Contacts of the helix formed by residues 57 - 67 (chain D) in PDB entry 6PUO
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 GLU 57 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56D GLN* 1.3 78.0 - - - +
58D SER* 1.3 59.0 + - - +
60D SER* 2.8 21.2 + - - +
61D SER* 2.9 18.0 + - - -
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Residues in contact with SER 58 (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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56D GLN* 4.3 6.2 + - - +
57D GLU* 1.3 80.1 - - - +
59D LEU* 1.3 59.9 + - - +
61D SER* 2.4 24.9 + - - -
62D TRP* 2.9 17.3 + - - +
161D HIS* 5.5 7.3 + - - -
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Residues in contact with LEU 59 (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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56D GLN* 3.4 15.8 + - - +
57D GLU 3.2 0.4 - - - -
58D SER* 1.3 84.0 + - - +
60D SER* 1.3 62.0 + - - +
62D TRP* 4.3 4.3 - - - +
63D ILE* 3.0 59.2 + - + +
127D PHE* 4.6 4.3 - - + -
128D GLY* 5.7 4.0 - - - -
141D LYS* 5.9 2.5 - - + +
161D HIS* 3.7 42.6 - - + +
162D TRP* 4.2 18.6 - - + +
260D PHE* 4.5 16.4 - - + -
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Residues in contact with SER 60 (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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56D GLN 3.4 3.0 + - - -
57D GLU* 2.8 27.2 + - - +
59D LEU* 1.3 74.5 - - - +
61D SER* 1.3 62.2 + - - +
64D PRO* 3.3 18.6 - - - +
127D PHE* 3.9 22.2 - - - -
257D THR* 4.9 8.7 - - - -
260D PHE* 3.7 28.5 - - - -
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Residues in contact with SER 61 (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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57D GLU 2.9 12.4 + - - -
58D SER* 2.4 32.4 + - - -
60D SER* 1.3 77.9 + - - +
62D TRP* 1.3 65.3 + - - +
64D PRO* 3.3 9.2 - - - +
65D GLU* 2.9 31.5 + - - +
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Residues in contact with TRP 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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58D SER 2.9 14.8 + - - +
59D LEU 3.1 2.9 + - - +
61D SER* 1.3 81.4 + - - +
63D ILE* 1.3 70.5 + - + +
65D GLU* 3.3 9.8 + - - +
66D ASN* 2.3 73.6 + - + +
67D ILE* 4.5 11.0 - - + -
153D VAL* 4.4 18.8 - - + -
156D HIS* 3.5 32.6 - + + -
157D LEU* 4.3 17.5 - - + -
161D HIS* 3.2 39.1 + + + +
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Residues in contact with ILE 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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59D LEU* 3.0 45.9 + - + +
62D TRP* 1.3 91.6 - - + +
64D PRO* 1.3 67.7 - - + +
65D GLU 3.2 1.0 + - - -
66D ASN 3.3 1.0 + - - -
67D ILE* 3.3 37.1 + - + +
124D THR* 5.4 4.7 - - - -
127D PHE* 3.6 43.3 - - + -
128D GLY* 5.5 0.7 - - - +
142D TYR 6.1 0.2 - - - +
143D VAL* 4.4 10.1 - - + -
157D LEU* 4.4 17.9 - - + -
162D TRP* 5.3 4.9 - - + +
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Residues in contact with PRO 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 SER 3.3 21.5 - - - +
61D SER 3.3 9.4 - - - +
63D ILE* 1.3 93.6 - - + +
65D GLU* 1.3 62.4 + - + +
66D ASN 3.2 0.6 + - - -
67D ILE 4.0 10.0 - - - +
68D LYS* 4.8 3.3 + - - -
123D PRO* 3.8 23.3 - - + +
124D THR* 3.9 24.2 - - - +
127D PHE* 4.3 9.6 - - + -
257D THR* 6.3 1.3 - - - -
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Residues in contact with GLU 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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61D SER* 2.9 33.5 + - - +
62D TRP* 3.3 11.7 + - - +
63D ILE 3.2 1.2 - - - -
64D PRO* 1.3 80.5 - - + +
66D ASN* 1.3 66.1 + - - +
68D LYS* 5.7 3.4 + - - +
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Residues in contact with ASN 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 TRP* 2.3 85.1 + - + +
63D ILE 3.3 1.0 + - - -
64D PRO 3.2 0.2 - - - -
65D GLU* 1.3 90.5 + - - +
67D ILE* 1.3 64.7 + - + +
68D LYS* 4.2 10.5 + - - +
149D THR* 6.0 0.2 - - - +
153D VAL* 4.8 11.3 - - + +
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Residues in contact with ILE 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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62D TRP* 4.5 10.1 - - + -
63D ILE* 3.3 28.7 + - + +
64D PRO 4.0 7.6 - - - +
66D ASN* 1.3 87.1 - - + +
68D LYS* 1.3 75.7 + - - +
123D PRO* 4.1 0.3 - - - +
124D THR* 3.0 26.9 + - - +
143D VAL* 4.7 7.0 - - + -
144D ARG 4.3 2.9 - - - +
145D VAL* 4.0 28.9 - - + -
149D THR* 4.4 11.9 - - + -
153D VAL* 4.3 14.8 - - + -
154D ILE* 6.4 2.2 - - + -
157D LEU* 4.3 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