Contacts of the helix formed by residues 57 - 67 (chain C) in PDB entry 3THT
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 SER 57 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52C LEU* 4.6 6.3 - - - -
55C GLY 3.7 4.5 + - - -
56C VAL* 1.3 79.0 - - - +
58C ARG* 1.3 60.4 + - - +
59C ASN* 3.6 10.0 + - - +
60C GLN* 3.0 41.4 + - - +
61C LEU* 3.1 13.3 + - - +
76C MET* 4.4 2.5 - - - -
108C ASP* 5.7 2.7 - - - -
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Residues in contact with ARG 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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52C LEU* 4.7 3.7 - - + +
57C SER* 1.3 69.2 - - - +
59C ASN* 1.3 70.3 + - - +
60C GLN 3.0 4.9 - - - -
61C LEU* 4.7 0.9 - - - +
62C LEU* 3.0 41.5 + - + +
74C LEU* 2.9 50.8 + - + +
76C MET* 3.8 32.9 - - - +
316D ASP 3.1 18.8 + - - -
317D VAL 3.6 21.2 + - - -
318D GLY* 4.1 5.9 - - - +
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Residues in contact with ASN 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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57C SER* 3.2 9.0 + - - +
58C ARG* 1.3 91.5 - - - +
60C GLN* 1.3 57.1 + - - +
62C LEU* 5.1 0.4 - - - -
63C PRO* 3.0 24.2 - - - +
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Residues in contact with GLN 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 VAL* 4.3 7.6 - - + +
57C SER* 3.1 30.9 + - - +
58C ARG 3.0 0.4 - - - -
59C ASN* 1.3 78.6 - - - +
61C LEU* 1.3 62.7 + - - +
63C PRO* 3.1 14.2 - - - +
64C VAL* 3.7 16.5 - - - +
105C VAL* 3.8 15.2 - - - +
106C VAL* 2.6 53.3 + - - +
107C ASP* 5.6 0.4 - - - -
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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
----------------------------------------------------------
47C VAL* 4.3 15.9 - - + -
50C GLY* 3.5 9.2 - - - +
56C VAL* 4.0 13.2 - - + +
57C SER 3.1 10.7 + - - +
58C ARG* 5.2 0.4 - - - -
60C GLN* 1.3 74.4 - - - +
62C LEU* 1.3 66.9 + - - +
63C PRO 3.2 2.0 - - - -
64C VAL* 3.0 12.1 + - + +
65C LEU* 2.9 47.1 + - + +
74C LEU* 4.2 10.8 - - + -
76C MET* 4.9 2.7 - - + -
83C SER* 3.2 27.4 - - - +
105C VAL* 5.4 3.6 - - + -
115C LEU* 3.5 36.3 - - + -
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Residues in contact with LEU 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 ARG* 3.0 27.3 + - + +
59C ASN* 5.1 0.4 - - - -
61C LEU* 1.3 75.0 - - - +
63C PRO* 1.3 71.3 - - + +
65C LEU* 3.2 4.5 + - + +
66C GLU* 3.0 71.4 + - + +
71C VAL* 4.2 21.5 - - + +
74C LEU* 3.8 25.6 - - + +
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Residues in contact with PRO 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 ASN* 3.0 30.3 - - - +
60C GLN 3.1 11.7 - - - +
62C LEU* 1.3 100.6 - - + +
64C VAL* 1.3 62.5 + - + +
65C LEU 3.3 0.2 + - - -
66C GLU* 3.4 11.6 + - - +
67C LYS* 3.4 18.2 + - - +
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Residues in contact with VAL 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 GLN* 3.7 18.6 - - - +
61C LEU* 3.0 11.8 + - + +
63C PRO* 1.3 77.4 - - + +
65C LEU* 1.3 62.7 + - + +
67C LYS* 3.4 17.2 - - - +
68C CYS 4.4 0.7 + - - -
100C LEU* 3.7 21.9 - - + +
103C LYS* 3.2 46.9 - - + +
105C VAL* 4.5 15.5 - - + -
115C LEU* 5.1 9.4 - - + -
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Residues in contact with LEU 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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47C VAL* 4.6 11.9 - - + -
61C LEU* 2.9 44.5 + - + +
62C LEU* 3.6 7.2 - - + +
63C PRO 3.2 0.2 - - - -
64C VAL* 1.3 74.6 - - + +
66C GLU* 1.3 61.5 + - - +
67C LYS 3.0 4.3 - - - -
68C CYS* 3.0 13.9 + - - +
71C VAL* 3.8 11.9 - - + -
74C LEU* 3.7 28.9 - - + -
85C ALA* 4.2 22.0 - - + -
87C TYR* 2.7 34.4 + - + +
100C LEU* 4.1 15.9 - - + -
115C LEU* 6.1 1.3 - - + -
117C LEU* 4.7 6.5 - - + -
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Residues in contact with GLU 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 LEU* 3.0 45.4 + - + +
63C PRO* 3.4 9.4 + - - +
65C LEU* 1.3 70.2 - - - +
67C LYS* 1.3 57.6 + - - +
68C CYS 2.9 10.1 + - - -
69C GLY* 2.9 27.4 + - - +
71C VAL* 3.6 23.9 + - + +
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Residues in contact with LYS 67 (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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63C PRO 3.4 9.1 + - - +
64C VAL* 3.4 15.5 - - - +
65C LEU 3.0 0.4 - - - -
66C GLU* 1.3 78.5 - - - +
68C CYS* 1.3 65.8 + - - +
95C ARG* 5.3 1.4 - - - -
99C THR* 5.1 6.1 + - - -
100C LEU* 4.4 9.7 - - - +
103C LYS* 3.9 24.7 - - - +
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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