Contacts of the helix formed by residues 82 - 94 (chain S) in PDB entry 5C3I
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 THR 82 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85R GLN* 3.4 29.4 - - - +
88R ALA* 3.5 10.0 - - - +
78S ARG* 3.5 21.8 - - - +
80S THR 3.9 0.7 - - - +
81S VAL* 1.3 78.8 - - - +
83S ALA* 1.3 63.6 + - - +
84S MET 3.4 3.3 + - - -
85S ASP* 3.0 35.2 + - - +
86S VAL* 3.5 8.1 + - - +
102T VAL* 3.8 16.4 - - + -
104T GLU* 3.4 26.1 + - - +
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Residues in contact with ALA 83 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85R GLN* 3.6 5.9 + - - +
87R SER* 4.1 23.8 - - - +
88R ALA* 3.6 18.8 - - - +
91R ALA* 4.7 6.1 - - + +
82S THR* 1.3 74.3 - - - +
84S MET* 1.3 61.1 + - + +
86S VAL* 3.2 6.8 + - - +
87S VAL* 2.8 35.2 + - + +
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Residues in contact with MET 84 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82S THR* 3.3 1.8 + - - -
83S ALA* 1.3 79.0 - - + +
85S ASP* 1.3 55.9 + - - +
87S VAL* 3.5 34.4 - - + +
88S TYR* 2.8 64.5 + - + +
91S LYS* 5.4 0.9 - - - -
104T GLU* 2.9 38.3 + - + +
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Residues in contact with ASP 85 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69S ALA* 3.8 12.5 - - - +
72S TYR* 3.7 13.7 - - + -
73S THR* 2.7 30.4 + - - +
78S ARG* 2.8 37.0 + - - -
81S VAL* 4.2 4.5 - - + -
82S THR* 3.0 22.9 + - - +
83S ALA 3.3 0.2 - - - -
84S MET* 1.3 75.5 - - - +
86S VAL* 1.3 57.8 + - - +
88S TYR* 3.7 2.6 + - - -
89S ALA* 3.1 27.7 + - - +
104T GLU* 4.5 1.0 - - - +
105T LEU* 2.9 19.0 - - - +
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Residues in contact with VAL 86 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88R ALA* 3.9 16.4 - - + +
91R ALA* 3.9 16.8 - - + -
92R LEU* 3.7 37.0 - - + +
65S VAL* 4.9 1.8 - - + -
69S ALA* 4.2 13.5 - - + -
81S VAL* 4.3 9.9 - - + -
82S THR 3.5 11.9 + - - +
83S ALA 3.2 7.5 + - - +
85S ASP* 1.3 75.8 - - - +
87S VAL* 1.3 59.1 + - - +
89S ALA* 3.3 7.0 + - - +
90S LEU* 2.9 47.1 + - + +
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Residues in contact with VAL 87 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91R ALA* 5.2 8.7 - - + -
83S ALA* 2.8 23.5 + - + +
84S MET* 3.2 35.9 + - + +
86S VAL* 1.3 76.5 - - - +
88S TYR* 1.3 63.3 + - + +
90S LEU* 3.5 12.4 + - + +
91S LYS* 3.4 47.8 + - - +
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Residues in contact with TYR 88 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72S TYR* 3.7 24.7 + + + +
84S MET* 2.8 47.3 + - + +
85S ASP* 3.9 5.2 - - - +
87S VAL* 1.3 71.0 - - + +
89S ALA* 1.3 61.3 + - - +
91S LYS* 2.9 42.0 + - - +
92S ARG* 3.2 10.2 + - - +
104T GLU* 5.5 2.5 - - - +
105T LEU* 4.1 39.8 + - + -
110T ARG* 3.3 52.3 + - + +
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Residues in contact with ALA 89 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65S VAL* 3.7 28.3 - - + +
68S ASP* 3.7 8.1 - - + +
69S ALA* 3.7 15.5 - - + +
72S TYR* 3.5 10.4 - - + -
85S ASP 3.1 16.3 + - - +
86S VAL 3.6 4.7 - - - +
88S TYR* 1.3 78.1 - - - +
90S LEU* 1.3 56.4 + - - +
92S ARG* 3.4 8.9 + - - +
93S GLN* 3.3 31.0 + - - +
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Residues in contact with LEU 90 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91R ALA* 4.3 5.8 - - + +
92R LEU* 5.8 0.2 - - + -
95R ALA* 3.5 35.0 - - + -
61S PHE* 4.4 14.4 - - + -
65S VAL* 4.0 22.9 - - + -
86S VAL* 2.9 35.2 + - + +
87S VAL* 3.7 13.2 - - + +
88S TYR 3.1 0.4 - - - -
89S ALA* 1.3 76.0 - - - +
91S LYS* 1.3 62.2 + - + +
92S ARG 3.3 0.7 - - - -
93S GLN* 3.7 5.1 + - + +
94S GLY 3.4 22.9 + - - +
95S ARG* 4.5 2.8 + - - +
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Residues in contact with LYS 91 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148Q ARG 4.4 1.4 - - - +
149Q PHE* 4.2 1.0 - - - -
150Q HIS* 3.4 32.2 + - + +
84S MET* 5.4 1.4 - - - -
87S VAL* 3.4 38.8 + - - +
88S TYR* 2.9 27.3 + - - +
90S LEU* 1.3 75.7 - - + +
92S ARG* 1.3 64.1 + - - +
93S GLN 3.7 0.2 + - - -
94S GLY* 3.8 9.0 + - - +
95S ARG* 3.5 47.5 + - + +
110T ARG* 4.8 12.0 - - - +
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Residues in contact with ARG 92 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149Q PHE* 4.2 13.5 - - - +
150Q HIS* 4.4 22.3 + - + +
68S ASP* 3.2 26.7 + - - +
72S TYR* 4.0 9.2 - - - +
88S TYR 3.2 9.6 + - - +
89S ALA* 3.5 11.7 - - - +
90S LEU 3.3 0.2 - - - -
91S LYS* 1.3 79.0 - - - +
93S GLN* 1.3 67.6 + - - +
114T GLU* 4.6 7.8 + - + +
117T MET* 3.4 56.5 - - - +
118T ARG* 3.9 12.7 - - - +
120T ARG* 3.5 16.2 - - - +
121T ASP* 3.5 20.6 + - - -
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Residues in contact with GLN 93 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147Q THR* 5.2 0.2 - - - +
149Q PHE* 3.3 17.8 - - - -
131R ARG 5.3 0.9 - - - +
133R GLU* 6.1 1.0 - - - +
61S PHE* 5.1 10.9 - - + -
64S ASN* 3.5 38.9 + - - +
65S VAL* 3.7 25.8 - - + -
68S ASP* 2.9 27.3 + - - -
89S ALA 3.3 13.9 + - - +
90S LEU* 3.7 6.7 + - + +
91S LYS 3.4 0.2 - - - -
92S ARG* 1.3 84.0 - - - +
94S GLY* 1.3 58.1 + - - +
120T ARG* 5.5 1.6 - - - +
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Residues in contact with GLY 94 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147Q THR* 4.4 5.6 - - - +
148Q ARG 3.2 15.7 - - - -
149Q PHE* 3.8 10.1 - - - -
61S PHE* 6.2 0.2 - - - -
90S LEU 3.4 10.9 + - - +
91S LYS 3.8 3.5 + - - -
92S ARG 3.4 2.2 - - - -
93S GLN* 1.3 82.1 - - - +
95S ARG* 1.3 64.0 + - - -
96S THR* 3.7 3.1 + - - -
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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