Contacts of the helix formed by residues 61 - 70 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60D ALA* 1.3 88.3 - - + +
62D ALA* 1.3 67.8 + - - +
63D HIS* 2.8 29.5 + - + +
64D ALA* 3.0 21.3 + - + +
65D ILE* 3.6 6.8 + - - +
152D GLU* 3.3 24.9 - - + +
164D VAL* 4.1 16.4 - - + -
166D SER* 3.2 5.2 - - - +
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Residues in contact with ALA 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D PRO* 1.3 69.9 - - - +
63D HIS* 1.3 58.1 + - - +
65D ILE* 3.0 5.0 + - - +
66D TRP* 2.8 28.8 + - - +
128D ARG* 3.3 29.6 - - - +
150D VAL* 3.6 19.3 - - + +
152D GLU* 2.8 33.4 + - + +
166D SER* 2.7 12.3 + - - -
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Residues in contact with HIS 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D PRO* 2.8 31.5 + - + +
62D ALA* 1.3 75.9 - - - +
64D ALA* 1.3 68.0 + - + +
66D TRP* 3.8 5.7 + - - +
67D ARG* 3.2 29.6 + - + +
128D ARG* 3.9 21.3 - - - +
152D GLU* 4.0 4.0 + - - +
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Residues in contact with ALA 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D ALA* 5.1 0.4 - - + -
61D PRO* 3.0 21.6 + - + +
63D HIS* 1.3 90.7 - - + +
65D ILE* 1.3 60.2 + - - +
67D ARG* 3.6 12.4 - - - +
68D PHE* 3.2 27.3 - - + -
204D SER* 4.0 15.5 - - - +
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Residues in contact with ILE 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D VAL* 3.7 26.0 - - + -
60D ALA* 3.8 9.4 - - + +
61D PRO 3.9 5.6 - - - +
62D ALA 3.0 4.2 + - - +
64D ALA* 1.3 75.2 - - - +
66D TRP* 1.3 66.0 + - - +
67D ARG 3.1 1.3 - - - -
68D PHE* 2.9 17.2 + - - +
69D VAL* 3.2 12.3 + - + +
150D VAL* 3.9 21.8 - - + -
166D SER* 3.4 36.1 - - - +
168D VAL* 4.1 11.2 - - + -
200D LEU* 4.1 22.2 - - + -
204D SER* 3.5 21.5 - - - +
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Residues in contact with TRP 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D ALA 2.8 15.5 + - - +
63D HIS* 3.9 6.7 - - - +
65D ILE* 1.3 74.1 - - - +
67D ARG* 1.3 68.8 + - + +
68D PHE 2.9 1.2 + - - -
69D VAL* 3.8 27.4 - - + -
70D ARG* 2.9 58.2 + - + +
123D LEU* 4.1 11.4 - - + -
124D ASP 3.7 18.6 - - - -
125D GLU* 3.1 29.9 + - - +
128D ARG* 3.2 53.8 - - + +
129D ILE* 3.4 31.6 - - - -
130D LEU* 3.8 7.4 - - + -
148D THR 5.3 0.2 - - - -
150D VAL* 4.0 8.0 - - + +
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Residues in contact with ARG 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D HIS* 3.2 20.2 + - + +
64D ALA* 3.6 16.4 - - - +
65D ILE 3.1 0.6 - - - -
66D TRP* 1.3 79.0 - - - +
68D PHE* 1.3 69.3 + - + +
70D ARG* 3.4 21.2 + - - +
71D ASP* 3.6 11.8 - - - +
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Residues in contact with PHE 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C GLY* 6.4 2.9 - - - -
64D ALA* 3.2 27.4 - - + -
65D ILE 2.9 6.1 + - - +
66D TRP 2.9 1.0 + - - -
67D ARG* 1.3 82.2 - - + +
69D VAL* 1.3 68.5 + - - +
70D ARG 3.2 1.1 - - - -
71D ASP* 2.9 24.6 + - + +
74D ASN 5.3 0.9 - - - +
77D LYS* 4.0 27.3 - - + +
78D TYR* 4.1 14.0 - - + -
200D LEU* 3.6 14.4 - - + -
203D ILE* 3.3 43.7 - - + -
204D SER* 3.6 25.6 - - - -
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Residues in contact with VAL 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D ILE* 3.5 27.4 - - + +
66D TRP* 3.2 25.2 + - + +
68D PHE* 1.3 77.4 - - - +
70D ARG* 1.3 61.4 + - - +
71D ASP 3.3 1.0 + - - -
72D PHE* 4.4 3.5 + - - -
78D TYR* 4.2 20.6 + - - +
130D LEU* 3.2 29.3 - - + +
148D THR* 3.7 30.7 - - + -
150D VAL* 4.2 11.2 - - + -
168D VAL* 5.9 1.3 - - + -
200D LEU* 4.3 10.5 - - + -
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Residues in contact with ARG 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D TRP* 2.9 51.5 + - + +
67D ARG* 3.4 15.4 + - - +
69D VAL* 1.3 73.9 - - - +
71D ASP* 1.3 54.0 + - - +
72D PHE* 2.5 26.7 + - - +
97D ILE* 4.5 9.9 - - - +
123D LEU* 4.2 11.8 - - + +
125D GLU* 2.6 40.1 + - - -
130D LEU* 3.8 11.5 - - - +
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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