Contacts of the helix formed by residues 82 - 99 (chain L) in PDB entry 6R8Y
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 SER 82 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117K GLU 4.1 15.9 + - - -
118K THR* 5.8 0.7 - - - -
76L HIS* 4.8 0.4 - - - -
80L ARG 4.5 4.2 + - - -
81L ALA* 1.3 77.4 - - - +
83L TRP* 1.3 66.4 + - - +
84L PRO* 3.4 11.7 - - - -
85L SER* 3.3 21.1 + - - -
86L VAL* 3.5 11.9 + - - +
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Residues in contact with TRP 83 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
953K TRP* 3.4 46.4 - + + -
970K ASN* 3.3 49.1 - - + +
972K PHE* 6.4 2.2 - - + -
1079K GLU* 3.7 29.5 + - - -
76L HIS* 4.0 20.4 + + + +
82L SER* 1.3 71.8 - - - +
84L PRO* 1.3 77.0 - - + +
86L VAL* 2.8 28.3 + - + +
87L GLN* 2.9 48.5 + - + -
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Residues in contact with PRO 84 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115K PRO* 4.9 6.7 - - + +
116K SER 4.1 19.7 - - - +
117K GLU* 4.6 16.2 - - + +
82L SER* 3.6 12.1 - - - -
83L TRP* 1.3 107.5 - - + +
85L SER* 1.3 57.6 + - - +
87L GLN* 3.4 8.7 + - + +
88L GLN* 2.9 28.9 + - - +
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Residues in contact with SER 85 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117K GLU* 5.9 3.1 - - - +
69L ILE* 4.6 6.5 - - - +
72L THR* 5.2 6.7 - - - -
81L ALA* 5.3 4.5 - - - -
82L SER* 3.3 18.2 + - - -
83L TRP 3.2 0.8 - - - -
84L PRO* 1.3 78.5 - - - +
86L VAL* 1.3 59.0 + - - +
88L GLN* 3.0 10.4 + - - +
89L GLY* 2.9 23.9 + - - -
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Residues in contact with VAL 86 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
970K ASN* 4.7 9.0 - - - +
72L THR* 3.9 30.5 - - + +
73L LEU* 4.0 16.6 - - + -
76L HIS* 3.8 34.1 - - + +
81L ALA* 5.3 1.6 - - + +
82L SER 3.5 12.3 + - - +
83L TRP* 2.8 12.0 + - + +
85L SER* 1.3 75.3 - - - +
87L GLN* 1.3 66.0 + - - +
89L GLY* 3.0 2.9 + - - +
90L LEU* 2.9 43.7 + - + +
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Residues in contact with GLN 87 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114K ARG* 4.7 14.6 - - - +
953K TRP* 4.8 3.6 - - + -
1079K GLU* 5.7 0.7 - - - -
83L TRP* 2.9 55.5 + - + +
84L PRO* 3.7 10.7 - - + +
85L SER 3.3 0.2 - - - -
86L VAL* 1.3 76.4 - - - +
88L GLN* 1.3 57.9 + - - +
90L LEU* 3.8 5.7 - - - +
91L GLN* 2.9 31.1 + - - +
299L ASP* 5.8 1.0 + - - -
347L ARG 3.5 24.4 + - - +
348L TYR* 4.2 18.8 - - + +
349L ASN* 5.1 0.8 - - - +
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Residues in contact with GLN 88 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69L ILE* 5.7 1.1 - - + -
84L PRO 2.9 14.4 + - - +
85L SER* 3.0 14.6 + - - +
87L GLN* 1.3 77.0 - - - +
89L GLY* 1.3 62.7 + - - +
91L GLN* 3.3 30.3 + - - +
92L GLN* 3.0 23.4 + - - +
349L ASN* 5.9 0.7 - - - +
376L ASP* 4.4 8.3 + - - -
378L ASN* 4.9 13.2 + - - +
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Residues in contact with GLY 89 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69L ILE* 3.5 30.2 - - - +
70L VAL* 6.0 0.5 - - - +
72L THR* 5.7 2.7 - - - -
85L SER 2.9 12.0 + - - -
86L VAL* 3.0 3.7 + - - -
88L GLN* 1.3 76.1 - - - +
90L LEU* 1.3 61.9 + - - +
92L GLN* 3.0 11.1 + - - +
93L SER* 2.9 26.2 + - - -
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Residues in contact with LEU 90 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
910K MET* 4.9 2.9 - - + -
926K LEU* 3.4 42.4 - - + -
927K MET* 4.9 1.7 - - - +
953K TRP* 3.3 39.3 - - + -
970K ASN* 6.0 0.7 - - - +
70L VAL* 6.1 4.0 - - + -
72L THR* 6.2 2.5 - - + -
73L LEU* 4.3 14.4 - - + -
86L VAL* 2.9 37.5 + - + +
87L GLN* 4.1 3.4 - - - +
89L GLY* 1.3 76.9 - - - +
91L GLN* 1.3 60.7 + - - +
93L SER* 3.1 14.6 + - - +
94L PHE* 2.9 28.8 + - - +
348L TYR* 3.7 6.7 + - - +
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Residues in contact with GLN 91 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87L GLN 2.9 13.6 + - - +
88L GLN* 3.3 41.0 + - - +
