Contacts of the helix formed by residues 56 - 66 (chain G) in PDB entry 5YWB
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 56 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54G ARG 2.6 11.1 + - - -
55G PHE* 1.3 72.3 - - - +
57G GLN* 1.3 58.3 + - - -
58G ASP 3.6 0.4 - - - -
59G VAL* 3.1 24.5 - - + +
60G PHE* 2.9 25.5 + - - +
132H PHE* 5.6 2.2 - - - -
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Residues in contact with GLN 57 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A TRP* 6.4 1.8 - - + -
174A ALA* 6.3 3.1 - - + -
176A ARG* 3.7 28.5 - - + +
55G PHE 3.0 8.0 + - - +
56G LEU* 1.3 74.3 - - - +
58G ASP* 1.3 62.0 + - - +
59G VAL 3.1 1.3 - - - -
60G PHE* 2.9 23.8 + - - +
61G THR* 3.0 16.9 + - - +
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Residues in contact with ASP 58 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A ARG* 4.9 5.1 - - + +
177A ARG* 4.3 22.7 - - - +
206A ARG* 4.6 7.2 - - - +
54G ARG* 3.3 33.8 - - + +
57G GLN* 1.3 77.6 - - - +
59G VAL* 1.3 56.3 + - - +
61G THR* 3.1 11.9 + - - +
62G THR* 2.7 34.5 + - - +
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Residues in contact with VAL 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54G ARG* 3.4 25.8 - - + +
56G LEU* 3.1 24.7 - - + +
57G GLN 3.1 0.6 - - - -
58G ASP* 1.3 74.4 - - - +
60G PHE* 1.3 63.4 + - - +
61G THR 3.1 1.3 - - - -
62G THR* 3.9 7.0 - - - -
63G LEU* 2.9 30.8 + - - +
49H ILE* 4.6 26.9 - - + +
132H PHE* 5.7 6.5 - - + -
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Residues in contact with PHE 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A THR* 5.7 4.7 - - - +
56G LEU 2.9 15.1 + - - +
57G GLN* 2.9 14.6 + - - +
59G VAL* 1.3 77.6 - - - +
61G THR* 1.3 59.2 + - + +
63G LEU* 3.2 32.2 - - + +
64G VAL* 3.6 9.2 - - - +
162G ILE* 5.8 7.2 - - + -
166G CYS* 5.7 0.2 - - - +
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Residues in contact with THR 61 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A THR 5.0 7.0 - - - +
172A ALA 5.6 2.0 - - - +
173A GLN 5.0 6.1 - - - +
174A ALA* 4.9 17.9 - - + -
177A ARG* 5.0 9.3 + - + +
293A THR* 5.8 5.6 - - - -
57G GLN 3.0 10.4 + - - +
58G ASP* 3.1 21.0 + - - +
60G PHE* 1.3 79.5 - - + +
62G THR* 1.3 64.3 + - - +
63G LEU 3.1 1.8 - - - -
64G VAL* 3.1 19.0 + - - +
65G ASP* 3.1 11.8 + - - +
169G MET* 5.6 9.0 - - - -
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Residues in contact with THR 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58G ASP* 2.7 29.8 + - - +
59G VAL* 3.3 8.2 + - - -
61G THR* 1.3 73.2 + - - +
63G LEU* 1.3 61.7 + - - +
65G ASP* 3.3 25.3 + - + +
66G LEU* 3.5 17.9 + - + +
49H ILE* 5.1 13.2 - - + +
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Residues in contact with LEU 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59G VAL* 2.9 13.0 + - + +
60G PHE* 3.2 29.6 - - + +
61G THR 3.1 0.2 - - - -
62G THR* 1.3 76.9 - - - +
64G VAL* 1.3 68.2 + - + +
66G LEU* 3.2 27.8 + - + +
71G THR* 3.8 8.4 + - - +
74G ILE* 4.8 12.4 - - + +
75G PHE* 3.5 37.0 - - + -
162G ILE* 5.7 8.3 - - + -
166G CYS* 4.6 11.2 - - + -
49H ILE* 4.9 18.5 - - + +
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Residues in contact with VAL 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60G PHE 3.6 16.6 - - - +
61G THR* 3.1 12.0 + - - +
63G LEU* 1.3 84.6 - - + +
65G ASP* 1.3 62.5 + - - +
66G LEU 3.4 8.5 + - - +
71G THR* 5.0 3.9 + - - -
75G PHE* 6.2 0.9 - - + -
166G CYS* 4.2 24.0 - - + +
169G MET* 4.6 18.4 - - + -
170G LYS* 3.3 42.5 - - + +
173G GLN* 4.3 15.0 + - - +
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Residues in contact with ASP 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61G THR 3.1 10.2 + - - +
62G THR* 3.3 20.5 - - + +
63G LEU 3.2 0.2 - - - -
64G VAL* 1.3 76.0 - - - +
66G LEU* 1.3 68.3 + - + +
67G LYS* 3.6 2.3 + - - +
173G GLN* 5.8 2.0 - - - +
175G HIS* 5.4 6.8 + - - -
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Residues in contact with LEU 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62G THR* 3.6 20.9 - - + +
63G LEU* 3.2 17.6 + - + +
64G VAL 3.5 8.7 - - - +
65G ASP* 1.3 82.6 - - + +
67G LYS* 1.3 66.2 + - - +
68G TRP 3.6 1.0 + - - -
70G HIS* 4.2 23.3 - - + +
71G THR* 4.0 12.2 - - - +
74G ILE* 5.6 9.2 - - + -
48H PHE 4.8 7.0 - - - +
49H ILE* 4.9 13.7 - - + +
52H GLY* 3.9 38.6 - - - +
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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