Contacts of the helix formed by residues 56 - 67 (chain A) 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 GLN 56 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A GLU* 1.3 67.4 + - - +
58A SER* 3.3 9.1 + - - +
59A LEU* 3.4 17.0 + - - +
60A SER* 3.4 19.2 + - - -
260A PHE* 4.8 11.2 - - + -
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Residues in contact with GLU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A GLN* 1.3 79.5 - - - +
58A SER* 1.3 58.9 + - - +
60A SER* 2.8 20.7 + - - +
61A SER* 2.9 18.2 + - - -
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Residues in contact with SER 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A GLN 4.3 6.2 + - - +
57A GLU* 1.3 79.6 - - - +
59A LEU* 1.3 59.5 + - - +
61A SER* 2.4 25.3 + - - -
62A TRP* 2.9 16.5 + - - +
161A HIS* 5.5 8.4 + - - -
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Residues in contact with LEU 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A GLN* 3.4 16.4 + - - +
57A GLU 3.2 0.4 - - - -
58A SER* 1.3 83.4 + - - +
60A SER* 1.3 61.9 + - - +
62A TRP* 4.4 4.7 - - - -
63A ILE* 3.0 59.0 + - + +
127A PHE* 4.6 4.9 - - + -
128A GLY* 5.7 2.9 - - - -
141A LYS* 5.9 2.2 - - + +
157A LEU* 5.3 0.2 - - + -
161A HIS* 3.7 41.7 - - + +
162A TRP* 4.2 18.4 - - + +
260A PHE* 4.5 16.4 - - + -
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Residues in contact with SER 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A GLN 3.4 2.5 + - - -
57A GLU* 2.8 27.4 + - - +
59A LEU* 1.3 76.2 - - - +
61A SER* 1.3 62.8 + - - +
64A PRO* 3.3 18.5 - - - +
127A PHE* 3.9 21.4 - - - -
257A THR* 4.9 8.1 - - - -
260A PHE* 3.7 28.6 - - - -
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Residues in contact with SER 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A GLU 2.9 12.9 + - - -
58A SER* 2.4 32.8 + - - -
60A SER* 1.3 77.7 + - - +
62A TRP* 1.3 65.7 + - - +
64A PRO* 3.3 9.8 - - - +
65A GLU* 2.9 32.2 + - - +
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Residues in contact with TRP 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A SER 2.9 14.6 + - - +
59A LEU 3.1 3.1 + - - +
61A SER* 1.3 82.1 + - - +
63A ILE* 1.3 70.5 + - + +
65A GLU* 3.3 9.9 + - - -
66A ASN* 2.3 74.2 + - + +
67A ILE* 4.5 10.8 - - + -
153A VAL* 4.4 18.8 - - + -
156A HIS* 3.5 33.7 - + - -
157A LEU* 4.3 16.8 - - + -
161A HIS* 3.2 39.4 + + + +
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Residues in contact with ILE 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A LEU* 3.0 46.4 + - + +
62A TRP* 1.3 91.3 - - + +
64A PRO* 1.3 66.6 - - + +
65A GLU 3.2 0.5 + - - -
66A ASN 3.3 1.2 + - - -
67A ILE* 3.3 38.9 + - + +
124A THR* 5.4 4.5 - - - -
127A PHE* 3.6 42.2 - - + -
128A GLY 5.5 0.7 - - - +
142A TYR 6.1 0.2 - - - +
143A VAL* 4.4 10.8 - - + -
157A LEU* 4.4 18.4 - - + -
161A HIS* 5.1 0.4 - - + -
162A TRP* 5.3 4.9 - - + +
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Residues in contact with PRO 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A SER 3.3 20.9 - - - +
61A SER 3.3 9.4 - - - +
63A ILE* 1.3 94.0 - - + +
65A GLU* 1.3 62.6 + - + +
66A ASN 3.2 0.4 - - - -
67A ILE 4.0 9.9 - - - +
68A LYS* 4.8 3.3 + - - -
123A PRO* 3.8 22.5 - - + +
124A THR* 3.9 25.4 - - - +
127A PHE* 4.3 10.8 - - + -
257A THR* 6.3 1.3 - - - -
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Residues in contact with GLU 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A SER* 2.9 34.0 + - - +
62A TRP* 3.3 12.6 + - - +
63A ILE 3.2 1.4 - - - -
64A PRO* 1.3 80.7 - - + +
66A ASN* 1.3 66.4 + - - +
68A LYS* 5.7 3.6 + - - +
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Residues in contact with ASN 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A TRP* 2.3 84.7 + - + +
63A ILE 3.3 0.8 + - - -
65A GLU* 1.3 90.2 + - - +
67A ILE* 1.3 63.9 + - + +
68A LYS* 4.2 10.9 + - - +
149A THR* 6.0 0.2 - - - +
153A VAL* 4.8 11.0 - - + +
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Residues in contact with ILE 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A TRP* 4.5 10.5 - - + -
63A ILE* 3.3 28.7 + - + +
64A PRO 4.0 7.4 - - - +
66A ASN* 1.3 85.4 - - + +
68A LYS* 1.3 77.1 + - - +
123A PRO* 4.1 0.3 - - - +
124A THR* 3.0 28.1 + - + +
143A VAL* 4.7 7.6 - - + -
144A ARG 4.3 2.7 - - - +
145A VAL* 4.0 30.1 - - + -
149A THR* 4.4 11.9 - - + -
153A VAL* 4.3 15.9 - - + -
154A ILE* 6.4 2.2 - - + -
157A LEU* 4.3 23.6 - - + -
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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