Contacts of the helix formed by residues 45 - 67 (chain C) in PDB entry 4F9K
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 ARG 45 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43C PRO* 3.2 26.3 - - - +
44C GLU* 1.3 125.6 + - + +
46C PRO* 1.4 64.5 - - - +
47C MSE 3.4 2.9 - - - -
48C LYS* 3.4 27.1 + - + +
49C PHE* 3.3 18.9 + - - +
61D GLU* 3.5 18.2 - - - +
65D ILE* 5.0 11.7 - - + -
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Residues in contact with PRO 46 (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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38C LEU* 4.1 6.7 - - + +
43C PRO* 3.8 3.8 - - + +
44C GLU 3.3 12.6 - - - +
45C ARG* 1.4 82.0 - - - +
47C MSE 1.3 86.7 + - + +
49C PHE* 3.3 9.8 - - + +
50C LEU* 3.2 28.4 + - - +
21D TYR* 3.1 19.7 - - - +
25D HIS* 3.4 30.7 - - + -
27D ILE* 4.0 9.6 - - + -
61D GLU* 3.1 11.2 - - - +
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Residues in contact with MSE 47 (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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46C PRO* 1.3 105.0 - - + +
48C LYS* 1.3 60.5 + - - +
50C LEU* 3.5 5.6 + - + +
51C ARG* 3.3 17.3 + - - +
25D HIS* 4.2 5.4 - - + +
27D ILE* 3.7 16.4 - - + -
30D VAL* 3.7 36.3 - - + -
54D PHE* 3.8 28.9 - - + +
57D LEU* 3.6 44.9 - - + +
58D GLU* 3.8 2.7 - - - +
60D GLU* 4.1 8.1 - - - +
61D GLU* 3.1 23.3 + - - +
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Residues in contact with LYS 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C ARG* 3.4 37.3 + - + +
46C PRO 3.4 0.4 - - - -
47C MSE 1.3 74.2 - - - +
49C PHE* 1.3 60.8 + - - +
51C ARG* 3.1 23.7 - - - +
52C GLU* 3.0 45.4 + - - +
58D GLU* 3.5 35.4 - - + +
61D GLU* 3.4 4.6 + - - +
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Residues in contact with PHE 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C CYS 4.8 0.2 - - - -
37C HIS* 3.5 21.8 - + + -
38C LEU* 3.3 36.6 - - + -
41C SER* 3.0 31.9 - - - -
43C PRO* 3.7 29.2 - - + -
45C ARG 3.3 3.4 + - - +
46C PRO 3.3 10.5 - - - +
48C LYS* 1.3 80.1 - - - +
50C LEU* 1.3 59.0 + - + +
52C GLU* 3.5 4.9 + - - +
53C HIS* 2.6 43.5 + - + +
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Residues in contact with LEU 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C CYS* 4.0 29.2 - - + +
38C LEU* 4.2 19.1 - - + -
46C PRO 3.2 19.8 + - - +
47C MSE 3.5 7.6 + - + +
49C PHE* 1.3 93.6 - - + +
51C ARG* 1.3 58.7 + - - +
53C HIS* 3.6 12.3 - - + -
54C PHE* 2.8 42.6 + - + +
27D ILE* 5.5 1.8 - - + -
30D VAL* 5.1 5.4 - - + -
31D LEU* 5.6 2.0 - - + -
54D PHE* 3.8 43.5 - - + -
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Residues in contact with ARG 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C MSE 3.3 15.2 + - - +
48C LYS* 3.1 33.2 + - - +
50C LEU* 1.3 74.4 - - - +
52C GLU* 1.3 69.6 + - - +
55C GLU* 2.3 77.6 + - - +
51D ARG* 3.9 10.0 - - + +
54D PHE* 3.7 13.9 - - - +
55D GLU* 3.5 39.8 + - + +
58D GLU* 2.9 40.6 + - - +
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Residues in contact with GLU 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 LYS* 3.0 34.9 + - - +
49C PHE* 3.7 5.2 - - - +
51C ARG* 1.3 87.9 + - - +
53C HIS* 1.3 62.7 + - - +
55C GLU* 3.2 32.8 + - - +
56C LYS* 3.3 40.8 + - - +
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Residues in contact with HIS 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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30C VAL 4.6 1.4 + - - -
33C ASP* 4.8 1.3 - - + +
34C CYS* 3.5 33.7 + - + +
37C HIS* 4.2 27.3 - + - +
49C PHE* 2.6 30.6 + - + +
50C LEU* 3.4 16.2 - - + +
52C GLU* 1.3 74.1 - - - +
54C PHE* 1.3 78.4 + + - +
56C LYS* 3.2 11.4 + - - +
57C LEU* 3.2 48.8 + - + +
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Residues in contact with PHE 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C VAL* 3.7 25.4 - - + -
31C LEU* 4.2 19.5 - - + -
34C CYS* 4.3 12.1 - - + -
50C LEU* 2.8 41.4 + - + +
51C ARG 3.8 0.2 - - - -
53C HIS* 1.3 86.2 - + - +
55C GLU* 1.3 58.3 + - - +
56C LYS 3.2 0.2 - - - -
57C LEU* 3.6 20.9 - - + -
58C GLU* 2.8 31.9 + - - +
47D MSE 3.6 11.6 - - - +
50D LEU* 3.6 25.4 - - + -
51D ARG* 3.7 21.7 - - - +
54D PHE* 3.9 26.2 - + - -
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Residues in contact with GLU 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C ARG* 2.3 58.8 + - - +
52C GLU* 3.2 22.6 - - - +
53C HIS 3.2 0.4 - - - -
54C PHE* 1.3 76.5 - - - +
56C LYS* 1.3 58.6 + - - +
58C GLU* 3.9 4.0 - - - +
59C LYS* 3.2 23.7 + - - +
51D ARG* 3.6 24.4 - - + +
55D GLU* 5.5 1.1 - - - -
