Contacts of the helix formed by residues 61 - 70 (chain C) in PDB entry 4JDA
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 PRO 61 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C ALA* 1.3 89.2 - - + +
62C ALA* 1.3 67.4 + - - +
63C HIS* 3.4 34.5 - - + +
64C ALA* 2.9 26.4 + - + +
65C ILE* 3.5 4.0 + - - +
152C GLU* 3.6 13.2 - - - +
164C VAL* 4.5 15.6 - - + +
166C SER* 4.2 0.2 - - - +
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Residues in contact with ALA 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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61C PRO* 1.3 70.3 - - - +
63C HIS* 1.3 62.4 + - - +
65C ILE* 3.1 4.8 + - - +
66C TRP* 2.9 24.8 + - - +
128C ARG* 3.6 26.2 - - - +
150C VAL* 3.7 20.8 - - + +
151C ASN 4.8 0.2 - - - -
152C GLU* 3.3 28.3 + - + +
166C SER* 3.0 20.8 + - - +
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Residues in contact with HIS 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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61C PRO* 2.9 35.8 + - + +
62C ALA* 1.3 79.2 - - - +
64C ALA* 1.3 66.8 + - - +
66C TRP* 3.4 4.4 + - - +
67C ARG* 3.2 30.6 + - + +
128C ARG* 3.5 25.9 - - - +
152C GLU* 4.8 2.6 + - - -
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Residues in contact with ALA 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C ALA* 4.7 1.1 - - + -
61C PRO* 2.9 27.1 + - + +
63C HIS* 1.3 89.6 - - - +
65C ILE* 1.3 58.9 + - - +
67C ARG* 3.7 11.6 - - - +
68C PHE* 3.4 24.3 - - - -
204C SER* 3.8 21.5 - - - +
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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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58C VAL* 3.7 29.2 - - + -
60C ALA* 3.9 6.5 - - + +
61C PRO 4.1 5.6 - - - +
62C ALA 3.1 5.9 + - - +
64C ALA* 1.3 74.8 - - - +
66C TRP* 1.3 66.6 + - - +
68C PHE* 3.1 9.0 + - - +
69C VAL* 3.0 23.9 + - + +
150C VAL* 3.9 9.2 - - + -
166C SER* 3.7 30.5 - - - +
168C VAL* 3.9 12.1 - - + -
200C LEU* 3.6 30.3 - - + -
204C SER* 3.4 25.4 - - - +
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Residues in contact with TRP 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 ALA 2.9 16.6 + - - +
63C HIS* 3.7 5.4 - - - +
65C ILE* 1.3 72.6 - - - +
67C ARG* 1.3 67.5 + - - +
68C PHE 2.8 4.0 + - - -
69C VAL* 2.8 43.4 + - + +
70C ARG* 2.9 42.0 + - + +
123C LEU* 3.8 15.9 - - + -
124C ASP 3.7 14.1 - - - -
125C GLU* 3.1 30.8 + - - +
128C ARG* 3.5 52.9 - - + +
129C ILE 3.2 27.1 - - - -
130C LEU* 3.9 7.4 - - + -
148C THR 5.1 0.2 - - - -
150C VAL* 4.0 5.8 - - + +
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Residues in contact with ARG 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 HIS* 3.2 19.6 + - + +
64C ALA* 3.7 13.7 - - - +
65C ILE 3.3 0.2 - - - -
66C TRP* 1.3 78.2 - - + +
68C PHE* 1.3 65.5 + - + +
70C ARG* 3.7 16.4 + - - +
71C ASP* 3.7 14.7 - - - +
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Residues in contact with PHE 68 (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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64C ALA 3.4 25.6 - - - -
65C ILE 3.1 5.2 + - - +
66C TRP 2.8 0.8 + - - -
67C ARG* 1.3 82.0 - - + +
69C VAL* 1.3 68.0 + - - +
70C ARG 3.3 0.2 - - - -
71C ASP* 3.1 21.7 + - + +
74C ASN 5.2 1.0 - - - +
77C LYS* 4.4 29.1 - - + +
78C TYR* 3.8 16.2 - + + -
200C LEU* 3.7 12.3 - - + -
203C ILE* 3.7 53.8 - - + -
204C SER* 4.0 9.4 - - - -
110D GLY* 5.9 5.6 - - - -
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Residues in contact with VAL 69 (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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65C ILE* 3.0 32.2 + - + +
66C TRP* 2.8 35.2 + - + +
68C PHE* 1.3 73.7 - - - +
70C ARG* 1.3 60.3 + - - +
71C ASP* 3.2 3.1 + - - +
72C PHE* 4.8 1.6 + - - -
78C TYR* 4.3 20.9 + - - +
130C LEU* 4.1 22.7 - - + +
148C THR* 4.2 22.4 - - + +
150C VAL* 4.0 10.5 - - + -
200C LEU* 3.9 16.6 - - + -
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Residues in contact with ARG 70 (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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66C TRP* 2.9 55.3 + - + +
67C ARG* 3.7 13.5 - - - +
69C VAL* 1.3 75.8 - - - +
71C ASP* 1.3 57.5 + - - +
72C PHE* 2.6 24.9 + - - +
97C ILE* 4.6 6.6 - - - +
120C LEU* 5.8 0.3 - - - +
123C LEU* 4.1 19.1 - - + +
125C GLU* 2.9 36.7 + - - -
130C LEU* 4.9 4.9 - - - +
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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