Contacts of the helix formed by residues 69 - 76 (chain J) in PDB entry 6H25
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 ASP 69 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68J PRO* 1.3 75.8 - - - +
70J THR* 1.3 86.0 + - - +
71J ASN* 4.4 12.9 + - + +
72J VAL* 3.3 19.1 - - + +
73J LEU* 3.5 12.6 + - - +
94J VAL* 3.9 6.6 - - - +
146J ASN* 4.3 12.4 + - - -
149J ILE* 4.0 14.4 - - - +
173J PHE* 4.3 16.6 - - + -
174J ILE 3.2 20.8 + - - +
175J THR* 3.7 18.8 + - - -
176J ASN 5.1 0.9 + - - +
180J ASN* 4.5 11.4 + - - +
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Residues in contact with THR 70 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69J ASP* 1.3 85.4 + - - +
71J ASN* 1.3 65.7 + - - +
73J LEU* 3.0 5.2 + - - +
74J LEU* 2.9 42.5 + - + +
94J VAL* 3.7 26.5 - - + +
97J GLU* 3.1 46.8 + - + +
98J VAL* 4.6 5.3 - - + +
101J ARG* 5.6 1.3 - - - +
146J ASN* 5.6 1.9 + - - -
149J ILE* 4.1 5.5 - - - +
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Residues in contact with ASN 71 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69J ASP* 3.5 9.5 + - - +
70J THR* 1.3 82.5 - - - +
72J VAL* 1.3 57.7 + - + +
74J LEU* 3.3 16.0 + - - +
75J HIS* 2.9 44.9 + - + -
101J ARG* 4.6 9.7 + - - -
176J ASN* 3.4 22.4 - - + +
180J ASN* 5.9 2.6 - - - +
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Residues in contact with VAL 72 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68J PRO* 3.8 11.7 - - + -
69J ASP* 3.3 33.8 - - + +
71J ASN* 1.3 76.7 - - - +
73J LEU* 1.3 60.3 + - - +
75J HIS* 4.8 1.3 - - - -
76J GLN* 2.8 36.5 + - + +
80J LEU* 4.6 5.0 - - + +
174J ILE* 4.1 12.6 - - + +
175J THR* 3.5 24.0 - - - +
176J ASN* 3.4 30.5 - - - +
194J CYS* 3.9 16.2 - - + -
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Residues in contact with LEU 73 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68J PRO* 4.8 12.1 - - + -
69J ASP 3.5 10.1 - - - +
70J THR 3.0 10.1 + - - +
72J VAL* 1.3 83.2 - - + +
74J LEU* 1.3 62.2 + - - +
77J ILE* 4.0 14.6 + - + +
80J LEU* 3.8 24.7 - - + -
90J VAL* 4.9 18.6 - - + -
94J VAL* 3.7 24.7 - - + +
95J LEU* 5.3 2.0 - - - +
98J VAL* 4.0 9.2 - - + -
105J VAL* 3.7 12.8 - - - +
109J ILE* 3.7 35.7 - - + -
120J PHE* 6.4 2.0 - - + -
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Residues in contact with LEU 74 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70J THR* 2.9 24.6 + - + +
71J ASN* 3.3 13.9 + - - +
73J LEU* 1.3 80.1 - - - +
75J HIS* 1.3 74.5 + - + +
77J ILE* 4.3 10.4 - - - +
98J VAL* 3.8 27.4 - - + -
101J ARG* 3.9 53.4 - - + +
102J SER* 4.4 11.0 - - - -
105J VAL* 4.0 23.9 - - + +
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Residues in contact with HIS 75 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71J ASN* 2.9 28.7 + - + +
72J VAL* 4.5 2.5 - - - +
74J LEU* 1.3 94.7 - - + +
76J GLN* 1.3 59.7 + - + +
77J ILE* 3.3 12.9 + - - +
78J ASP* 4.6 3.1 + - - +
101J ARG* 5.8 2.8 + - - -
176J ASN* 4.1 13.8 + - - +
210J ARG 5.2 9.2 - - - -
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Residues in contact with GLN 76 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72J VAL* 2.8 23.5 + - + +
75J HIS* 1.3 72.2 - - + +
77J ILE* 1.3 56.7 + - - +
78J ASP* 3.2 4.0 - - - +
79J VAL* 3.0 25.8 + - + +
80J LEU* 2.9 33.1 + - + +
194J CYS* 4.0 24.2 - - - -
210J ARG* 5.7 5.6 - - - -
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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