Contacts of the helix formed by residues 54 - 66 (chain C) in PDB entry 5UHF
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 LEU 54 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52C GLY 3.3 1.0 - - - -
53C LEU* 1.3 75.1 - - - +
55C ASP* 1.3 56.8 + - - +
56C VAL* 3.2 3.4 - - - -
57C GLN* 3.1 13.2 + - + +
58C THR* 2.6 39.4 + - - +
162C GLU 4.4 7.9 - - - +
163C LYS* 3.9 27.8 - - - +
164C GLY* 5.3 2.2 - - - -
449C LEU* 3.6 24.5 - - + -
452C LYS* 3.6 33.7 - - + +
453C ARG* 5.5 1.6 - - + -
637C ASP* 3.2 27.5 + - + +
638C ALA 5.0 1.8 - - - +
639C GLY* 5.3 1.6 - - - +
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Residues in contact with ASP 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 PRO* 5.9 0.3 - - - +
52C GLY* 3.1 36.7 + - - +
53C LEU 3.1 2.2 - - - -
54C LEU* 1.3 76.8 + - - +
56C VAL* 1.3 64.4 + - + +
57C GLN 3.1 0.2 - - - -
58C THR* 3.7 9.1 + - - -
59C ASP* 3.2 48.2 + - - +
60C SER 4.1 0.5 + - - -
505C ARG* 6.3 2.7 - - + -
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Residues in contact with VAL 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C GLY 5.6 0.4 - - - +
53C LEU 3.9 14.6 - - - +
54C LEU* 3.2 0.6 - - - -
55C ASP* 1.3 77.6 - - + +
57C GLN* 1.3 62.0 + - + +
60C SER* 3.3 21.3 - - - -
177C SER* 4.1 19.0 + - - +
378C LEU* 5.0 2.9 - - + -
380C THR* 4.0 8.4 - - + +
381C VAL* 4.7 2.4 - - - +
452C LYS 5.3 6.5 - - - +
453C ARG* 4.3 11.4 - - + +
455C LEU* 5.7 2.5 - - + -
500C LEU* 3.6 33.2 - - + -
504C ALA 5.1 3.6 - - - +
505C ARG* 5.5 2.9 - - - -
506C VAL* 3.7 28.7 - - + +
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Residues in contact with GLN 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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54C LEU* 3.1 12.2 + - + +
56C VAL* 1.3 81.5 - - + +
58C THR* 1.3 66.1 + - - +
60C SER* 3.6 2.3 - - - -
61C PHE 3.3 14.6 + - - -
160C MET* 3.4 33.6 - - + +
164C GLY* 3.6 19.0 - - - +
166C PHE* 5.2 0.3 - - - -
174C VAL* 4.4 2.3 - - - +
175C VAL 2.6 30.9 + - - +
176C VAL* 4.7 0.8 - - - +
177C SER* 4.7 4.4 + - - -
381C VAL* 3.2 23.9 - - - +
452C LYS* 3.1 47.2 + - + +
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Residues in contact with THR 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C LEU* 2.6 32.2 + - - +
55C ASP* 3.6 6.0 + - - -
57C GLN* 1.3 73.2 - - - +
59C ASP* 1.3 75.7 + - - +
61C PHE* 3.1 15.4 + - - +
62C GLU* 3.1 34.7 + - + +
69C ARG* 5.3 5.6 - - - +
160C MET* 4.4 9.8 - - - +
161C THR 6.2 0.2 - - - +
162C GLU 5.5 4.2 + - - +
164C GLY* 5.5 3.1 - - - -
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Residues in contact with ASP 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 ASP* 3.2 36.3 + - - +
58C THR* 1.3 86.3 - - - +
60C SER* 1.3 62.2 + - - +
62C GLU* 3.3 14.8 + - - +
63C TRP* 3.1 23.2 + - - +
70C TRP* 4.6 4.0 - - + -
73C SER* 5.2 5.1 + - - -
77C ARG* 4.3 17.5 + - - +
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Residues in contact with SER 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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55C ASP 4.1 1.8 + - - -
56C VAL 3.3 23.1 - - - -
57C GLN 3.6 5.6 - - - -
58C THR 3.1 0.2 + - - -
59C ASP* 1.3 78.0 - - - +
