Contacts of the helix formed by residues 76 - 94 (chain C) in PDB entry 2RFQ
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 CYS 76 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C LEU* 4.0 19.3 - - + +
24C ALA* 4.4 19.1 - - + -
27C THR* 4.3 18.4 - - - -
72C ILE 3.2 7.9 + - - +
73C ALA* 3.6 4.5 + - - -
75C ALA* 1.3 81.1 - - - +
77C GLY* 1.3 62.5 + - - +
78C SER* 3.9 4.7 - - - -
79C THR* 3.1 37.9 - - - +
80C GLY 2.9 24.9 + - - -
354C ARG* 6.1 2.7 - - - +
355C PHE* 4.8 1.1 - - - -
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Residues in contact with GLY 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C ALA* 3.6 4.2 + - - -
76C CYS* 1.3 71.8 - - - +
78C SER* 1.3 58.1 + - - +
80C GLY* 3.3 1.1 + - - -
81C TRP* 2.9 30.3 + - - +
184C LEU* 4.0 6.7 - - - -
245C MSE 3.6 33.3 - - - +
354C ARG* 6.0 1.8 - - - +
355C PHE* 4.3 6.8 - - - -
358C ASP* 3.9 14.2 + - - -
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Residues in contact with SER 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C THR* 4.2 7.0 - - - -
28C GLU* 5.5 3.4 - - - +
33C ILE* 3.6 5.2 - - - -
76C CYS* 3.3 3.8 - - - -
77C GLY* 1.3 76.0 - - - +
79C THR* 1.3 64.8 + - - +
81C TRP* 3.6 0.9 - - - +
82C VAL* 3.0 29.5 + - - +
184C LEU* 3.5 16.8 - - - +
185C ARG 3.9 0.3 + - - -
186C GLY* 3.1 40.6 + - - -
187C THR* 3.5 15.5 + - - -
358C ASP* 4.0 7.4 + - - -
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Residues in contact with THR 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C LEU* 4.4 16.5 - - + +
27C THR* 4.5 4.0 + - - +
33C ILE* 3.5 30.0 - - + +
34C PRO* 5.2 0.2 - - - +
37C SER* 5.0 1.8 + - - -
38C MSE 5.5 0.8 - - - +
41C LEU* 3.7 28.5 - - + -
72C ILE* 3.8 12.1 - - + -
76C CYS* 3.1 29.1 + - - +
78C SER* 1.3 78.2 - - - +
80C GLY* 1.3 58.3 + - - +
82C VAL* 3.5 0.9 + - - +
83C SER* 2.8 34.9 + - - -
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Residues in contact with GLY 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C VAL* 4.0 4.4 - - - +
72C ILE* 3.7 9.8 - - - +
73C ALA* 3.7 31.0 - - - -
76C CYS 2.9 11.7 + - - -
77C GLY 3.8 0.4 - - - -
79C THR* 1.3 77.8 - - - +
81C TRP* 1.3 56.1 + - - +
83C SER* 3.4 1.4 + - - -
84C SER* 2.9 31.4 + - - -
241C PRO* 4.0 8.3 - - - +
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Residues in contact with TRP 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C GLY 2.9 17.3 + - - +
78C SER 3.6 4.0 - - - +
80C GLY* 1.3 74.7 - - - +
82C VAL* 1.3 65.5 + - - +
84C SER* 3.4 1.7 + - - -
85C ILE* 3.1 48.6 + - + +
140C SER* 3.1 28.1 + - - -
184C LEU* 3.7 25.8 - - + +
187C THR* 3.6 19.3 + - + -
189C SER* 4.7 1.2 + - - -
238C ILE* 3.6 41.7 - - + -
241C PRO* 3.8 25.0 - - + +
242C ILE* 4.0 4.3 - - + -
245C MSE 4.1 9.2 - - + -
362C GLY* 3.7 33.7 - - - -
365C HIS* 4.2 12.8 - + + -
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Residues in contact with VAL 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C ILE* 3.7 20.2 - - + -
38C MSE 4.2 18.8 - - + -
78C SER 3.0 17.8 + - - +
