Contacts of the helix formed by residues 81 - 94 (chain C) in PDB entry 3R9A
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 81 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A TYR* 3.4 25.9 + - - -
262A HIS* 3.6 7.4 - - - -
263A THR* 3.6 19.1 - - - -
80C GLY* 1.3 73.1 - - - +
82C GLY* 1.3 57.2 + - - +
83C HIS 3.1 0.4 + - - -
84C CYS* 2.6 34.2 + - - +
208C GLN* 5.2 1.6 - - - -
209C LLP 2.7 27.8 + - - -
216C GLY* 3.6 16.7 + - - +
217C THR 4.4 2.9 - - - -
218C SER* 3.5 3.6 + - - -
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Residues in contact with GLY 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C SER* 1.3 73.8 - - - +
83C HIS* 1.3 59.6 + - - +
84C CYS 3.4 0.5 + - - -
85C ALA 3.5 2.8 + - - -
86C LEU 3.5 4.3 + - - -
185C VAL* 4.2 16.8 - - - -
204C TYR* 3.4 27.2 - - - -
205C SER 4.5 0.4 - - - -
206C GLY* 4.4 8.1 - - - -
208C GLN* 4.8 0.8 + - - -
209C LLP 3.2 17.7 + - - -
217C THR 4.6 2.4 + - - -
218C SER* 3.9 14.5 - - - -
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Residues in contact with HIS 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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240A PHE* 5.8 7.9 - - + -
241A TYR* 4.7 11.1 - - + +
260A TYR* 5.6 0.9 - - - +
261A HIS 5.2 4.9 - - - +
262A HIS* 4.8 5.2 - - + -
81C SER* 2.9 2.8 + - - +
82C GLY* 1.3 72.6 - - - +
84C CYS* 1.3 59.2 + - - +
86C LEU* 3.4 13.1 + - + +
87C GLU* 3.1 27.7 + - - +
108C TRP* 5.8 3.4 - - + -
111C ARG* 5.7 5.4 - - + +
115C ILE* 4.5 5.2 - - + +
209C LLP 3.4 29.5 + - + +
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Residues in contact with CYS 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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241A TYR* 3.7 37.9 - - + -
78C ILE* 3.8 10.1 - - + -
79C SER 4.7 2.5 - - - -
80C GLY* 3.7 19.1 - - - -
81C SER 2.6 22.8 + - - +
83C HIS* 1.3 69.5 - - - +
85C ALA* 1.3 51.9 + - - +
87C GLU* 3.1 6.4 + - - +
88C ALA* 2.7 34.7 + - - +
241C TYR* 5.0 2.9 - - - -
242C LEU* 3.7 30.1 - - - +
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Residues in contact with ALA 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C ILE* 4.1 10.7 - - + +
81C SER 3.5 1.6 + - - -
82C GLY 3.5 9.3 + - - +
84C CYS* 1.3 77.2 - - - +
86C LEU* 1.3 57.6 + - - +
88C ALA* 3.0 9.3 + - - +
89C ALA* 2.8 27.2 + - - +
204C TYR* 3.7 26.0 - - + -
218C SER* 3.5 23.6 + - - +
219C LEU 4.5 2.9 - - - +
220C ILE* 3.5 13.7 - - + +
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Residues in contact with LEU 86 (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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82C GLY 3.5 3.4 + - - +
83C HIS* 3.4 14.7 + - + +
84C CYS 3.2 0.6 - - - -
85C ALA* 1.3 76.8 - - - +
87C GLU* 1.3 64.2 + - - +
89C ALA* 3.2 4.4 + - - +
90C LEU* 3.0 38.4 + - + +
108C TRP* 4.4 8.7 - - + +
111C ARG* 4.5 6.5 - - + -
112C ALA* 4.1 22.2 - - + +
115C ILE* 4.0 20.6 - - + -
152C PHE* 3.9 15.9 - - + -
181C LEU* 4.0 11.4 - - + -
183C ASP* 5.4 0.4 - - - +
204C TYR* 3.3 38.9 - - + +
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Residues in contact with GLU 87 (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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238A PHE 4.2 1.9 - - - +
239A SER* 2.7 35.2 + - - -
240A PHE* 3.2 17.1 + - - +
241A TYR* 2.8 31.1 + - - +
83C HIS 3.1 13.6 + - - +
84C CYS* 3.1 9.2 + - - +
86C LEU* 1.3 76.0 - - - +
88C ALA* 1.3 54.1 + - - +
90C LEU 3.2 0.2 + - - -
91C VAL* 2.8 49.8 + - + +
115C ILE* 3.9 28.1 - - + +
239C SER* 5.9 1.4 - - - -
242C LEU* 4.2 15.5 - - + +
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Residues in contact with ALA 88 (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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78C ILE* 3.9 28.0 - - + -
