Contacts of the helix formed by residues 56 - 68 (chain G) in PDB entry 40ER
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 GLN 56 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54G SER 3.7 0.9 + - - +
55G LEU* 1.3 83.8 - - - +
57G VAL* 1.3 64.6 + - - +
58G LYS* 4.3 7.0 - - - +
59G LYS* 3.3 45.4 + - + +
60G ALA* 3.2 21.5 + - - +
110G GLU 3.0 24.9 - - - +
111G GLU* 5.1 5.1 + - - +
112G HIS 3.7 11.9 - - - +
113G LYS* 3.9 20.1 - - + +
114G ILE* 4.4 0.4 - - - -
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Residues in contact with VAL 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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56G GLN* 1.3 70.9 - - - +
58G LYS* 1.3 70.0 + - - +
60G ALA* 3.2 7.5 + - - +
61G PHE* 3.0 45.0 + - + -
86G LEU* 6.2 1.8 - - + -
94G ILE* 4.0 14.6 - - + -
109G LEU* 3.3 26.2 - - + +
112G HIS* 3.4 15.5 + - + +
113G LYS 3.5 25.6 - - - +
114G ILE* 3.5 13.9 - - + +
117G TRP* 4.1 16.8 - - + -
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Residues in contact with LYS 58 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56G GLN* 3.4 6.6 - - - +
57G VAL* 1.3 84.0 - - - +
59G LYS* 1.3 66.2 + - + +
61G PHE* 3.4 8.7 + - - +
62G PHE* 3.1 55.5 + - + -
109G LEU* 4.7 12.3 - - + +
110G GLU* 2.9 58.5 + - - +
112G HIS 4.8 0.2 + - - -
255G TYR* 3.8 6.7 - - + +
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Residues in contact with LYS 59 (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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248B ASP* 4.8 17.3 - - - +
249B SER* 3.3 24.1 + - - +
250B VAL* 4.1 15.1 - - + +
269B TYR* 5.4 2.3 - - + -
55G LEU* 3.9 24.6 - - + +
56G GLN* 3.3 49.9 + - + +
57G VAL 3.3 0.4 - - - -
58G LYS* 1.3 79.5 - - + +
60G ALA* 1.3 64.4 + - - +
62G PHE* 3.5 9.7 + - - +
63G ALA* 3.1 23.0 + - - +
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Residues in contact with ALA 60 (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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51G PHE* 3.3 42.2 - - + -
55G LEU* 4.2 8.5 - - + +
56G GLN 3.2 14.1 + - - +
57G VAL* 3.2 10.2 + - - +
59G LYS* 1.3 78.3 - - - +
61G PHE* 1.3 62.9 + - + +
63G ALA* 3.2 9.6 + - - -
64G LEU* 3.3 9.9 + - - +
86G LEU* 4.3 9.0 - - + -
114G ILE* 4.1 14.4 - - + -
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Residues in contact with PHE 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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57G VAL* 3.0 40.8 + - + +
58G LYS* 3.9 7.6 - - - +
59G LYS 3.3 0.2 - - - -
60G ALA* 1.3 75.2 - - + +
62G PHE* 1.3 66.5 + - + +
64G LEU* 3.3 33.6 + - + +
65G VAL* 3.6 12.0 + - - +
86G LEU* 3.5 31.4 - - + -
87G THR 4.2 2.5 - - - -
90G ASP* 3.9 6.5 - - + -
91G PHE* 3.4 67.1 - + + -
94G ILE* 4.2 10.3 - - + -
109G LEU* 5.5 3.1 - - + -
117G TRP* 6.2 2.5 - + - -
247G ILE* 4.5 4.7 - - + +
250G ALA* 4.6 9.0 - - + +
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Residues in contact with PHE 62 (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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58G LYS* 3.1 55.6 + - + -
59G LYS* 3.9 9.2 - - - +
61G PHE* 1.3 76.6 - - + +
63G ALA* 1.3 62.4 + - - +
65G VAL* 3.1 26.7 - - + +
66G THR* 3.3 14.3 + - + +
250G ALA* 3.2 32.5 - - + -
253G LYS* 3.3 32.3 - - + -
255G TYR* 3.6 28.0 - + - -
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Residues in contact with ALA 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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269B TYR* 3.5 35.7 - - + -
51G PHE* 3.7 15.0 - - + -
59G LYS 3.1 14.3 + - - +
60G ALA 3.5 9.9 - - - +
61G PHE 3.2 0.4 - - - -
62G PHE* 1.3 74.9 - - - +
64G LEU* 1.3 64.2 + - - +
66G THR* 2.9 14.5 + - - -
67G ASN* 2.9 26.1 + - - -
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Residues in contact with LEU 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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51G PHE* 4.1 17.9 - - + -
60G ALA 3.3 12.7 + - - +
61G PHE* 3.4 38.6 - - + +
62G PHE 3.2 1.0 - - - -
63G ALA* 1.3 77.8 - - - +
65G VAL* 1.3 58.7 + - + +
67G ASN 3.4 0.7 + - - -
68G GLY* 2.8 24.8 + - - -
69G VAL* 3.1 48.4 + - + +
70G ARG* 4.1 2.5 - - - -
71G ALA* 4.0 19.3 - - - +
72G ALA* 4.6 1.3 - - + +
86G LEU* 4.9 9.0 - - + +
87G THR 5.0 7.6 - - - +
88G ILE* 5.6 2.0 - - + +
247G ILE* 4.7 12.8 - - + -
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Residues in contact with VAL 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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368A PHE* 3.4 34.4 - - + -
61G PHE 3.6 6.0 + - - +
62G PHE* 3.1 28.7 - - + +
64G LEU* 1.3 75.0 - - - +
66G THR* 1.3 68.4 + - + +
68G GLY* 3.4 4.7 + - - -
247G ILE* 3.6 33.4 - - + +
250G ALA* 4.5 1.1 - - + -
251G ALA* 3.8 39.3 - - + +
253G LYS* 6.4 0.2 - - - -
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Residues in contact with THR 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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398A TRP* 6.1 1.2 - - - -
269B TYR* 4.1 4.7 + - - -
62G PHE* 3.3 15.4 + - + +
63G ALA* 2.9 21.4 + - - -
65G VAL* 1.3 84.9 - - + +
67G ASN* 1.3 65.1 + - - +
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Residues in contact with ASN 67 (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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398A TRP* 4.4 11.8 - - - -
227B PRO* 4.8 3.6 - - - +
267B LEU* 3.5 17.0 - - - +
269B TYR* 3.2 26.0 + - - -
47G LYS* 3.2 35.9 + - - +
49G VAL* 3.6 25.6 - - + +
63G ALA 2.9 22.3 + - - +
66G THR* 1.3 83.9 + - - +
68G GLY* 1.3 55.8 + - - +
69G VAL* 3.1 21.6 + - + +
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Residues in contact with GLY 68 (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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364A GLU* 4.7 8.1 - - - +
368A PHE* 3.9 30.7 - - - -
227B PRO* 4.3 21.1 - - - +
64G LEU 2.8 8.3 + - - -
65G VAL 3.4 5.0 + - - -
67G ASN* 1.3 76.9 - - - +
69G VAL* 1.3 63.3 + - - +
70G ARG* 3.7 1.2 + - - +
244G PHE* 5.0 6.6 - - - -
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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
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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