Contacts of the helix formed by residues 56 - 66 (chain C) in PDB entry 1TW8
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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C LYS* 1.3 69.9 - - - +
57C TYR* 1.3 67.7 + - + +
59C TYR* 3.3 13.1 + - - +
60C LEU* 3.3 21.4 + - - +
88C LEU 4.1 1.0 - - - +
89C LEU* 2.9 58.6 + - - +
91C ARG* 4.6 1.3 - - - +
111C ASP* 3.1 36.0 + - - +
112C THR* 3.3 8.6 + - - -
113C ALA* 3.3 38.4 + - - +
114C ASP 5.1 0.2 - - - +
116C LEU* 3.4 24.3 - - + +
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Residues in contact with TYR 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C LYS* 2.6 59.0 + - + +
56C GLN* 1.3 81.2 - - + +
58C GLU* 1.3 70.0 + - + +
60C LEU* 3.2 19.7 + - - +
61C ASN* 3.2 26.3 + - - -
91C ARG* 3.6 21.5 - - - +
105C PHE* 4.1 10.5 - - + -
106C GLU* 3.8 24.0 - - + +
107C GLU* 3.5 35.0 - - + -
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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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42C TYR* 2.7 28.0 + - - -
53C THR 4.4 2.0 - - - +
54C PHE* 3.4 22.0 - - + -
55C LYS* 3.1 23.1 + - + +
57C TYR* 1.3 94.7 - - + +
59C TYR* 1.3 61.7 + - - +
60C LEU 3.3 0.5 + - - -
61C ASN* 3.4 7.9 + - + +
62C ASP* 3.3 34.2 + - - +
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Residues in contact with TYR 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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54C PHE* 3.5 46.9 - + + +
56C GLN 3.3 13.1 + - - +
58C GLU* 1.3 75.8 - - - +
60C LEU* 1.3 66.1 + - + +
62C ASP* 4.0 6.7 - - + -
63C LEU* 2.9 52.1 + - + +
80C PHE* 6.2 2.2 - + - -
89C LEU* 5.5 9.9 - - + -
116C LEU* 5.1 9.2 - - + -
118C VAL* 4.1 18.2 - - + +
123C TYR* 3.6 41.5 + + - -
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Residues in contact with LEU 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C GLN* 3.3 20.4 + - - +
57C TYR* 3.4 11.2 - - - +
58C GLU 3.1 0.4 - - - -
59C TYR* 1.3 81.8 - - + +
61C ASN* 1.3 65.2 + - - +
63C LEU* 3.2 4.3 + - + +
64C PHE* 3.1 30.9 + - + -
80C PHE* 3.3 37.7 - - + -
89C LEU* 3.8 29.2 - - + +
91C ARG* 4.0 28.0 - - + +
105C PHE* 3.4 26.9 - - + -
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Residues in contact with ASN 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C TYR* 3.2 17.1 + - - +
58C GLU* 3.4 9.4 + - + +
60C LEU* 1.3 77.1 - - - +
62C ASP* 1.3 59.8 + - - +
64C PHE 3.5 0.3 + - - -
65C MET* 2.8 44.4 + - - +
99C TRP* 3.7 11.4 - - - +
104C LEU* 3.7 25.9 - - + +
105C PHE* 3.0 51.3 + - - +
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Residues in contact with ASP 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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54C PHE* 3.5 26.2 - - + -
58C GLU* 3.3 23.0 + - - +
59C TYR* 4.1 7.9 - - + +
61C ASN* 1.3 77.1 - - - +
63C LEU* 1.3 67.6 + - - +
65C MET* 3.6 15.7 - - - +
66C LYS* 2.9 28.2 + - - +
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Residues in contact with LEU 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 TYR* 2.9 45.6 + - + +
60C LEU* 3.2 9.2 + - + +
62C ASP* 1.3 77.9 - - - +
64C PHE* 1.3 70.2 + - + +
66C LYS* 3.8 3.9 + - + +
67C ASN* 3.4 22.7 + - - +
79C LEU* 3.4 47.8 - - + +
80C PHE* 4.9 17.7 - - + +
81C ASN* 5.7 2.9 - - - +
123C TYR* 6.1 0.2 - - - +
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Residues in contact with PHE 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 LEU 3.1 21.4 + - - +
63C LEU* 1.3 77.8 - - + +
65C MET* 1.3 62.2 + - - +
66C LYS 3.1 6.3 + - - -
67C ASN* 3.2 22.8 + - - +
68C PRO* 3.5 3.3 - - - +
70C ILE* 5.3 0.9 - - + -
76C ARG* 3.5 36.8 - - + -
79C LEU* 3.4 31.0 - - + -
80C PHE* 4.0 25.6 - + - -
96C THR* 4.3 12.6 - - + -
99C TRP* 3.4 41.4 - + + -
105C PHE* 3.4 35.2 - + - -
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Residues in contact with MET 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 ASN* 2.8 34.5 + - - +
62C ASP* 3.1 16.8 + - - +
64C PHE* 1.3 74.9 - - - +
66C LYS* 1.3 56.3 - - - +
67C ASN 3.2 2.5 + - - -
68C PRO* 4.0 10.9 - - - +
99C TRP* 3.8 18.8 - - + -
101C ILE* 5.7 10.8 - - + -
104C LEU* 4.7 13.5 - - + -
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Residues in contact with LYS 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 ASP 2.9 15.2 + - - +
63C LEU* 4.1 7.9 - - + +
64C PHE 3.1 1.2 - - - -
65C MET* 1.3 77.7 - - - +
67C ASN* 1.3 70.2 + - - +
68C PRO* 4.0 1.3 - - - -
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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
------------------------------------------------------------
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