61C PHE* 1.3 61.5 + - - +
63C TRP* 3.3 23.6 + - - +
64C LEU 3.4 7.6 + - - -
380C THR* 3.4 14.7 + - - -
381C VAL* 3.3 9.4 + - - +
382C GLY* 2.6 36.8 + - - -
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Residues in contact with PHE 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C GLN 3.3 12.0 + - - +
58C THR 3.1 4.9 + - - +
60C SER* 1.3 77.7 - - - +
62C GLU* 1.3 65.3 + - + +
64C LEU* 3.3 41.2 - - + +
65C ILE* 3.3 32.7 - - + +
157C PHE* 4.1 10.5 - + - -
158C PRO 3.6 15.9 - - - -
159C MET* 3.7 12.3 - - + -
160C MET* 3.3 50.7 - - + -
166C PHE* 3.8 23.1 - + - -
381C VAL* 5.1 3.1 - - + +
382C GLY* 5.0 3.4 - - - +
385C ILE* 4.5 6.7 - - + -
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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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58C THR* 3.1 34.5 + - + +
59C ASP* 3.6 16.9 - - - +
60C SER 3.2 0.4 - - - -
61C PHE* 1.3 78.0 - - + +
63C TRP* 1.3 60.1 + - - +
64C LEU 3.1 0.2 - - - -
65C ILE* 3.3 10.9 - - + +
66C GLY* 2.9 27.4 + - - -
67C SER* 2.6 36.4 + - - +
69C ARG* 3.2 48.3 + - - +
70C TRP* 3.7 12.3 + - + +
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Residues in contact with TRP 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 ASP 3.1 11.1 + - - +
60C SER* 3.5 15.7 - - - +
62C GLU* 1.3 76.3 - - - +
64C LEU* 1.3 72.0 + - - +
66C GLY* 3.7 2.1 + - - -
70C TRP* 3.4 42.4 - + + +
83C VAL 3.7 13.9 + - - -
84C GLY* 3.5 6.5 - - - -
85C GLY* 2.9 34.1 + - - -
88C GLU* 3.6 18.4 - - - -
382C GLY* 3.7 31.0 - - - -
383C GLU* 3.9 5.2 - - + -
386C GLN* 3.2 29.8 - - + -
508C PRO* 6.6 0.9 - - + -
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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 SER 3.4 5.8 + - - +
61C PHE* 3.3 41.9 + - + +
62C GLU 3.1 0.4 - - - -
63C TRP* 1.3 88.0 - - + +
65C ILE* 1.3 61.6 + - - +
84C GLY 4.3 0.3 - - - -
85C GLY* 3.4 8.5 + - - +
86C LEU* 3.1 49.4 + - + +
157C PHE* 3.8 13.9 - - + -
382C GLY* 3.6 23.1 - - - +
385C ILE* 3.8 25.6 - - + -
386C GLN* 4.3 18.2 - - + +
389C ILE* 4.8 0.4 - - + -
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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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61C PHE* 3.3 43.3 - - + +
62C GLU* 3.3 18.8 - - + +
64C LEU* 1.3 77.9 - - + +
66C GLY* 1.3 61.1 + - - +
67C SER* 3.6 24.2 - - - +
84C GLY* 5.5 0.7 - - - -
86C LEU* 4.4 5.8 - - + +
87C GLU* 5.6 1.6 - - - +
110C PRO* 5.2 10.4 - - - +
112C PHE* 3.8 42.4 - - + -
157C PHE* 4.5 7.4 - - + -
159C MET* 4.6 14.6 - - + -
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Residues in contact with GLY 66 (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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62C GLU 2.9 8.6 + - - -
63C TRP 3.7 2.8 + - - -
64C LEU 3.3 3.0 + - - -
65C ILE* 1.3 79.8 - - - +
67C SER* 1.3 69.0 + - - +
68C PRO* 4.5 1.0 - - - +
70C TRP* 3.7 22.0 - - - -
71C ARG* 3.1 23.5 + - - -
84C GLY* 4.7 5.4 - - - -
87C GLU* 5.2 2.2 - - - -
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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
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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