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Residues in contact with LYS 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C GLU* 3.3 46.4 - - - +
53C HIS* 3.2 10.0 + - - +
54C PHE 3.2 0.2 - - - -
55C GLU* 1.3 74.1 - - - +
57C LEU* 1.3 62.5 + - + +
58C GLU 3.1 1.8 - - - -
59C LYS* 2.9 25.7 + - + +
60C GLU* 3.0 13.9 + - - +
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Residues in contact with LEU 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C VAL* 4.9 10.1 - - + +
53C HIS* 3.2 46.0 + - + +
54C PHE* 3.5 24.2 + - + -
56C LYS* 1.3 76.8 - - + +
58C GLU* 1.3 57.5 + - - +
60C GLU* 4.0 13.8 - - + +
61C GLU* 3.0 26.7 + - - +
47D MSE 3.2 24.6 - - + +
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Residues in contact with GLU 58 (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 PHE 2.8 16.2 + - - +
55C GLU* 3.9 4.5 - - - +
57C LEU* 1.3 75.7 - - - +
59C LYS* 1.3 61.7 + - - +
60C GLU 3.3 0.4 - - - -
61C GLU* 3.7 5.9 - - - +
62C ASN* 3.2 29.6 + - - +
47D MSE 3.5 17.5 - - + +
48D LYS* 3.2 44.1 - - + +
51D ARG* 2.9 42.1 + - - +
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Residues in contact with LYS 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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55C GLU 3.2 14.3 + - - +
56C LYS* 2.9 14.8 + - + +
58C GLU* 1.3 76.9 - - - +
60C GLU* 1.3 62.3 + - - +
62C ASN* 3.7 9.8 - - - +
63C ARG* 2.9 54.0 + - - +
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Residues in contact with GLU 60 (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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56C LYS 3.0 12.8 + - - +
57C LEU* 4.2 13.9 - - + +
59C LYS* 1.3 74.4 - - - +
61C GLU* 1.3 68.8 + - - +
62C ASN 3.0 2.5 - - - -
63C ARG* 3.0 23.4 + - + +
64C GLN* 2.6 50.2 + - - +
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Residues in contact with GLU 61 (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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57C LEU 3.0 20.5 + - - +
58C GLU* 3.7 10.2 - - - +
60C GLU* 1.3 76.7 - - - +
62C ASN* 1.3 62.7 + - - +
64C GLN* 3.4 28.3 - - - +
65C ILE* 3.1 30.6 - - + +
45D ARG* 3.9 15.0 - - - +
46D PRO* 3.1 33.2 - - - +
47D MSE 3.1 33.7 + - + +
48D LYS* 3.7 6.6 + - - +
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Residues in contact with ASN 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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58C GLU* 3.2 25.6 + - - +
59C LYS* 3.7 12.6 + - - +
60C GLU 3.0 0.8 - - - -
61C GLU* 1.3 77.7 - - - +
63C ARG* 1.3 63.1 + - - +
65C ILE* 3.0 12.0 + - - +
66C LEU* 2.7 50.2 + - + +
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Residues in contact with ARG 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 LYS* 2.9 60.3 + - - +
60C GLU* 3.0 15.0 + - + +
62C ASN* 1.3 88.4 - - - +
64C GLN* 1.3 53.6 + - - +
66C LEU* 3.3 16.8 - - - +
67C ALA* 2.5 41.6 + - + +
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Residues in contact with GLN 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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60C GLU* 2.6 40.9 + - - +
61C GLU* 3.4 27.3 - - - +
63C ARG* 1.3 77.4 - - - +
65C ILE* 1.3 66.4 + - + +
67C ALA* 4.3 4.3 - - - -
68C ARG* 3.4 37.5 + - - +
69C GLN* 3.5 12.2 + - - +
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Residues in contact with ILE 65 (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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20A LEU* 4.6 29.6 - - + -
23A GLN* 5.4 3.4 - - - +
61C GLU* 3.1 31.0 - - + +
62C ASN* 3.0 12.6 + - - +
64C GLN* 1.3 85.1 - - + +
66C LEU* 1.3 65.8 + - + +
67C ALA 3.0 4.5 - - - -
69C GLN* 3.3 23.3 - - + +
70C LYS* 2.5 37.6 + - + +
45D ARG* 6.6 0.2 - - + -
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Residues in contact with LEU 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C ASN* 2.7 43.6 + - + +
63C ARG* 3.8 20.0 - - - +
65C ILE* 1.3 84.2 - - + +
67C ALA* 1.3 58.3 + - - +
70C LYS* 3.0 36.7 - - + +
71C SER* 4.8 0.9 + - - -
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Residues in contact with ALA 67 (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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63C ARG* 2.5 23.0 + - + +
64C GLN* 3.6 6.5 - - - +
65C ILE 3.0 0.6 - - - -
66C LEU* 1.3 74.3 - - - +
68C ARG* 1.3 58.1 + - + +
69C GLN 3.1 1.6 - - - -
70C LYS 2.7 24.3 + - - -
71C SER* 2.8 24.1 + - - -
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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
------------------------------------------------------------
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