Contacts of the helix formed by residues 50 - 64 (chain C) in PDB entry 4D2W
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 ASP 50 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22C PHE* 4.7 17.9 - - + -
49C SER* 1.3 83.1 + - - +
51C LEU* 1.3 60.9 + - - +
52C PRO* 4.1 10.8 - - - +
53C ARG* 3.4 33.5 + - + +
54C ILE* 3.3 27.5 + - - +
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Residues in contact with LEU 51 (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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44C LYS* 3.7 38.8 - - + -
49C SER* 3.8 15.8 - - - +
50C ASP* 1.3 71.8 - - - +
52C PRO* 1.4 66.9 - - + +
54C ILE* 3.3 7.5 + - + +
55C LYS* 2.9 40.5 + - + +
82C ILE* 3.8 21.1 - - + -
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Residues in contact with PRO 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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49C SER 5.5 0.4 - - - +
50C ASP* 3.6 15.7 - - - +
51C LEU* 1.4 91.4 - - + +
53C ARG* 1.4 55.1 + - - +
55C LYS* 3.4 7.1 + - + +
56C THR* 2.9 35.7 + - - +
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Residues in contact with ARG 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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21B GLY* 5.0 10.7 + - - -
46B THR* 4.2 18.7 + - - -
22C PHE* 5.1 13.3 - - - -
50C ASP* 3.4 28.3 + - - +
51C LEU 3.4 0.4 - - - -
52C PRO* 1.4 75.9 - - - +
54C ILE* 1.3 67.8 + - + +
56C THR* 3.4 4.7 + - - -
57C GLU* 3.0 24.6 + - - +
132C ASP* 4.3 10.3 + - - -
150C ASP* 3.4 31.0 + - - -
152C GLY* 3.3 41.3 - - - +
153C LEU* 4.4 22.0 - - + +
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Residues in contact with ILE 54 (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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22C PHE* 3.7 33.0 - - + -
40C LYS* 5.0 7.9 - - - +
42C MET* 3.7 35.2 - - + -
50C ASP 3.3 16.4 + - - +
51C LEU* 3.3 11.6 + - + +
53C ARG* 1.3 87.1 - - + +
55C LYS* 1.3 56.9 + - + +
57C GLU* 3.4 10.5 + - + +
58C ILE* 3.0 50.8 + - + +
82C ILE* 4.2 20.9 - - + -
84C MET* 4.7 0.8 - - - +
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Residues in contact with LYS 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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51C LEU* 2.9 26.7 + - + +
52C PRO* 3.8 6.5 - - + +
54C ILE* 1.3 72.7 - - + +
56C THR* 1.4 57.5 + - - +
58C ILE* 3.9 17.6 - - + +
59C GLU* 2.9 32.1 + - - +
75C VAL* 6.1 2.2 - - - +
77C GLU* 3.5 21.7 + - - -
82C ILE* 4.4 19.5 - - - +
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Residues in contact with THR 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 PRO* 2.9 22.9 + - - +
53C ARG* 3.5 6.2 - - - -
54C ILE 3.4 0.2 - - - -
55C LYS* 1.4 72.7 - - - +
57C GLU* 1.4 64.4 + - - +
59C GLU* 3.7 5.1 - - - +
60C ALA* 3.0 22.9 + - - +
151C PHE 3.7 8.7 - - - +
152C GLY 3.5 18.7 + - - +
153C LEU 4.8 0.2 - - - -
154C CYS* 3.5 28.6 - - - +
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Residues in contact with GLU 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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40C LYS* 2.7 33.0 + - - -
53C ARG 3.0 17.1 + - - +
54C ILE* 3.8 10.1 - - + +
56C THR* 1.4 75.1 - - - +
58C ILE* 1.3 57.1 + - - +
60C ALA* 3.3 2.8 + - - +
61C LEU* 2.9 43.7 + - + +
