY* 1.4 59.9 + - - +
88G ILE* 5.1 4.0 - - - -
90G ARG* 4.4 13.7 - - - +
91G ASP 5.6 1.2 + - - +
125G ILE* 5.3 8.3 - - - -
126G VAL 3.5 10.3 - - - -
127G THR* 3.9 16.5 + - - +
128G VAL* 4.8 0.7 - - - +
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Residues in contact with GLY 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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74G SER* 1.4 74.8 - - - +
76G VAL* 1.3 64.6 + - - -
88G ILE* 4.5 15.8 - - - +
89G ARG 3.9 13.0 - - - -
90G ARG* 4.8 1.3 - - - -
91G ASP 5.9 0.2 - - - -
125G ILE* 3.8 5.5 - - - +
126G VAL* 3.0 36.0 + - - +
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Residues in contact with VAL 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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75G GLY* 1.3 77.2 - - - -
77G VAL* 1.4 72.8 + - - +
78G THR* 3.2 0.9 + - - -
88G ILE* 3.3 3.0 - - - -
89G ARG* 3.0 34.8 + - + +
91G ASP* 5.1 9.2 - - - +
123G GLY* 3.6 25.1 - - - +
124G ASP 3.6 4.3 - - - +
125G ILE* 3.8 20.9 - - + +
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Residues in contact with VAL 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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76G VAL* 1.4 71.7 - - - +
78G THR* 1.4 56.7 + - - +
79G LYS 3.3 30.1 - - - +
80G MET* 4.2 4.0 - - + +
86G ILE* 3.9 26.0 - - + -
87G VAL 3.7 6.5 - - - +
88G ILE* 4.1 2.0 - - + -
121G GLN 4.3 7.2 - - - +
122G ILE* 3.3 18.4 - - + +
123G GLY* 3.2 27.1 + - - +
124G ASP* 3.0 23.9 + - + +
126G VAL* 3.8 21.3 - - + -
145G VAL* 6.3 0.2 - - + -
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Residues in contact with THR 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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76G VAL 3.2 3.0 + - - -
77G VAL* 1.4 72.6 - - - +
79G LYS* 1.4 70.3 + - + +
87G VAL* 3.1 31.7 + - + +
89G ARG* 3.8 34.0 + - + +
108G ASN* 3.7 18.4 + - - +
122G ILE* 3.5 14.4 - - - +
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Residues in contact with LYS 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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385A G 3.8 28.3 + - - +
386A U 3.2 53.7 + - - +
387A G 5.3 3.2 + - - -
77G VAL* 3.3 10.1 - - - +
78G THR* 1.4 90.1 - - + +
80G MET* 1.3 62.9 + - - +
81G LYS* 4.1 13.7 - - + +
86G ILE* 3.7 0.5 - - - +
87G VAL* 3.0 37.4 + - + +
108G ASN* 5.0 8.5 - - - +
122G ILE* 4.4 4.3 - - - -
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Residues in contact with MET 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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77G VAL* 4.7 3.4 - - + -
79G LYS* 1.3 72.9 - - - +
81G LYS* 1.3 82.8 + - - +
82G MET 5.1 1.1 - - - +
85G THR 5.0 1.8 - - - +
86G ILE* 4.1 25.6 - - + +
113G LEU* 5.9 0.9 - - + -
120G VAL* 3.8 24.2 - - + +
121G GLN* 3.7 37.7 - - - +
122G ILE* 3.5 28.9 - - + +
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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