Contacts of the helix formed by residues 65 - 75 (chain p) in PDB entry 6FF7
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 65 (chain p).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60p VAL* 3.7 3.9 - - + +
64p GLY* 1.3 65.9 - - - +
66p GLU* 1.3 62.5 + - - +
67p PHE 3.0 3.1 - - - -
68p GLU* 3.0 28.5 + - + +
69p ALA* 3.5 6.6 + - - +
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Residues in contact with GLU 66 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63p ASN 5.0 6.3 - - - +
64p GLY* 3.0 4.3 + - - +
65p PRO* 1.3 77.5 - - - +
67p PHE* 1.3 59.7 + - - +
69p ALA* 3.6 8.4 + - - +
70p ARG* 3.3 19.1 + - - +
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Residues in contact with PHE 67 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59p PHE* 5.0 1.8 - - + +
60p VAL* 4.3 15.7 - - + +
63p ASN* 4.6 14.5 + - + -
64p GLY 3.1 13.6 + - - +
65p PRO 3.0 0.4 - - - -
66p GLU* 1.3 76.1 - - - +
68p GLU* 1.3 59.3 + - - +
69p ALA 3.2 1.6 - - - -
70p ARG* 3.6 7.4 - - + +
71p ILE* 2.9 34.3 + - + +
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Residues in contact with GLU 68 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60p VAL* 4.4 13.0 - - + +
64p GLY 4.2 1.0 + - - -
65p PRO* 3.0 21.7 + - + +
67p PHE* 1.3 77.8 - - - +
69p ALA* 1.3 57.2 + - - +
71p ILE* 4.1 3.4 - - - +
72p ARG* 2.9 33.3 + - - +
84p LEU* 5.1 3.1 - - + +
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Residues in contact with ALA 69 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65p PRO 3.5 5.7 + - - +
66p GLU* 3.7 11.2 - - - +
67p PHE 3.2 0.2 - - - -
68p GLU* 1.3 77.4 - - - +
70p ARG* 1.3 58.3 + - - +
72p ARG* 3.3 5.1 + - - +
73p GLN* 2.9 34.2 + - - +
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Residues in contact with ARG 70 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66p GLU 3.3 10.9 + - - +
67p PHE* 3.3 11.8 + - - +
69p ALA* 1.3 78.6 - - - +
71p ILE* 1.3 52.8 + - - +
73p GLN* 3.6 3.2 - - - +
74p ASN* 2.7 39.0 + - - +
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Residues in contact with ILE 71 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56p THR* 6.4 1.8 - - - -
67p PHE* 2.9 21.5 + - + +
68p GLU* 4.1 3.6 - - - +
70p ARG* 1.3 71.0 - - - +
72p ARG* 1.3 62.6 + - - +
74p ASN* 3.6 6.7 - - - +
75p GLU* 3.1 28.4 + - - +
81p PHE* 4.9 3.6 - - + +
84p LEU* 5.8 0.2 - - - -
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Residues in contact with ARG 72 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68p GLU 2.9 22.1 + - - +
69p ALA* 3.7 5.2 - - - +
71p ILE* 1.3 75.6 - - - +
73p GLN* 1.3 56.7 + - - +
75p GLU 3.6 1.1 - - - -
76p ILE* 2.9 32.2 + - - +
81p PHE* 5.6 3.8 - - - +
84p LEU* 4.1 28.4 - - + +
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Residues in contact with GLN 73 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69p ALA 2.9 20.0 + - - +
70p ARG* 3.9 2.7 - - - +
72p ARG* 1.3 71.9 - - - +
74p ASN* 1.3 60.7 + - - +
75p GLU 3.3 0.4 + - - -
76p ILE* 4.0 14.5 + - - +
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Residues in contact with ASN 74 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70p ARG 2.7 23.8 + - - +
71p ILE* 3.2 8.3 + - - +
73p GLN* 1.3 72.3 - - - +
75p GLU* 1.3 58.9 + - + +
76p ILE 3.7 0.2 - - - -
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Residues in contact with GLU 75 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71p ILE 3.1 10.8 + - - +
72p ARG 3.6 2.5 - - - -
74p ASN* 1.3 79.9 - - + +
76p ILE* 1.3 62.7 + - - +
77p ASN 3.2 3.4 - - - -
78p ASN* 2.9 35.9 + - + +
80p LYS* 6.4 0.2 - - + -
81p PHE* 3.6 27.9 - - + +
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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