84C MET* 3.8 22.5 - - + +
86C LEU* 6.0 1.2 - - - +
150C ASP* 3.3 16.7 + - - +
151C PHE* 3.1 36.9 + - + +
152C GLY* 3.9 11.1 - - - +
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Residues in contact with ILE 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 ILE* 3.0 39.8 + - + +
55C LYS* 3.9 19.1 - - + +
57C GLU* 1.3 72.4 - - - +
59C GLU* 1.3 65.6 + - - +
61C LEU* 3.3 1.7 + - - +
62C LYS* 3.0 51.7 + - + +
72C LEU* 4.3 6.0 - - + +
75C VAL* 4.1 21.1 - - + -
82C ILE* 4.0 18.4 - - + -
84C MET* 3.7 26.9 - - + -
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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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55C LYS 2.9 19.0 + - - +
56C THR* 3.7 5.8 - - - +
58C ILE* 1.3 77.9 - - - +
60C ALA* 1.3 61.9 + - - +
62C LYS* 3.6 14.1 + - - +
63C ASN* 2.9 51.1 + - - -
128C TYR* 3.5 11.4 + - - -
156C LYS* 4.6 24.2 + - + +
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Residues in contact with ALA 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 THR 3.0 17.6 + - - +
57C GLU 3.6 4.3 - - - +
59C GLU* 1.3 76.2 - - - +
61C LEU* 1.3 57.1 + - - +
63C ASN* 3.1 5.9 + - - +
64C LEU* 3.0 41.0 + - + +
128C TYR* 4.0 19.5 - - + -
151C PHE* 4.1 10.8 - - + -
154C CYS* 3.6 25.4 - - - -
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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
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57C GLU* 2.9 44.8 + - + +
58C ILE 3.3 0.4 + - - -
60C ALA* 1.3 73.2 - - - +
62C LYS* 1.4 62.0 + - - +
63C ASN 3.2 0.2 - - - -
64C LEU* 3.0 27.2 - - + +
69C ILE* 3.8 23.1 - - + -
70C CYS 4.1 8.3 - - - +
71C GLN* 4.7 2.3 - - - +
72C LEU* 3.8 27.9 + - + +
84C MET* 4.1 6.1 - - + -
86C LEU* 4.1 26.0 - - + -
149C ILE* 6.6 0.2 - - - -
151C PHE* 3.7 28.5 - - + -
310C TYR* 3.9 6.1 + - - -
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Residues in contact with LYS 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 ILE* 3.0 40.5 + - + +
59C GLU* 3.8 12.6 - - - +
60C ALA 3.3 0.2 - - - -
61C LEU* 1.4 76.9 - - - +
63C ASN* 1.3 62.6 + - - +
72C LEU* 4.2 5.6 - - + -
75C VAL* 4.5 8.6 - - - +
279C PHE* 3.3 12.6 - - - -
309C GLN 4.5 7.2 + - - -
310C TYR* 2.7 64.3 + - + -
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Residues in contact with ASN 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* 2.9 46.7 + - - -
60C ALA 3.1 7.2 + - - +
62C LYS* 1.3 79.5 - - - +
64C LEU* 1.3 62.4 + - - +
122C TYR* 3.9 4.5 + - - -
126C GLN* 4.4 12.1 + - - +
128C TYR* 3.6 18.8 + - + +
279C PHE* 3.5 19.8 - - - -
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Residues in contact with LEU 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 ALA* 3.0 27.0 + - + +
61C LEU* 3.0 24.9 + - + +
63C ASN* 1.3 79.2 - - - +
65C ARG* 1.3 63.4 + - - +
66C HIS 4.3 0.2 - - - -
69C ILE* 4.1 15.5 - - + +
71C GLN* 4.6 5.9 + - - +
72C LEU 5.9 0.2 + - - -
122C TYR* 3.7 21.1 - - + -
123C VAL* 4.4 9.2 - - + -
126C GLN* 3.8 26.0 - - + -
128C TYR* 3.9 19.1 - - + -
151C PHE* 3.6 37.9 - - + -
279C PHE* 4.5 0.3 - - - -
310C TYR* 5.2 0.3 + - - -
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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
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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