Contacts of the helix formed by residues 45 - 66 (chain C) in PDB entry 3EVK
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 LYS 45 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A ASN* 3.8 43.7 - - + +
41C LEU* 2.9 30.2 + - + +
44C GLN* 1.3 95.0 - - + +
46C HIS* 1.3 60.0 + - + +
47C HIS 3.6 0.4 - - - -
48C GLN* 3.8 1.8 - - - +
49C GLY* 3.0 26.7 + - - -
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Residues in contact with HIS 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A GLU* 4.1 4.9 - - - -
183A TYR* 2.7 33.1 + + - -
188A ASN* 3.5 27.2 - - + +
41C LEU 3.0 21.1 + - - -
42C HIS* 3.3 26.0 - - + +
45C LYS* 1.3 75.0 - - - +
47C HIS* 1.3 67.1 + - - +
49C GLY* 3.2 10.4 + - - -
50C TYR* 3.1 31.3 + - + -
180C HIS* 3.5 43.0 + + + +
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Residues in contact with HIS 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C LEU* 3.3 12.4 - - + +
21C PRO* 3.6 23.3 - - + +
42C HIS 2.9 16.5 + - - +
43C HIS* 3.4 15.2 + - - +
46C HIS* 1.3 72.6 - - - +
48C GLN* 1.3 65.0 + - - +
50C TYR* 3.0 18.9 + + - -
51C VAL* 3.1 8.9 + - + +
86C GLY 4.6 0.7 - - - -
87C HIS* 2.9 39.3 + - - -
90C HIS* 3.4 26.9 - + + +
91C SER* 3.7 11.2 - - - -
94C TRP* 3.0 27.4 + - + -
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Residues in contact with GLN 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C LEU* 3.3 33.7 - - + +
43C HIS 3.3 5.6 + - - +
44C GLN 3.2 27.2 - - - +
45C LYS* 3.8 1.8 - - - +
46C HIS 3.3 0.4 - - - -
47C HIS* 1.3 76.4 - - - +
49C GLY* 1.3 58.3 + - - +
51C VAL* 3.2 17.6 + - - +
52C ASN* 2.9 63.5 + - - +
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Residues in contact with GLY 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C LYS 3.0 15.7 + - - -
46C HIS 3.6 4.9 - - - -
47C HIS 3.2 0.4 - - - -
48C GLN* 1.3 77.0 - - - +
50C TYR* 1.3 59.3 + - - +
52C ASN* 3.4 10.6 + - - +
53C GLY* 2.9 25.1 + - - -
83C HIS* 3.9 5.0 + - - -
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Residues in contact with TYR 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C HIS* 3.1 31.8 + - + +
47C HIS* 3.0 12.8 + - - +
49C GLY* 1.3 73.3 - - - +
51C VAL* 1.3 60.9 + - - +
54C ALA* 2.8 32.8 + - - +
82C PHE* 3.8 14.8 - + - -
83C HIS* 3.4 38.3 - + - +
86C GLY* 4.0 7.6 - - - -
87C HIS* 3.8 8.5 - - - +
90C HIS* 3.4 33.4 - + - -
161C HIS* 3.0 28.2 - + - -
178C TRP* 4.0 6.8 - - - -
180C HIS* 3.5 23.7 - - - -
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Residues in contact with VAL 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C TYR* 3.4 31.8 - - + +
19C THR* 3.9 6.7 - - - -
20C LEU* 3.9 16.8 - - + +
47C HIS* 3.1 18.3 + - + +
48C GLN* 3.5 19.1 - - - +
50C TYR* 1.3 75.9 - - - +
52C ASN* 1.3 63.2 + - - +
54C ALA* 3.3 4.4 + - - +
55C ASN* 3.0 32.8 + - - +
87C HIS* 3.5 36.5 - - + +
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Residues in contact with ASN 52 (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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48C GLN* 2.9 51.3 + - - +
49C GLY* 3.6 9.2 - - - +
51C VAL* 1.3 78.6 - - - +
53C GLY* 1.3 57.2 + - - +
55C ASN* 3.4 7.1 + - - +