79C THR 3.9 2.7 - - - +
81C TRP* 1.3 75.5 - - - +
83C SER* 1.3 58.3 + - - +
85C ILE* 3.3 2.9 + - - -
86C ILE* 2.9 48.6 + - + +
140C SER* 4.4 4.3 - - - -
141C GLY* 3.9 18.2 - - - +
144C HIS* 5.3 0.7 - - + -
187C THR* 3.7 36.3 - - - +
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Residues in contact with SER 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C MSE 5.2 1.0 - - - -
41C LEU* 3.4 27.0 - - - +
46C PHE* 3.2 31.3 - - - -
47C PHE* 4.3 8.0 - - - -
69C VAL* 5.3 0.4 - - - -
72C ILE* 3.8 17.2 - - - +
79C THR 2.8 27.6 + - - -
80C GLY 3.7 5.4 - - - -
82C VAL* 1.3 73.0 - - - +
84C SER* 1.3 57.3 + - - +
87C GLY* 2.8 25.8 + - - -
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Residues in contact with SER 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C PHE* 3.4 2.8 - - - -
66C TYR* 5.0 0.3 - - - -
69C VAL* 3.6 32.1 - - - +
80C GLY 2.9 17.4 + - - -
81C TRP 3.6 4.9 - - - -
82C VAL 3.3 0.2 - - - -
83C SER* 1.3 76.0 - - - +
85C ILE* 1.3 57.3 - - - +
88C VAL* 2.9 25.3 + - - +
237C THR* 2.7 56.3 + - - -
240C ALA* 4.9 0.3 - - - +
241C PRO* 4.1 2.2 - - - -
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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
----------------------------------------------------------
81C TRP* 3.1 57.2 + - + +
82C VAL 4.1 1.3 - - - +
84C SER* 1.3 75.2 - - - +
86C ILE* 1.3 66.4 + - + +
88C VAL* 3.2 8.5 + - + +
89C HIS* 3.1 47.6 + - + +
115C SER* 4.1 6.5 - - - +
140C SER* 4.0 22.7 - - - +
234C HIS* 5.9 4.5 - - + -
237C THR* 3.9 21.3 - - + +
238C ILE* 3.9 15.5 - - + -
365C HIS* 5.6 1.1 - - + +
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Residues in contact with ILE 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C MSE 4.8 3.4 - - + -
47C PHE* 3.9 13.2 - - + -
82C VAL* 2.9 38.7 + - + +
85C ILE* 1.3 72.1 - - + +
87C GLY* 1.3 63.2 + - - +
89C HIS* 3.2 21.3 + - + +
90C ASN* 3.8 9.4 + - - +
112C ARG* 3.7 37.9 - - + -
113C ILE 3.3 23.0 - - - +
114C SER* 3.7 15.5 - - - -
140C SER 3.4 22.4 - - - +
141C GLY 4.3 9.0 - - - +
144C HIS* 5.9 0.7 - - + -
145C ALA* 5.0 2.0 - - + -
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Residues in contact with GLY 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C PHE* 4.4 0.7 - - - -
47C PHE* 4.1 19.7 - - - +
50C LEU* 4.4 5.4 + - - +
65C PHE* 3.8 20.1 - - - -
83C SER 2.8 23.4 + - - -
84C SER 3.8 0.9 - - - -
86C ILE* 1.3 73.5 - - - +
88C VAL* 1.3 62.6 + - - +
90C ASN* 3.2 23.2 + - - +
91C TRP 3.9 2.3 + - - -
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Residues in contact with VAL 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C LEU* 4.3 13.2 - - + -
65C PHE* 3.7 4.9 - - + -
66C TYR* 4.8 0.9 - - - +
84C SER 2.9 14.1 + - - +
85C ILE* 3.2 12.3 + - + +
87C GLY* 1.3 76.1 - - - +
89C HIS* 1.3 71.6 + - + +
91C TRP* 2.9 23.7 + - + +
92C HIS* 3.1 10.6 + - - +
230C TRP* 4.8 14.8 - - + -
233C ILE* 3.4 33.2 - - + +
234C HIS* 4.9 4.9 - - + +
237C THR* 3.6 31.4 - - + +
