Contacts of the helix formed by residues 72 - 90 (chain C) in PDB entry 2PJ7
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 GLU 72 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C HIS* 3.1 28.3 + - + +
70C ALA 3.2 0.2 - - - -
71C ARG* 1.3 75.6 - - + +
73C TRP* 1.3 58.5 + - - +
74C ILE 3.3 2.7 - - - -
75C SER* 3.0 23.8 + - - -
76C HIS* 3.1 13.9 + - - -
127C ARG* 4.2 2.8 + - - -
195C ILE 4.7 0.3 - - - +
196C HIS* 3.1 9.0 + - - +
197C SER* 2.9 52.3 + - - +
279C PHE* 3.7 16.8 - - + -
600C ZN 2.2 36.5 - - - -
601C 235 3.2 7.6 + - - -
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Residues in contact with TRP 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C TYR* 3.7 46.1 - + + -
70C ALA 3.2 18.8 + - - -
71C ARG 3.0 13.2 + - - -
72C GLU* 1.3 68.5 - - - +
74C ILE* 1.3 65.3 + - - +
75C SER 3.2 0.5 + - - -
76C HIS* 3.3 10.1 + - - +
77C ALA* 3.1 20.6 + - - +
116C TYR* 3.4 12.9 + + + +
119C THR* 3.0 27.6 + - - -
120C TRP* 3.3 54.5 - + - -
124C ARG* 3.4 52.7 - - - +
279C PHE 4.5 3.5 + - - +
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Residues in contact with ILE 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C TYR* 3.9 9.0 + - - +
73C TRP* 1.3 78.1 - - - +
75C SER* 1.3 63.9 + - - +
77C ALA* 3.4 7.4 + - + +
78C PHE* 3.0 22.2 + - - +
197C SER* 3.4 33.0 - - - +
271C LEU* 4.1 14.7 - - + +
272C ARG 4.2 6.1 - - - +
279C PHE 5.3 2.5 + - - +
281C LEU* 3.8 26.5 - - + -
286C ILE* 4.0 35.7 - - + +
289C THR* 3.8 26.2 - - + -
290C CYS* 4.7 3.1 - - - -
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Residues in contact with SER 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C CYS* 3.2 22.9 - - - +
67C GLY* 2.9 19.9 + - - -
72C GLU* 3.0 18.4 + - - -
74C ILE* 1.3 79.5 - - - +
76C HIS* 1.3 67.1 + - - +
78C PHE* 3.1 11.1 + - - +
79C CYS 3.4 0.2 + - - -
195C ILE* 2.7 43.6 + - - -
196C HIS* 4.4 9.0 - - - -
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Residues in contact with HIS 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C ILE* 4.6 0.4 - - + -
66C CYS* 4.1 0.7 - - - -
67C GLY* 3.4 26.9 + - - -
69C HIS 3.8 5.8 + - - -
70C ALA* 3.7 18.6 + - - -
72C GLU 3.1 21.0 + - - -
73C TRP* 3.7 7.5 - - - +
75C SER* 1.3 73.4 + - - +
77C ALA* 1.3 65.5 + - - +
78C PHE 3.2 0.7 + - - -
79C CYS* 3.3 10.7 + - - +
80C GLN* 3.1 27.1 + - - +
109C PRO 4.0 14.7 - - - +
110C VAL* 3.6 32.8 - - + +
116C TYR* 3.2 45.3 - + + +
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Residues in contact with ALA 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C TYR* 5.4 4.1 - - - +
11C LYS 5.3 4.7 - - - +
12C TYR* 4.2 17.5 - - + -
13C ASN* 6.2 0.2 - - - +
73C TRP 3.1 10.3 + - - +
74C ILE* 3.5 21.5 - - + +
75C SER 3.1 0.6 - - - -
76C HIS* 1.3 80.6 - - - +
78C PHE* 1.3 62.0 + - - +
80C GLN* 3.4 14.8 + - - +
81C TRP* 3.1 21.1 + - - +
286C ILE* 4.3 15.0 - - + -
290C CYS* 4.2 2.9 - - - -
