Contacts of the helix formed by residues 66 - 83 (chain C) in PDB entry 2IZV
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 PRO 66 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B SER* 3.6 14.1 - - - +
23C SER* 3.8 1.6 - - - -
24C SER* 3.2 15.9 - - - +
25C ASP* 3.6 4.7 - - + +
64C GLU 3.8 7.6 - - - +
65C ILE* 1.4 90.1 - - + +
67C SER* 1.3 66.6 + - - +
68C HIS* 3.6 24.5 - - + +
69C VAL* 3.0 22.6 + - + -
70C LEU* 3.1 10.4 + - - +
102C GLU* 4.0 10.5 - - + +
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Residues in contact with SER 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B PHE* 3.4 12.6 - - - -
94B SER* 2.9 21.2 + - - -
23C SER* 3.6 15.4 - - - -
25C ASP* 2.6 37.6 + - - -
27C HIS* 3.7 20.6 - - - -
29C PHE* 3.8 3.9 - - - -
66C PRO* 1.3 73.0 - - - +
68C HIS* 1.3 58.6 + - - +
69C VAL 3.1 0.2 - - - -
70C LEU 4.4 0.7 - - - +
71C SER* 3.0 31.5 + - - -
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Residues in contact with HIS 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B PHE* 4.0 9.8 - - + +
94B SER* 2.7 49.0 + - - +
95B SER 3.8 16.4 - - - -
96B PRO* 3.7 12.3 - - + +
97B PRO* 5.1 0.2 - - + -
66C PRO* 3.6 15.0 - - + +
67C SER* 1.3 77.4 + - - +
69C VAL* 1.3 62.8 + - + +
71C SER* 3.4 12.6 + - - -
72C LYS* 4.0 9.4 - - - +
99C ILE* 3.3 38.4 - - + +
102C GLU* 2.8 38.4 + - - -
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Residues in contact with VAL 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C ILE* 3.6 20.0 - - + -
66C PRO* 3.0 13.6 + - + +
68C HIS* 1.3 108.5 - - + +
70C LEU* 1.3 59.1 + - - +
71C SER 3.3 0.4 - - - -
72C LYS* 3.2 6.0 + - - +
73C VAL* 3.1 25.4 + - + +
99C ILE* 5.0 5.4 - - + -
102C GLU* 3.6 27.6 - - + +
103C LEU* 3.6 21.9 - - + +
106C ALA* 3.8 16.6 - - + -
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Residues in contact with LEU 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C LEU* 4.0 16.2 - - + +
22C ILE 3.9 1.6 - - - -
23C SER* 3.6 35.4 - - - +
29C PHE* 3.9 23.6 - - + -
62C PHE* 3.8 33.9 - - + -
65C ILE* 4.0 17.9 - - + +
66C PRO 3.1 13.7 + - - +
67C SER 3.3 0.4 + - - +
69C VAL* 1.3 74.0 - - - +
71C SER* 1.3 66.7 + - - +
73C VAL* 3.3 19.6 + - + +
74C CYS* 3.0 29.1 + - - -
110C LEU* 4.8 3.1 - - + -
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Residues in contact with SER 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PHE* 3.5 5.7 - - - -
93B PHE* 3.8 23.1 - - - -
29C PHE* 3.6 26.6 - - - -
67C SER 3.0 20.0 + - - -
68C HIS* 3.4 11.8 + - - -
70C LEU* 1.3 77.9 - - - +
72C LYS* 1.3 68.4 + - - +
74C CYS* 3.3 6.1 + - - +
75C MET* 3.2 35.9 + - - +
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Residues in contact with LYS 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A LEU* 5.2 0.2 - - - +
70B GLN 4.9 3.6 + - - -
68C HIS 4.0 11.4 - - - +
69C VAL 3.2 8.9 + - - +
71C SER* 1.3 80.8 + - - +
73C VAL* 1.3 64.5 + - - +
75C MET* 3.2 26.0 + - + +
76C TYR* 3.1 16.8 + - - +
93C PHE* 3.6 22.0 - - + -
94C PRO* 3.0 35.0 + - - +
95C ILE* 4.7 4.2 - - - +
96C ALA 5.3 1.8 - - - +
99C ILE* 3.9 16.1 - - + +
103C LEU* 3.7 27.4 - - + -
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Residues in contact with VAL 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A LEU* 4.1 18.6 - - + -
69C VAL* 3.1 21.3 + - + +
70C LEU* 3.6 17.0 - - + +
72C LYS* 1.3 76.1 - - - +
74C CYS* 1.3 63.9 + - - +
76C TYR* 2.9 13.5 + - - +
77C PHE* 3.0 44.4 + - + -
103C LEU* 3.8 15.7 - - + -
106C ALA* 4.6 6.5 - - + -
110C LEU* 3.6 26.2 - - + -
112C CYS* 5.2 1.1 - - - -
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Residues in contact with CYS 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PHE* 3.5 23.2 - - + -
21C LEU* 4.2 15.3 - - - -
29C PHE* 4.0 18.2 - - - -
31C VAL* 3.5 26.8 - - + +
70C LEU* 3.0 21.5 + - - -
71C SER 3.4 9.4 - - - +
72C LYS 3.2 0.2 - - - -
73C VAL* 1.3 76.5 - - - +
75C MET* 1.3 61.4 + - - +
77C PHE* 3.2 21.8 + - - +
78C THR* 3.1 17.7 + - - -
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Residues in contact with MET 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B MET* 3.8 33.4 - - + -
15B PHE* 3.8 9.8 - - + -
69B PRO 3.5 14.3 - - - +