56C ALA* 2.9 29.7 + - - +
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Residues in contact with GLY 53 (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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49C GLY 2.9 16.2 + - - -
52C ASN* 1.3 70.3 - - - +
54C ALA* 1.3 64.7 + - - +
56C ALA* 3.3 7.8 + - - +
57C ALA* 3.1 24.3 + - - +
79C ASP* 5.6 0.3 - - - +
83C HIS* 3.5 33.9 + - - -
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Residues in contact with ALA 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C TYR* 4.4 18.2 - - + -
50C TYR 2.8 20.6 + - - +
51C VAL* 3.8 5.4 - - - +
53C GLY* 1.3 71.0 - - - +
55C ASN* 1.3 59.1 + - - +
57C ALA* 3.4 4.0 + - - +
58C LEU* 3.1 33.4 + - - +
80C LEU* 4.0 9.0 - - + +
83C HIS* 3.3 13.9 - - + +
84C LEU* 3.9 20.9 - - + +
87C HIS* 5.4 1.8 - - + -
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Residues in contact with ASN 55 (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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17C ARG* 3.4 31.5 + - - +
18C TYR* 2.8 51.3 + - - -
51C VAL* 3.0 28.9 + - - +
52C ASN* 3.8 7.5 + - - +
54C ALA* 1.3 72.8 - - - +
56C ALA* 1.3 60.2 + - - +
58C LEU* 3.4 4.8 + - - +
59C GLU* 3.0 29.1 + - - +
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Residues in contact with ALA 56 (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 ASN 2.9 18.5 + - - +
53C GLY* 3.6 8.3 - - - +
54C ALA 3.3 0.2 - - - -
55C ASN* 1.3 76.6 - - - +
57C ALA* 1.3 60.3 + - - +
59C GLU* 2.8 38.9 - - - +
60C LYS* 3.2 21.7 + - - +
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Residues in contact with ALA 57 (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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53C GLY 3.1 16.5 + - - +
54C ALA 3.8 4.5 - - - +
55C ASN 3.3 0.2 - - - -
56C ALA* 1.3 77.6 - - - +
58C LEU* 1.3 57.1 + - - +
60C LYS* 3.3 7.8 + - - +
61C LEU* 3.0 32.3 + - - +
76C VAL* 3.5 18.4 - - + +
79C ASP* 4.4 7.4 - - + -
80C LEU* 3.9 36.8 - - + +
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Residues in contact with LEU 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B GLN* 3.9 3.1 - - - +
154B LEU* 3.7 28.9 - - + -
15C THR* 4.2 18.5 - - + +
16C LYS 3.4 25.4 - - - +
17C ARG* 4.1 19.1 - - - +
18C TYR* 3.5 24.9 - - + -
54C ALA 3.1 20.9 + - - +
55C ASN* 3.7 5.6 - - - +
56C ALA 3.3 0.2 - - - -
57C ALA* 1.3 73.9 - - - +
59C GLU* 1.3 55.1 + - - +
61C LEU* 3.2 13.3 + - + +
62C GLU* 2.7 36.2 + - - +
65C ARG* 5.3 0.2 - - - +
80C LEU* 4.0 13.0 - - + -
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Residues in contact with GLU 59 (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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17C ARG* 3.6 24.6 - - - +
55C ASN 3.0 15.5 + - - +
56C ALA* 2.8 38.6 - - - +
58C LEU* 1.3 77.1 - - - +
60C LYS* 1.3 69.8 + - - +
62C GLU* 3.8 2.2 - - - +
63C LYS* 3.0 50.4 + - - +
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Residues in contact with LYS 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C ALA* 3.2 26.5 + - - +
57C ALA* 3.5 10.8 - - - +
59C GLU* 1.3 87.3 - - - +
61C LEU* 1.3 61.6 + - - +