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Residues in contact with PHE 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C MET* 3.8 31.9 - - + -
74C ILE 3.0 13.8 + - - +
75C SER 3.1 8.5 + - - +
77C ALA* 1.3 75.0 - - - +
79C CYS* 1.3 60.9 + - - +
81C TRP* 3.1 1.9 + + + +
82C PHE* 2.8 28.8 + + + +
195C ILE* 4.3 17.0 - - + -
271C LEU* 4.1 11.4 - - + -
290C CYS* 3.5 39.2 - - + -
293C THR* 3.4 39.5 - - + -
294C MET* 3.8 24.7 - - + -
297C ILE* 3.8 15.3 - - + -
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Residues in contact with CYS 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C TRP* 4.9 0.9 - - - -
64C MET* 3.9 18.6 - - - -
65C ASP* 4.0 3.8 - - - -
66C CYS* 2.0 55.7 - - + -
75C SER 3.4 2.4 + - - -
76C HIS 3.3 5.6 + - - +
78C PHE* 1.3 77.5 - - - +
80C GLN* 1.3 64.3 + - - +
82C PHE* 3.4 2.4 + - - +
83C VAL* 3.3 28.4 + - - +
107C VAL* 3.8 15.9 - - + +
108C LEU 3.7 9.2 - - - -
109C PRO* 3.8 16.8 - - + -
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Residues in contact with GLN 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C HIS* 2.8 29.0 + - - +
9C TYR* 3.4 20.6 - - + -
13C ASN* 3.0 19.3 + - - +
18C ILE* 3.5 35.1 - - + +
21C TRP* 3.6 35.5 - - + -
76C HIS* 3.1 24.7 + - - +
77C ALA* 3.4 11.5 + - - +
78C PHE 3.2 0.6 - - - -
79C CYS* 1.3 78.4 - - - +
81C TRP* 1.3 62.2 + - - +
83C VAL* 3.3 12.0 + - - +
84C ARG 3.3 8.8 + - - -
109C PRO* 5.2 4.4 - - + +
110C VAL* 5.9 0.2 - - - +
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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
----------------------------------------------------------
9C TYR* 3.8 33.8 - - + +
10C GLU* 3.8 14.6 - - - -
77C ALA 3.1 14.1 + - - +
78C PHE* 3.1 8.7 + + - +
80C GLN* 1.3 77.8 - - - +
82C PHE* 1.3 62.0 + - - +
84C ARG* 3.2 34.2 + - - +
85C GLU* 3.1 49.7 + - + +
287C GLN* 3.4 34.8 - - + -
290C CYS* 3.4 36.1 - - + +
291C GLU* 3.5 25.3 - - + +
294C MET* 3.7 18.3 - - + +
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Residues in contact with PHE 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C VAL* 5.4 2.0 - - + -
64C MET* 3.9 17.7 - - + -
78C PHE* 2.8 20.3 + + + +
79C CYS 3.7 4.9 - - - +
80C GLN 3.3 0.2 - - - -
81C TRP* 1.3 75.9 - - - +
83C VAL* 1.3 67.6 + - - +
85C GLU* 3.2 3.8 + - - +
86C ALA* 3.0 30.7 + - + +
96C MET* 4.9 6.5 - - + -
105C PHE* 3.6 55.4 - + + -
107C VAL* 4.0 20.6 - - + -
294C MET* 3.5 37.0 - - + -
297C ILE* 3.9 26.2 - - + -
298C LYS* 5.6 1.6 - - + -
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Residues in contact with VAL 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C TRP* 3.8 26.7 - - + -
25C VAL* 4.2 7.6 - - + -
33C ILE* 3.9 26.2 - - + -
50C LEU* 4.0 16.8 - - + -
52C VAL* 4.5 9.0 - - + -
79C CYS 3.3 15.3 - - - +
80C GLN 3.3 6.9 + - - +
81C TRP 3.2 0.6 - - - -
82C PHE* 1.3 80.8 - - - +
84C ARG* 1.3 63.3 + - - +
86C ALA* 3.2 6.3 + - - +