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Residues in contact with HIS 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* 3.1 39.9 + - + +
86C ILE* 3.2 10.0 + - + +
87C GLY 3.2 1.2 - - - -
88C VAL* 1.3 85.0 - - + +
90C ASN* 1.3 58.5 + - - +
92C HIS* 3.6 6.2 - - - +
93C LEU* 2.9 31.4 + - - +
113C ILE* 2.7 42.9 + - + +
114C SER* 3.6 3.6 - - - -
115C SER* 2.8 42.9 + - - -
117C TYR* 3.3 24.5 + + - +
149C VAL* 4.6 4.3 - - + -
234C HIS* 6.1 0.4 - - - -
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Residues in contact with ASN 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C PHE* 2.9 39.5 + - - +
50C LEU 3.7 7.9 - - - +
51C GLN* 4.2 17.4 + - + +
52C PRO* 4.1 1.4 - - - +
86C ILE* 4.3 8.5 + - - +
87C GLY 3.2 11.8 + - - +
88C VAL 3.1 0.8 - - - -
89C HIS* 1.3 73.9 - - - +
91C TRP* 1.3 63.8 + - - +
94C ALA* 3.5 16.5 + - - +
105C TRP* 3.3 39.7 - - + -
109C THR 6.0 0.2 + - - -
111C VAL 4.4 6.9 + - - +
112C ARG* 5.0 3.7 - - - +
113C ILE* 3.4 16.8 + - - +
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Residues in contact with TRP 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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50C LEU* 3.8 34.6 + - + +
87C GLY 3.9 1.0 + - - -
88C VAL* 2.9 12.9 + - + +
90C ASN* 1.3 76.8 - - - +
92C HIS* 1.3 84.4 + - - +
94C ALA* 3.1 18.7 + - - +
95C LEU* 3.4 29.9 + - + +
210C MSE 4.1 5.8 - - + -
225C VAL* 2.9 39.7 + - + +
226C TYR* 3.6 32.5 - + - -
228C MSE 3.3 25.6 - - - -
230C TRP* 3.2 39.9 - + - -
233C ILE* 3.9 26.7 - - + +
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Residues in contact with HIS 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 VAL 3.1 10.9 + - - +
89C HIS* 3.3 8.9 + - + +
91C TRP* 1.3 87.2 - - + +
93C LEU* 1.3 63.5 + - - +
95C LEU* 3.0 16.9 + - + +
96C PHE* 3.4 21.3 - + - -
117C TYR* 2.8 35.3 + + - +
149C VAL* 4.1 7.7 - - + +
165C SER* 3.2 33.6 + - - -
205C LEU* 4.1 4.0 + - + +
207C PHE* 4.3 6.7 - + - -
210C MSE 3.5 36.1 - - + -
230C TRP* 4.3 6.7 - + + -
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Residues in contact with LEU 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 HIS 2.9 16.8 + - - +
90C ASN 4.3 0.2 - - - +
91C TRP 3.3 0.2 - - - -
92C HIS* 1.3 76.8 - - - +
94C ALA* 1.3 61.5 + - - +
96C PHE* 3.0 34.7 + - + +
100C ALA 4.6 2.2 - - - +
101C GLN* 3.2 26.9 - - + +
104C VAL* 3.6 35.9 - - + -
105C TRP* 3.6 34.5 - - + -
113C ILE* 3.8 9.0 - - + -
149C VAL* 5.4 3.1 - - + +
167C LEU* 3.8 33.0 - - + -
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Residues in contact with ALA 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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52C PRO* 3.5 22.2 - - + -
90C ASN 3.5 6.5 + - - +
91C TRP 3.1 15.6 + - - +
93C LEU* 1.3 78.1 - - - +
95C LEU* 1.3 57.9 + - - +
96C PHE 3.4 0.2 - - - -
101C GLN* 3.4 4.8 + - - -
105C TRP* 4.9 0.4 - - - -
217C GLY* 3.2 16.6 - - - -
221C ASN* 3.0 27.9 + - - +
226C TYR* 3.4 31.2 - - + -
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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