Contacts of the helix formed by residues 83 - 91 (chain I) in PDB entry 6AHU
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 83 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41I PHE* 5.1 14.5 - - + -
81I VAL* 3.4 16.8 - - - +
82I SER* 1.3 85.5 + - - +
84I PRO* 1.3 74.0 - - + +
85I SER* 4.0 16.0 + - - +
86I HIS* 3.3 16.4 + - + +
112I LEU* 3.9 2.9 - - - -
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Residues in contact with PRO 84 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82I SER 4.5 2.2 - - - +
83I ASP* 1.3 86.9 - - + +
85I SER* 1.3 63.2 + - - +
86I HIS 3.2 0.2 - - - -
87I CYS* 3.4 17.2 + - + +
88I ASN* 3.7 13.4 + - - -
112I LEU* 3.8 19.0 - - + -
115I ILE* 6.4 1.1 - - + -
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Residues in contact with SER 85 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83I ASP* 3.2 13.2 + - - +
84I PRO* 1.3 81.8 - - - +
86I HIS* 1.3 63.0 + - - +
87I CYS 3.5 0.5 + - - -
88I ASN* 3.6 21.7 + - - +
89I VAL* 4.0 8.1 - - - +
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Residues in contact with HIS 86 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39I VAL* 5.0 6.0 - - + +
40I ASP 3.5 19.4 + - - -
41I PHE* 3.7 28.7 - - + -
44I LYS* 4.9 13.2 - - + +
79I ILE* 3.6 27.4 - - + -
80I ILE 3.9 10.0 + - - -
81I VAL* 3.7 17.6 - - + +
82I SER 5.3 0.2 - - - +
83I ASP* 3.3 17.4 + - + +
84I PRO 3.2 0.6 - - - -
85I SER* 1.3 79.8 + - - +
87I CYS* 1.3 63.3 + - - +
88I ASN 3.2 0.9 - - - -
89I VAL* 3.3 33.2 + - + +
90I LEU* 3.7 6.1 - - + +
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Residues in contact with CYS 87 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81I VAL* 4.2 15.7 - - + +
83I ASP 3.7 2.6 + - - -
84I PRO* 3.4 17.4 + - + +
85I SER 3.3 0.8 - - - -
86I HIS* 1.3 78.7 - - - +
88I ASN* 1.3 63.4 + - - +
90I LEU* 3.3 24.3 + - - +
91I ARG* 3.9 13.3 + - - +
112I LEU* 4.5 7.4 - - + -
115I ILE* 3.9 26.7 - - + -
120I LEU* 3.9 29.8 - - - -
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Residues in contact with ASN 88 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84I PRO 3.7 15.6 + - - +
85I SER* 3.6 14.7 + - - +
86I HIS 3.2 0.8 - - - -
87I CYS* 1.3 76.2 - - - +
89I VAL* 1.3 61.9 + - + +
90I LEU 3.3 0.4 - - - -
91I ARG* 3.5 33.6 + - - +
92I ALA* 3.5 13.3 + - - +
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Residues in contact with VAL 89 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46I GLN* 3.8 25.4 - - + +
85I SER 4.0 11.0 - - - +
86I HIS* 3.4 32.1 - - + +
87I CYS 3.2 0.4 - - - -
88I ASN* 1.3 78.5 - - + +
90I LEU* 1.3 65.7 + - + +
92I ALA* 3.2 7.2 + - + +
93I THR* 3.1 27.1 + - + +
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Residues in contact with LEU 90 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79I ILE* 3.8 42.6 - - + -
81I VAL* 4.1 8.5 - - + -
86I HIS* 3.7 19.3 - - + +
87I CYS* 3.3 12.9 + - - +
88I ASN 3.3 0.6 - - - -
89I VAL* 1.3 80.8 - - + +
91I ARG* 1.3 59.3 + - - +
92I ALA 3.3 0.6 + - - -
93I THR* 3.7 8.0 + - - -
94I SER* 3.6 20.8 + - - -
103I VAL* 4.9 3.4 - - + -
105I VAL* 3.9 24.7 - - + -
120I LEU* 4.1 21.8 - - + -
122I VAL* 4.3 11.2 - - + -
235I ARG* 5.6 1.9 + - - -
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Residues in contact with ARG 91 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87I CYS* 3.9 9.3 + - - +
88I ASN* 3.5 25.9 + - - +
89I VAL 3.3 0.6 - - - -
90I LEU* 1.3 77.2 - - - +
92I ALA* 1.3 58.5 + - - +
94I SER* 4.3 10.9 + - - -
95I SER* 5.2 2.8 + - - -
115I ILE* 5.1 10.1 + - - +
119I HIS* 3.4 39.9 + - - +
120I LEU* 4.2 23.9 - - + +
121I ASP 6.1 0.2 - - - +
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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