84C CYS 2.7 17.0 + - - +
85C ALA 3.0 9.6 + - - +
87C GLU* 1.3 72.2 - - - +
89C ALA* 1.3 63.6 + - - +
91C VAL* 4.9 0.4 - - - -
92C ASN* 2.8 33.7 + - - +
220C ILE* 4.6 4.3 - - + -
222C PHE* 4.9 3.9 - - + -
242C LEU* 4.0 24.6 - - + +
244C ILE* 6.2 1.1 - - + -
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Residues in contact with ALA 89 (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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85C ALA 2.8 15.8 + - - +
86C LEU* 3.4 9.9 - - - +
88C ALA* 1.3 74.4 - - - +
90C LEU* 1.3 58.8 + - - +
92C ASN* 4.1 0.2 - - - +
93C VAL* 2.9 35.3 + - - +
150C LEU* 5.8 0.2 - - - -
181C LEU* 4.0 31.2 - - + -
202C ILE* 4.1 15.9 - - + -
204C TYR* 5.3 0.2 - - + -
220C ILE* 4.1 4.8 - - + +
222C PHE* 4.3 11.7 - - + -
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Residues in contact with LEU 90 (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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86C LEU* 3.0 33.8 + - + +
87C GLU 4.0 0.2 - - - +
89C ALA* 1.3 76.3 - - - +
91C VAL* 1.3 58.3 + - - +
93C VAL* 5.0 0.2 - - - -
94C LEU* 3.0 38.9 + - + +
100C PHE* 3.5 32.3 - - + -
112C ALA* 3.7 22.4 - - - +
115C ILE* 3.6 33.9 - - + -
116C GLY 4.2 2.0 - - - +
119C ILE* 3.3 10.4 - - + +
150C LEU* 3.7 19.1 - - + -
181C LEU* 3.7 13.7 - - + -
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Residues in contact with VAL 91 (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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238A PHE 5.0 2.7 - - - +
87C GLU* 2.8 34.0 + - + +
88C ALA 4.5 0.2 - - - +
90C LEU* 1.3 73.7 - - - +
92C ASN* 1.3 68.0 + - - +
94C LEU 3.7 2.6 - - - +
119C ILE* 3.7 30.3 - - + -
233C ARG* 3.1 18.4 + - - -
237C PRO* 3.7 27.5 - - + +
238C PHE* 4.5 17.0 + - + +
239C SER* 4.0 24.0 - - - +
242C LEU* 4.7 6.5 - - + +
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Residues in contact with ASN 92 (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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88C ALA* 2.8 26.5 + - - +
89C ALA 4.1 0.4 - - - +
90C LEU 3.2 0.4 - - - -
91C VAL* 1.3 82.4 - - - +
93C VAL* 1.3 60.8 + - - +
94C LEU 3.4 0.4 - - - -
222C PHE* 5.6 0.2 - - - -
229C LYS 4.9 0.2 - - - +
230C MET* 3.6 31.0 - - + +
233C ARG* 3.1 27.8 + - - +
237C PRO* 3.5 20.0 - - - +
242C LEU 2.8 26.1 + - - -
243C ASP* 3.9 0.7 - - - -
244C ILE* 3.0 38.0 + - - +
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Residues in contact with VAL 93 (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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89C ALA 2.9 22.8 + - - +
90C LEU 4.6 0.2 - - - +
92C ASN* 1.3 76.4 - - - +
94C LEU* 1.3 52.9 + - - +
95C GLU* 5.1 0.3 - - - +
149C VAL* 4.7 3.1 - - + -
150C LEU* 4.0 28.7 - - + -
179C LEU* 3.9 24.9 - - + -
202C ILE* 3.6 24.5 - - + -
222C PHE* 4.5 1.3 - - + -
226C ALA 4.8 3.8 - - - +
229C LYS* 2.7 41.6 + - + -
230C MET* 3.8 26.2 - - + -
233C ARG* 4.5 0.4 - - - -
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Residues in contact with LEU 94 (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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90C LEU* 3.0 28.9 + - + +
91C VAL 3.7 6.4 - - - +
93C VAL* 1.3 78.3 - - - +
95C GLU* 1.3 64.2 + - - +
96C PRO* 4.7 0.9 - - - +
98C ASP* 3.8 20.2 - - + -
99C SER 4.5 1.1 - - - +
100C PHE* 3.6 39.0 - - + -
116C GLY* 4.8 0.9 - - - -
119C ILE* 4.0 26.9 - - + +
121C ALA* 4.1 11.9 - - + -
149C VAL* 4.2 8.5 - - + -
150C LEU* 4.1 28.9 - - + -
233C ARG* 2.9 19.4 + - - -
238C PHE* 6.1 1.0 - - - -
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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