63C LYS* 3.6 11.2 + - + +
64C PHE* 3.2 16.6 + - - +
69C ALA* 5.8 0.2 - - - +
70C GLN 5.2 1.4 - - - +
71C ILE* 3.5 14.0 - - + +
76C VAL* 4.1 27.3 - - + +
79C ASP* 4.6 12.7 + - - +
72D ASP* 5.3 5.7 + - - -
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Residues in contact with LEU 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B GLU* 3.6 21.5 - - - +
154B LEU* 5.4 0.2 - - + -
155B ILE 5.7 0.2 - - - +
15C THR* 5.5 0.2 - - + -
57C ALA 3.0 22.2 + - - +
58C LEU* 3.2 15.9 + - + +
60C LYS* 1.3 74.4 - - - +
62C GLU* 1.3 59.3 + - - +
64C PHE* 3.2 5.0 + - + +
65C ARG* 2.9 53.8 + - - +
71C ILE* 3.9 11.4 - - + -
73C ILE* 3.8 23.8 - - + -
76C VAL* 3.7 9.9 - - + -
77C LEU* 4.0 13.9 - - + -
80C LEU* 3.8 28.5 - - + -
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Residues in contact with GLU 62 (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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13C VAL* 4.0 18.1 - - + +
14C THR* 4.9 0.7 - - - -
15C THR* 2.5 40.8 + - + +
17C ARG* 3.1 15.8 + - - -
58C LEU 2.7 20.1 + - - +
59C GLU* 3.8 5.8 - - - +
61C LEU* 1.3 70.7 - - - +
63C LYS* 1.3 59.3 + - + +
65C ARG* 3.2 10.8 + - - +
66C LYS* 2.9 63.6 + - - +
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Residues in contact with LYS 63 (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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59C GLU* 3.0 43.6 + - - +
60C LYS* 3.8 9.4 - - + +
62C GLU* 1.3 74.7 - - - +
64C PHE* 1.3 59.8 + - - +
66C LYS* 3.5 3.9 + - - -
67C GLY 3.3 2.1 + - - -
68C GLU* 2.8 55.5 + - + +
69C ALA* 3.2 24.9 + - + -
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Residues in contact with PHE 64 (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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124B LYS* 2.9 38.5 + - + -
127B GLU* 3.4 33.2 - - + -
128B GLU* 3.7 46.2 - - + -
131B GLN* 5.1 8.3 - - + -
60C LYS 3.2 12.1 + - - +
61C LEU* 3.2 8.3 + - + +
63C LYS* 1.3 79.0 - - - +
65C ARG* 1.3 58.5 + - - +
67C GLY* 3.0 10.4 + - - -
69C ALA 3.5 20.1 + - - +
70C GLN* 4.9 6.3 - - - +
71C ILE* 3.5 39.9 - - + -
73C ILE* 5.0 4.0 - - + -
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Residues in contact with ARG 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B PHE* 2.6 46.7 + - - +
119B PHE* 3.6 33.7 - - + +
124B LYS* 3.3 30.4 - - + +
128B GLU* 3.2 32.1 + - - +
152B GLN* 5.7 0.4 + - - -
153B LEU 4.4 9.1 + - - -
154B LEU* 4.4 15.2 - - - +
155B ILE 5.1 0.4 - - - +
13C VAL* 3.7 28.8 - - + +
14C THR 3.8 1.6 + - - -
15C THR* 3.5 26.0 - - - +
58C LEU* 5.3 0.2 - - - +
61C LEU* 2.9 36.0 + - - +
62C GLU* 3.2 2.0 + - - +
64C PHE* 1.3 76.2 - - + +
66C LYS* 1.3 59.4 + - - +
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Residues in contact with LYS 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LYS* 4.7 0.7 - - - -
13C VAL* 3.7 40.2 + - + +
62C GLU* 2.9 54.8 + - - +
63C LYS* 3.7 8.3 - - - +
64C PHE 3.2 0.2 - - - -
65C ARG* 1.3 76.3 - - - +
67C GLY* 1.3 59.0 + - - +
68C GLU* 3.6 27.3 + - + +
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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