Contacts of the helix formed by residues 83 - 92 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41J PHE* 4.3 19.3 - - + -
81J VAL* 4.0 2.4 - - - +
82J SER* 1.3 90.7 + - - +
84J PRO* 1.3 71.0 - - + +
85J SER* 3.9 18.4 + - - +
86J HIS* 3.3 19.5 + - + +
87J CYS 3.6 7.1 + - - -
112J LEU* 3.8 8.8 - - - +
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Residues in contact with PRO 84 (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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82J SER 4.5 2.7 - - - +
83J ASP* 1.3 87.6 - - + +
85J SER* 1.3 59.1 + - - +
86J HIS 3.2 2.2 + - - -
87J CYS* 3.7 13.6 + - + +
88J ASN* 4.0 6.8 + - - -
109J THR* 6.6 0.4 - - - -
112J LEU* 4.3 13.7 - - + -
10T G 4.3 12.8 + - - +
11T U 6.0 7.6 - - - -
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Residues in contact with SER 85 (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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44J LYS* 6.0 1.7 + - - -
83J ASP* 3.9 13.9 + - - +
84J PRO* 1.3 80.3 - - - +
86J HIS* 1.3 57.3 + - - +
88J ASN* 2.9 26.7 + - - +
89J VAL* 5.0 1.6 - - - +
10T G 5.7 0.7 - - - -
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Residues in contact with HIS 86 (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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39J VAL* 5.1 4.5 - - + +
40J ASP 3.7 9.1 + - - -
41J PHE* 3.5 48.0 + - + +
44J LYS* 4.2 25.1 - - + +
46J GLN* 5.2 6.5 + - - -
79J ILE* 4.2 13.5 - - + +
80J ILE 4.8 2.9 + - - -
81J VAL* 4.9 6.5 - - + +
83J ASP* 3.3 16.5 + - + +
84J PRO 3.2 1.0 - - - -
85J SER* 1.3 79.6 + - - +
87J CYS* 1.3 62.4 + - - +
88J ASN* 3.2 4.7 + - - -
89J VAL* 3.4 22.9 + - + +
90J LEU* 3.4 29.3 - - + +
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Residues in contact with CYS 87 (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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81J VAL* 4.2 20.3 - - + +
83J ASP 3.6 5.3 + - - +
84J PRO* 3.7 11.8 + - + +
86J HIS* 1.3 75.2 - - - +
88J ASN* 1.3 58.6 + - - +
89J VAL 3.2 0.2 - - - -
90J LEU* 3.1 16.0 + - - +
91J ARG* 2.8 43.9 + - - +
105J VAL* 6.0 0.7 - - - -
112J LEU* 5.0 4.5 - - + -
115J ILE* 4.4 13.5 - - + -
120J LEU* 3.7 30.1 - - - -
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Residues in contact with ASN 88 (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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84J PRO 4.0 3.5 + - - +
85J SER* 2.9 35.0 + - - +
86J HIS 3.6 0.5 - - - -
87J CYS* 1.3 76.2 - - - +
89J VAL* 1.3 88.6 + - - +
91J ARG* 3.5 8.9 + - - +
92J ALA* 3.1 21.3 + - - +
10T G 3.3 49.8 + - - +
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Residues in contact with VAL 89 (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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46J GLN* 3.4 30.5 - - - +
85J SER 5.0 1.6 - - - +
86J HIS* 3.4 18.4 + - + +
88J ASN* 1.3 96.0 + - - +
90J LEU* 1.3 62.1 + - + +
92J ALA* 3.1 18.6 + - + +
93J THR* 3.3 13.8 - - + +
96J ARG* 5.6 5.6 - - - +
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Residues in contact with LEU 90 (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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46J GLN* 4.7 9.0 - - - +
79J ILE* 3.8 38.4 - - + -
81J VAL* 3.8 21.3 - - + -
86J HIS* 3.4 40.2 - - + +
87J CYS* 3.1 19.6 + - - +
89J VAL* 1.3 80.1 - - + +
91J ARG* 1.3 57.9 + - - +
93J THR* 2.6 30.9 + - + -
94J SER 4.6 0.5 + - - -
103J VAL* 5.9 0.7 - - + -
105J VAL* 4.4 9.9 - - + -
120J LEU* 5.1 10.3 - - + +
122J VAL* 5.9 2.5 - - + -
235J ARG* 5.3 3.5 + - - -
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Residues in contact with ARG 91 (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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87J CYS* 2.8 27.3 + - - +
88J ASN* 3.8 7.4 - - - +
89J VAL 3.3 0.2 - - - -
90J LEU* 1.3 76.2 - - - +
92J ALA* 1.3 60.5 + - - +
93J THR 3.3 0.8 + - - -
94J SER* 3.9 16.2 + - - -
115J ILE* 3.5 39.0 - - - +
119J HIS* 4.0 12.3 + - - +
120J LEU* 3.6 49.8 - - + +
10T G 3.7 44.7 + - - +
11T U 5.3 5.0 + - - -
45T G 5.7 0.7 + - - -
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Residues in contact with ALA 92 (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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88J ASN 3.1 13.1 + - - +
89J VAL* 3.1 14.4 + - - +
91J ARG* 1.3 74.9 - - - +
93J THR* 1.3 56.1 + - - +
94J SER* 3.2 6.7 + - - -
95J SER* 3.9 4.0 + - - -
96J ARG* 3.3 55.6 + - - +
45T G 5.8 4.5 - - - +
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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