90L LEU* 1.3 76.9 - - - +
92L GLN* 1.3 61.7 + - - +
94L PHE* 3.2 3.8 + - - +
95L LEU* 3.0 34.0 + - + +
348L TYR* 3.5 22.4 - - + +
349L ASN* 3.0 41.5 + - - +
350L LEU* 3.7 24.6 - - + +
376L ASP* 3.6 12.4 + - - -
378L ASN* 5.9 0.4 - - - +
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Residues in contact with GLN 92 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841K ALA* 4.9 10.5 + - + +
64L PRO 5.8 0.4 - - - +
65L PRO* 5.4 2.7 - - + +
66L CYS* 3.4 37.0 + - + +
67L ARG* 2.8 30.4 + - - +
69L ILE* 3.9 18.3 - - - +
88L GLN* 3.0 14.9 + - - +
89L GLY* 3.0 13.4 + - - +
91L GLN* 1.3 77.4 - - - +
93L SER* 1.3 59.8 - - - +
95L LEU* 3.2 15.6 + - + +
96L HIS* 3.0 21.9 + - - +
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Residues in contact with SER 93 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841K ALA* 4.1 17.8 + - - +
842K GLU* 5.6 4.9 - - - +
909K ILE* 6.0 4.9 - - - -
910K MET* 4.6 13.8 - - - +
926K LEU* 5.5 2.7 - - - -
927K MET* 6.1 0.9 - - - -
70L VAL* 4.8 4.7 - - - +
89L GLY 2.9 16.1 + - - -
90L LEU* 3.1 24.4 + - - +
92L GLN* 1.3 77.9 - - - +
94L PHE* 1.3 62.2 + - - +
96L HIS* 3.1 8.9 + - - +
97L THR* 3.0 25.1 + - - +
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Residues in contact with PHE 94 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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909K ILE* 5.2 6.3 - - + -
927K MET* 4.5 11.7 - - + -
90L LEU 2.9 15.8 + - - +
91L GLN 3.6 3.6 - - - +
93L SER* 1.3 76.3 - - - +
95L LEU* 1.3 60.8 + - - +
97L THR* 3.3 13.3 - - + +
98L LEU* 2.8 45.1 + - + +
101L TYR* 3.6 29.8 - + - -
345L HIS* 3.6 27.8 - + - -
348L TYR* 3.8 22.7 - + + +
350L LEU* 4.0 24.7 - - + -
400L PHE* 4.3 16.6 - + - -
404L GLY 3.6 16.8 - - - -
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Residues in contact with LEU 95 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64L PRO* 5.0 6.7 - - + -
91L GLN* 3.0 25.7 + - + +
92L GLN* 3.5 15.0 - - + +
94L PHE* 1.3 78.3 - - - +
96L HIS* 1.3 62.3 + - - +
98L LEU* 3.1 12.4 + - + +
99L ASP* 3.0 29.7 + - - +
350L LEU* 3.9 35.7 - - + -
374L VAL* 4.1 17.3 - - + -
383L MET* 3.9 38.6 - - + +
384L CYS* 4.8 4.3 - - + -
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Residues in contact with HIS 96 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841K ALA* 3.8 31.2 + - + +
842K GLU* 5.5 13.5 + - + +
844K LYS* 5.8 8.1 - - - -
64L PRO* 4.6 15.2 - - + +
65L PRO* 4.2 18.6 - - + -
92L GLN 3.0 13.1 + - - +
93L SER* 3.1 8.8 + - - +
95L LEU* 1.3 79.0 - - - +
97L THR* 1.3 68.0 + - - +
99L ASP* 3.3 15.2 + - - +
100L SER* 4.0 3.1 + - - -
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Residues in contact with THR 97 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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909K ILE* 5.1 15.2 - - + +
93L SER 3.0 15.1 + - - +
94L PHE* 3.3 26.5 - - + +
96L HIS* 1.3 82.9 + - - +
98L LEU* 1.3 63.0 + - - +
100L SER* 2.9 14.9 + - - +
101L TYR* 3.3 6.9 + - + -
420L GLN* 2.3 60.2 + - - +
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Residues in contact with LEU 98 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94L PHE* 2.8 39.7 + - + +
95L LEU* 3.1 13.6 + - + +
97L THR* 1.3 72.2 - - - +
99L ASP* 1.3 59.7 + - - +
100L SER 3.0 4.7 - - - -
101L TYR* 2.9 61.9 + - + +
102L ARG* 4.3 3.1 + - - -
374L VAL* 4.1 33.9 - - + -
384L CYS* 4.4 7.0 - - - -
386L LEU* 4.0 24.5 - - + +
400L PHE* 4.8 10.1 - - + -
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Residues in contact with ASP 99 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58L ALA* 5.3 2.4 - - - +
59L GLY 5.6 0.9 - - - +
62L ILE 5.4 0.3 - - - +
64L PRO* 3.1 37.1 - - + +
95L LEU 3.0 14.1 + - - +
96L HIS 3.6 9.6 - - - +
97L THR 3.2 0.6 - - - -
98L LEU* 1.3 76.1 - - - +
100L SER* 1.3 54.9 + - - +
102L ARG* 2.9 51.2 + - - +
383L MET 5.1 0.5 - - - +
384L CYS* 3.0 29.4 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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