Contacts of the helix formed by residues 73 - 92 (chain C) in PDB entry 2B5F
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 GLY 73 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C HIS* 4.1 16.5 + - - -
71C SER 3.3 4.8 + - - -
72C VAL* 1.3 77.1 - - - +
74C LEU* 1.3 69.7 + - - -
75C LEU* 2.9 5.4 - - - -
76C GLY 2.6 13.2 + - - -
77C ILE* 3.0 11.9 + - - +
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Residues in contact with LEU 74 (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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69A CYS 5.7 0.4 - - - +
70A GLY* 3.3 34.5 - - - +
71A SER* 4.7 2.5 + - - -
72A VAL* 4.2 26.8 - - + +
62C HIS* 3.6 25.6 - - + +
73C GLY* 1.3 70.2 - - - -
75C LEU* 1.3 57.0 + - - +
77C ILE* 3.0 17.5 + - + +
78C ALA* 2.9 29.6 + - - +
214C ILE* 4.0 31.0 - - + +
215C PRO* 5.7 6.3 - - + -
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Residues in contact with LEU 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A VAL* 3.5 28.0 - - - +
75A LEU* 3.7 33.2 - - + -
76A GLY* 4.4 10.3 - - - +
79A TRP* 4.5 8.1 - - + +
72C VAL 4.9 1.1 - - - +
73C GLY* 4.0 3.1 - - - -
74C LEU* 1.3 77.1 - - - +
76C GLY* 1.3 60.7 + - - +
78C ALA* 3.3 5.5 + - - +
79C TRP* 3.1 28.3 + - + +
207C PHE* 3.9 17.0 - - + -
211C LEU* 3.9 23.1 - - + -
75D LEU* 3.5 26.2 - - + -
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Residues in contact with GLY 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C THR* 4.4 1.9 - - - +
72C VAL* 3.6 28.8 + - - -
73C GLY 2.6 15.5 + - - -
75C LEU* 1.3 75.2 - - - +
77C ILE* 1.3 59.8 + - - -
79C TRP* 3.3 6.2 + - - +
80C ALA* 3.0 19.4 + - - +
75D LEU* 4.1 15.2 - - - +
211D LEU* 3.6 8.8 - - - +
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Residues in contact with ILE 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C THR* 3.9 25.1 - - + +
59C VAL* 3.6 37.0 - - + -
62C HIS* 3.7 37.7 - - + -
63C SER* 5.8 0.4 - - - +
72C VAL* 4.7 1.1 - - + +
73C GLY 3.0 5.9 + - - +
74C LEU* 3.0 19.0 + - + +
76C GLY* 1.3 76.9 - - - +
78C ALA* 1.3 61.9 + - - +
80C ALA* 3.1 11.1 + - - +
81C PHE* 3.2 32.3 + - + -
214C ILE* 4.2 15.7 - - + -
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Residues in contact with ALA 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C LEU 2.9 12.2 + - - +
75C LEU 3.5 8.5 - - - +
77C ILE* 1.3 75.1 - - - +
79C TRP* 1.3 57.1 + - - +
81C PHE* 3.4 3.6 + - - +
82C GLY 3.1 23.2 + - - -
207C PHE* 3.6 26.9 - - + -
210C HIS* 3.8 25.5 - - + +
211C LEU* 3.8 20.2 - - + -
214C ILE* 4.2 5.6 - - + +
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Residues in contact with TRP 79 (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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79A TRP* 4.0 24.8 - + - +
75C LEU* 3.1 34.5 + - + +
76C GLY* 3.5 9.6 - - - +
77C ILE 3.2 0.4 - - - -
78C ALA* 1.3 73.9 - - - +
80C ALA* 1.3 60.0 + - - +
82C GLY 5.8 0.2 - - - -
83C GLY* 2.8 30.9 + - - -
203C GLY 6.4 0.9 - - - -
204C PHE* 3.9 24.7 - + - -
207C PHE* 3.3 47.1 - + + -
75D LEU* 4.5 8.0 - - + +
79D TRP* 3.7 28.5 - + - +
204D PHE* 3.7 34.3 - + - -
207D PHE* 4.0 16.4 - + + -
208D MET* 3.3 9.4 - - - +
211D LEU* 4.0 11.7 - - + -
