Contacts of the helix formed by residues 78 - 90 (chain A) in PDB entry 6PAX
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 78 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A PRO* 5.3 7.0 - - + -
76A ALA 4.0 0.2 - - - -
77A THR* 1.3 87.5 - - - +
79A GLU* 1.3 56.8 + - - +
81A VAL* 3.2 8.6 + - + +
82A SER* 2.9 32.7 + - - -
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Residues in contact with GLU 79 (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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77A THR* 3.3 6.1 + - - +
78A PRO* 1.3 79.1 - - - +
80A VAL* 1.3 58.0 + - + +
82A SER* 3.3 9.2 + - - -
83A LYS* 2.9 38.3 + - + +
108A VAL* 4.5 20.5 - - + +
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Residues in contact with VAL 80 (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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75A VAL 3.6 21.3 - - - +
76A ALA* 4.6 3.8 - - - -
77A THR* 3.1 23.7 + - - +
79A GLU* 1.3 73.9 - - + +
81A VAL* 1.3 60.8 + - - +
83A LYS* 3.1 7.6 + - - +
84A ILE* 2.8 46.8 + - + +
103A LEU* 4.2 11.9 - - + -
108A VAL* 4.2 13.5 - - + +
109A CYS* 3.8 20.2 - - - -
115A PRO* 4.2 13.5 - - + -
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Residues in contact with VAL 81 (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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76A ALA* 3.5 27.1 - - + +
77A THR 2.9 18.8 + - - +
78A PRO* 3.5 9.6 - - + +
80A VAL* 1.3 77.4 - - + +
82A SER* 1.3 61.2 + - - +
84A ILE* 3.2 7.8 + - - +
85A ALA* 3.0 22.0 + - - +
123A VAL* 4.3 18.6 - - + -
127A LEU* 4.1 25.1 - - + +
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Residues in contact with SER 82 (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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78A PRO 2.9 15.2 + - - -
79A GLU* 3.5 12.2 - - - -
81A VAL* 1.3 76.0 - - - +
83A LYS* 1.3 53.3 + - - +
85A ALA* 3.2 8.8 + - - +
86A GLN* 2.8 34.2 + - - +
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Residues in contact with LYS 83 (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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79A GLU* 2.9 25.3 + - + +
80A VAL* 3.4 7.6 - - - +
82A SER* 1.3 74.3 - - - +
84A ILE* 1.3 60.0 + - - +
86A GLN* 2.7 39.0 + - - +
87A TYR* 2.7 55.1 + - + +
103A LEU* 3.9 15.7 - - + -
106A GLU* 4.5 8.8 + - - -
108A VAL* 3.9 24.9 - - + -
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Residues in contact with ILE 84 (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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80A VAL* 2.8 38.3 + - + +
81A VAL 3.6 4.7 - - - +
83A LYS* 1.3 70.2 - - - +
85A ALA* 1.3 64.8 + - - +
87A TYR* 3.1 11.5 + - - +
88A LYS* 3.0 22.5 + - - +
99A ILE* 4.0 22.9 - - + +
103A LEU* 4.1 9.9 - - + -
115A PRO* 5.3 2.5 - - + -
120A ILE* 4.5 20.0 - - + +
123A VAL* 3.8 36.6 - - + -
124A LEU* 3.7 29.4 - - + -
127A LEU* 4.6 0.9 - - + -
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Residues in contact with ALA 85 (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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81A VAL 3.0 13.2 + - - +
82A SER* 3.4 10.5 - - - +
84A ILE* 1.3 77.4 - - - +
86A GLN* 1.3 56.8 + - - +
88A LYS* 3.8 5.5 - - - +
89A GLN* 2.9 35.7 + - + +
127A LEU* 4.0 25.1 - - + +
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Residues in contact with GLN 86 (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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82A SER 2.8 14.7 + - - +
83A LYS* 2.7 49.9 + - - +
85A ALA* 1.3 78.7 - - - +
87A TYR* 1.3 61.0 + - - +
89A GLN* 3.5 6.5 + - - +
90A GLU* 2.8 62.7 + - - +
102A ARG* 4.8 2.6 - - - +
106A GLU* 5.7 0.2 + - - -
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Residues in contact with TYR 87 (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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83A LYS* 2.7 38.6 + - + +
84A ILE 3.1 4.5 + - - +
86A GLN* 1.3 80.6 - - - +
88A LYS* 1.3 62.8 + - - +
90A GLU* 3.3 9.3 + - - +
91A CYS* 3.0 24.4 + - - +
94A ILE* 4.6 11.2 - - + +
99A ILE* 3.8 32.1 - - + -
102A ARG* 3.3 56.8 + - + +
103A LEU* 3.3 28.8 + - + -
106A GLU* 2.7 25.5 + - - +
108A VAL* 3.7 19.6 - - - +
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Residues in contact with LYS 88 (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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84A ILE 3.0 13.4 + - - +
85A ALA* 3.8 5.8 - - - +
87A TYR* 1.3 76.2 - - - +
89A GLN* 1.3 65.2 + - - +
91A CYS 4.0 4.3 - - - -
92A PRO* 3.0 59.8 + - + +
94A ILE* 4.2 21.0 + - + +
99A ILE* 4.4 2.2 - - + +
124A LEU* 3.4 40.5 - - + +
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Residues in contact with GLN 89 (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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85A ALA* 2.9 20.6 + - + +
86A GLN* 3.5 8.3 - - - +
87A TYR 3.2 0.2 - - - -
88A LYS* 1.3 80.0 - - - +
90A GLU* 1.3 60.7 + - + +
92A PRO* 3.9 10.0 - - - +
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Residues in contact with GLU 90 (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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86A GLN* 2.8 45.6 + - - +
87A TYR* 3.5 6.3 - - - +
89A GLN* 1.3 75.6 - - + +
91A CYS* 1.3 60.1 + - + +
92A PRO* 3.9 3.1 - - - +
102A ARG* 3.1 29.2 + - - +
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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