87C VAL* 3.0 22.5 + - + +
107C VAL* 4.1 22.7 - - + -
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Residues in contact with ARG 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C TYR* 3.3 64.2 + - + +
10C GLU* 4.1 9.1 + - - -
25C VAL* 5.8 0.4 - - - -
80C GLN 3.3 3.2 + - - -
81C TRP* 3.2 50.3 + - - +
82C PHE 3.3 0.4 - - - -
83C VAL* 1.3 80.0 - - - +
85C GLU* 1.3 66.6 + - - +
87C VAL* 3.1 8.8 - - + +
88C LEU* 2.9 63.8 + - + +
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Residues in contact with GLU 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 52.1 + - + +
82C PHE 3.2 7.8 + - - +
84C ARG* 1.3 87.9 + - - +
86C ALA* 1.3 52.8 + - - +
88C LEU* 4.7 4.0 - - - +
89C THR* 2.6 55.6 + - + +
96C MET* 4.6 2.5 - - + -
291C GLU* 6.2 0.4 - - - -
294C MET* 4.1 24.1 - - + +
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Residues in contact with ALA 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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52C VAL* 3.9 24.5 - - + -
82C PHE* 3.0 21.8 + - + +
83C VAL* 3.5 9.0 - - - +
84C ARG 3.2 0.2 - - - -
85C GLU* 1.3 77.4 - - - +
87C VAL* 1.3 62.8 + - - +
90C TYR* 3.1 28.9 + - - +
96C MET* 3.8 28.2 - - + +
100C LEU* 3.8 6.2 - - + +
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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
----------------------------------------------------------
25C VAL* 5.0 4.9 - - + -
29C ASN* 3.8 26.0 - - - +
32C LEU* 3.5 28.2 - - + +
33C ILE* 3.3 35.9 - - + -
52C VAL* 4.8 4.0 - - + -
83C VAL* 3.0 14.3 + - + +
84C ARG* 3.1 22.7 - - + +
86C ALA* 1.3 76.5 - - - +
88C LEU* 1.3 72.8 + - + +
90C TYR* 4.3 7.3 + - - +
92C TYR* 5.9 0.7 - - - -
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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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29C ASN* 5.6 2.7 - - - +
84C ARG* 2.9 52.1 + - + +
85C GLU* 4.2 5.4 - - - +
87C VAL* 1.3 90.2 - - + +
89C THR* 1.3 61.6 + - + +
90C TYR 4.9 0.2 - - - -
92C TYR* 3.4 22.0 - - - -
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Residues in contact with THR 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C GLU* 2.6 39.0 + - + +
88C LEU* 1.3 81.0 - - + +
90C TYR* 1.3 65.4 + - - +
91C GLY 3.2 0.2 + - - -
92C TYR* 3.0 21.2 + - - +
93C GLU* 3.1 25.0 + - + +
96C MET* 3.2 26.6 - - - +
298C LYS* 5.4 3.3 + - - +
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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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32C LEU* 4.0 24.0 - - + -
54C LYS* 3.6 26.9 - - + +
86C ALA 3.1 19.4 + - - +
87C VAL 4.5 5.9 - - - +
88C LEU 3.6 0.8 - - - -
89C THR* 1.3 78.5 + - - +
91C GLY* 1.3 62.8 + - - +
92C TYR* 3.2 12.2 + - - -
96C MET* 4.3 4.7 - - - -
97C THR* 3.6 37.1 - - + +
100C LEU* 3.7 31.0 - - + -
101C ASN* 2.7 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