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Residues in contact with ALA 80 (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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54C ILE* 4.8 4.9 - - + -
55C THR* 3.6 21.4 - - + +
58C THR* 4.0 22.9 - - + +
76C GLY 3.0 12.9 + - - +
77C ILE 3.1 9.2 + - - +
79C TRP* 1.3 73.7 - - - +
81C PHE* 1.3 63.6 + - + +
84C MET* 3.1 31.5 + - - +
208D MET* 3.7 10.8 - - - -
211D LEU* 3.9 7.4 - - + +
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Residues in contact with PHE 81 (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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51C PHE* 3.8 16.5 - + - -
55C THR* 3.4 36.8 - - + -
56C VAL* 4.9 2.2 - - + -
59C VAL* 3.8 11.7 - - + -
77C ILE* 3.2 40.4 + - + -
78C ALA 3.8 3.8 - - - +
79C TRP 3.2 0.2 - - - -
80C ALA* 1.3 80.1 - - + +
82C GLY* 1.3 62.3 + - - +
85C ILE* 3.3 28.6 + - - +
206C VAL* 3.8 3.8 - - + -
210C HIS* 3.1 43.5 - + + +
225C ARG* 3.6 48.5 - - + -
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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
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78C ALA 3.1 12.3 + - - -
79C TRP* 4.0 1.6 - - - -
81C PHE* 1.3 77.0 - - - +
83C GLY* 1.3 57.2 + - - +
85C ILE* 3.3 2.8 + - - +
86C PHE 3.1 22.2 + - - -
203C GLY* 3.1 34.3 - - - -
206C VAL* 3.8 5.9 - - - +
207C PHE* 3.7 16.6 - - - -
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Residues in contact with GLY 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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79C TRP* 2.8 25.7 + - - +
82C GLY* 1.3 70.1 - - - -
84C MET* 1.3 58.0 - - - +
86C PHE* 3.5 5.8 + - - +
87C VAL* 3.0 32.7 + - - +
204D PHE* 4.0 21.4 - - - -
208D MET* 3.5 13.9 - - - -
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Residues in contact with MET 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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50C LEU* 3.2 31.2 - - + +
51C PHE* 4.0 17.3 - - + +
54C ILE* 3.5 35.4 - - + -
55C THR* 4.8 2.7 - - + -
80C ALA 3.1 24.8 + - - +
83C GLY* 1.3 73.7 - - - +
85C ILE* 1.3 62.5 + - - +
87C VAL* 4.4 7.0 - - + -
88C LEU* 2.9 63.4 + - + +
174D VAL* 4.4 15.3 - - + -
208D MET* 3.5 21.9 - - - -
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Residues in contact with ILE 85 (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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51C PHE* 3.2 40.6 - - + -
81C PHE 3.3 9.7 + - - +
82C GLY 3.3 7.2 + - - +
84C MET* 1.3 75.5 - - - +
86C PHE* 1.3 57.0 + - - +
88C LEU* 4.6 1.3 - - + +
89C VAL* 2.9 45.9 + - + +
99C HIS 5.4 1.3 - - - +
100C ILE* 4.1 28.0 - - + +
101C ASN* 6.1 1.3 - - + -
175C LEU* 5.7 0.2 - - + -
202C ILE* 3.1 35.4 - - + -
206C VAL* 4.0 16.8 - - + -
222C ASN* 5.2 2.5 - - - +
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Residues in contact with PHE 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 3.1 7.1 + - - +
83C GLY* 3.5 7.9 - - - +
85C ILE* 1.3 76.0 - - - +
87C VAL* 1.3 65.1 + - + +
90C TYR* 3.0 30.1 + + + +
199C PRO* 3.1 41.2 - - + +
200C LEU* 3.4 34.1 - - + -
203C GLY* 3.5 22.4 - - - +
200D LEU* 3.4 26.9 - - + -
201D PRO* 3.3 32.3 - - + -