70B GLN 3.9 22.9 - - - +
71B ALA* 4.9 1.6 - - - -
72B PRO* 3.8 20.4 - - + -
93B PHE* 5.5 2.5 - - + -
71C SER* 3.2 25.4 + - - +
72C LYS* 3.2 32.5 + - + +
74C CYS* 1.3 76.6 - - - +
76C TYR* 1.3 62.5 + - - +
78C THR* 3.3 4.4 + - - -
79C TYR* 3.0 20.6 + - - +
93C PHE* 3.8 6.5 - - + -
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Residues in contact with TYR 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A PHE 2.4 32.9 + - - -
388A SER* 3.2 9.0 - - - -
389A LEU* 3.3 46.7 - - + -
392A ILE* 4.1 6.5 - - + -
38C THR* 4.3 6.7 - - + -
72C LYS 3.1 6.1 + - - +
73C VAL 2.9 9.4 + - - +
75C MET* 1.3 77.3 - - - +
77C PHE* 1.3 64.2 + + - +
79C TYR* 3.1 23.5 + + - +
80C LYS* 2.6 65.3 + - + +
93C PHE* 3.5 23.0 - + + -
112C CYS* 3.5 18.4 + - + -
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Residues in contact with PHE 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C LEU* 4.2 20.0 - - + -
31C VAL* 4.8 6.5 - - + -
35C HIS* 3.4 28.3 - - + +
36C ALA* 4.0 15.9 - - + -
38C THR* 3.6 23.3 - - + -
39C SER* 4.0 27.4 - - - -
42C ILE* 4.1 7.6 - - + -
73C VAL* 3.0 40.1 + - + -
74C CYS* 3.2 21.5 + - + +
76C TYR* 1.3 80.5 - + - +
78C THR* 1.3 58.1 + - - +
80C LYS* 4.0 3.9 - - - +
81C VAL* 3.1 34.5 + - - +
110C LEU* 4.8 0.7 - - + -
112C CYS* 4.3 9.9 - - - -
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Residues in contact with THR 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B PHE* 3.6 36.1 - - + -
15B PHE* 4.7 13.3 - - - +
17B ASP* 5.2 1.6 - - - +
69B PRO* 3.9 14.4 - - + +
35C HIS* 4.0 24.2 - - + +
74C CYS 3.1 13.6 + - - -
75C MET* 3.6 8.2 + - - -
76C TYR 3.2 0.4 - - - -
77C PHE* 1.3 76.0 - - - +
79C TYR* 1.3 60.1 + - - +
81C VAL* 3.6 0.9 + - - +
82C ARG* 2.9 34.4 + - + +
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Residues in contact with TYR 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A ARG* 5.6 1.9 + - - -
386A PRO* 3.7 22.6 - - + +
387A PHE 5.4 0.3 + - - -
392A ILE* 4.4 8.5 - - + +
69B PRO* 4.0 9.1 - - - +
70B GLN* 3.8 23.6 - - + -
75C MET 3.0 13.7 + - - +
76C TYR* 3.5 28.7 - + - +
78C THR* 1.3 74.1 - - - +
80C LYS* 1.3 65.8 + - - +
83C TYR* 2.9 51.6 + + - +
90C ILE* 3.7 12.2 - - + +
91C PRO* 2.8 33.9 + - + -
92C GLU* 4.2 2.5 - - - -
93C PHE* 3.8 35.3 + + + +
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Residues in contact with LYS 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A PHE* 5.7 1.8 - - - +
386A PRO* 3.8 28.2 + - + +
38C THR* 3.9 26.9 - - + +
76C TYR* 2.6 51.9 + - + +
77C PHE 4.0 3.8 - - - +
79C TYR* 1.3 75.0 - - - +
81C VAL* 1.3 58.5 + - + +
84C THR* 2.5 52.0 + - - +
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Residues in contact with VAL 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C GLU* 3.5 28.3 - - + +
35C HIS* 3.8 36.1 - - + +
38C THR* 3.5 18.8 - - - +
77C PHE 3.1 18.6 + - - +
78C THR 4.2 1.6 - - - +
80C LYS* 1.3 79.4 - - + +
82C ARG* 1.3 63.9 + - - +
83C TYR 3.5 0.2 + - - -
84C THR* 3.5 16.9 + - - +
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Residues in contact with ARG 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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2B ASP* 5.8 4.7 + - - +
4B PHE* 3.9 27.0 - - + -
69B PRO* 3.8 20.8 - - + +
78C THR* 2.9 19.5 + - + +
79C TYR 4.2 1.1 - - - +
81C VAL* 1.3 81.0 - - + +
83C TYR* 1.3 88.8 + - + +
84C THR 3.4 5.1 + - - +
85C ASN 5.3 0.2 - - - +
86C SER* 4.8 4.1 + - - -
87C SER* 4.0 18.6 + - - +
88C THR* 4.3 10.9 - - - +
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Residues in contact with TYR 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A THR 3.3 16.3 - - - +
386A PRO* 3.7 14.6 - - + +
68B ARG* 5.9 0.7 - - - +
69B PRO* 4.0 21.0 - - + +
70B GLN* 4.0 14.0 + - - -
79C TYR* 2.9 39.4 + + - +
80C LYS 3.9 1.8 - - - -
82C ARG* 1.3 100.4 + - + +
84C THR* 1.3 62.4 + - - +
86C SER* 3.4 24.6 - - - -
88C THR* 3.9 20.3 - - + +
90C ILE* 3.8 22.0 - - + +
91C PRO* 3.5 35.9 - - + +
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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) + - + + + + + -
------------------------------------------------------------
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