204D PHE* 3.9 31.4 - + + -
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Residues in contact with VAL 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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83C GLY 3.0 18.3 + - - +
84C MET* 3.8 8.7 - - - +
86C PHE* 1.3 77.4 - - + +
88C LEU* 1.3 66.3 + - + +
90C TYR* 3.3 7.8 + - - +
91C CYS* 2.9 31.8 + - - -
174D VAL* 5.0 9.0 - - + -
177D TYR* 6.4 0.2 - - + -
178D THR* 3.5 31.6 - - + +
201D PRO* 3.9 20.2 - - - +
204D PHE* 3.9 10.8 - - + -
205D ALA* 3.9 17.7 - - + +
208D MET* 4.5 4.7 - - + -
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Residues in contact with LEU 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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47C ALA* 3.4 37.9 - - + +
50C LEU* 4.8 7.4 - - + -
51C PHE* 3.5 26.9 - - + -
84C MET* 2.9 45.1 + - + +
85C ILE* 4.2 2.7 - - - +
87C VAL* 1.3 81.0 - - + +
89C VAL* 1.3 65.4 + - - +
91C CYS* 3.2 5.0 + - + +
92C THR* 2.9 29.0 + - + +
100C ILE* 4.0 18.4 - - + -
174D VAL* 6.1 1.1 - - + -
177D TYR* 4.7 18.4 - - + -
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Residues in contact with VAL 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 ILE* 2.9 40.5 + - + +
88C LEU* 1.3 71.4 - - - +
90C TYR* 1.3 62.9 + - - +
92C THR* 3.3 10.6 + - - -
93C ALA* 3.1 30.7 - - + +
98C GLY* 3.4 24.9 - - - +
99C HIS 5.2 0.7 - - - +
100C ILE* 4.3 9.4 - - + -
197C LEU* 3.9 28.3 - - + -
199C PRO* 4.0 19.0 - - + +
202C ILE* 4.6 12.6 - - + -
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Residues in contact with TYR 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 PHE* 3.0 24.9 + + + +
87C VAL* 3.3 6.3 - - - +
89C VAL* 1.3 77.1 - - - +
91C CYS* 1.3 72.5 + - - +
92C THR 3.4 5.4 + - - +
93C ALA* 5.0 0.9 - - - +
94C GLY 5.2 0.2 + - - -
199C PRO* 3.5 21.3 - - + +
178D THR* 4.7 2.9 - - + -
181D SER* 3.2 35.9 + - - -
182D ALA* 3.7 6.0 - - - -
184D ASP* 4.5 3.6 + - - -
198D ALA* 3.7 20.3 - - + +
201D PRO* 3.9 37.0 - - + -
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Residues in contact with CYS 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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87C VAL* 2.9 23.3 + - - +
88C LEU* 3.2 6.5 + - - +
90C TYR* 1.3 77.9 - - - +
92C THR* 1.3 61.9 + - + +
95C ILE* 4.8 6.2 - - - +
177D TYR* 3.5 38.6 + - + +
178D THR* 3.8 35.2 - - - -
181D SER* 3.7 30.5 + - - +
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Residues in contact with THR 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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43C ALA* 4.1 24.0 - - + +
44C GLU* 4.9 2.2 - - - +
47C ALA* 4.6 9.4 - - + -
88C LEU 2.9 18.6 + - - +
89C VAL* 3.3 1.0 + - - -
90C TYR 3.8 4.9 - - - +
91C CYS* 1.3 80.2 - - + +
93C ALA* 1.3 63.5 + - - +
94C GLY* 2.2 26.5 + - - -
95C ILE* 3.3 11.5 + - + +
96C SER* 2.9 21.8 - - - +
98C GLY* 3.0 18.5 - - - -
100C ILE* 4.1 3.1 - - - +
177D TYR* 3.7 19.1 - - + +
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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
------------------------------------------------------------
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