Contacts of the helix formed by residues 82 - 89 (chain H) 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 LEU 82 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20H HIS* 3.7 48.2 - - + +
22H MET* 4.4 10.5 - - + -
77H ILE* 5.2 2.0 - - - +
78H CYS 3.1 10.5 + - - +
79H SER 4.6 6.1 - - - +
80H SER 3.6 1.2 - - - -
81H GLY* 1.3 78.6 - - - +
83H VAL* 1.3 68.3 + - + +
84H LYS 3.6 0.2 + - - -
85H LEU* 3.7 4.2 + - - +
86H TRP* 3.5 59.4 - - + +
107H VAL* 4.3 11.7 - - + -
11L PRO* 4.3 16.2 - - + -
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Residues in contact with VAL 83 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52H PHE* 5.6 2.2 - - + -
79H SER 5.6 2.7 - - - +
80H SER 4.7 0.6 + - - -
81H GLY* 3.4 0.4 - - - -
82H LEU* 1.3 80.9 - - + +
84H LYS* 1.3 63.9 + - + +
85H LEU 3.2 1.2 + - - -
86H TRP* 3.4 8.9 + - + -
87H SER* 3.4 10.6 + - - -
205J ASN* 3.3 39.5 - - - +
208J LEU* 3.8 9.0 - - + -
209J LEU* 5.9 0.9 - - + -
6L ARG 4.3 7.4 - - - +
7L LEU* 3.3 51.1 + - + +
8L ARG* 5.5 0.9 - - - -
9L GLU 6.1 0.4 - - - +
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Residues in contact with LYS 84 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48H VAL* 4.5 6.1 - - + +
52H PHE* 3.5 39.3 - - + -
56H ASP* 3.2 40.2 + - + +
59H LEU* 4.6 13.0 - - + +
77H ILE* 5.7 0.4 - - - -
80H SER* 3.9 21.8 + - - +
81H GLY* 3.8 9.3 + - - +
82H LEU 3.4 0.8 - - - -
83H VAL* 1.3 76.4 - - + +
85H LEU* 1.3 57.2 + - - +
87H SER 4.3 0.7 - - - -
88H SER* 3.2 23.4 + - - -
7L LEU* 4.4 14.6 - - + +
8L ARG* 3.7 34.0 - - - +
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Residues in contact with LEU 85 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22H MET* 3.7 29.6 - - + -
44H LEU* 4.8 8.5 - - + +
48H VAL* 4.3 18.8 - - + -
61H LEU* 4.8 7.4 - - + -
75H LEU* 4.1 25.1 - - + -
76H ARG* 6.1 0.2 - - - -
77H ILE* 3.7 27.6 - - + +
81H GLY 3.5 15.6 + - - +
82H LEU* 3.7 4.2 + - - +
83H VAL 3.2 0.8 - - - -
84H LYS* 1.3 78.1 - - - +
86H TRP* 1.3 65.0 + - - +
87H SER 3.3 1.3 - - - -
88H SER* 4.7 0.4 - - - +
89H LEU* 3.4 46.0 + - + +
102H PHE* 5.4 0.5 - - - -
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Residues in contact with TRP 86 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22H MET* 3.3 41.7 - - + +
82H LEU* 3.5 31.6 - - + +
83H VAL* 3.4 3.2 + - + -
85H LEU* 1.3 75.9 - - - +
87H SER* 1.3 54.2 + - - +
89H LEU* 4.3 1.7 - - - +
90H THR* 2.3 35.7 + - - -
102H PHE* 6.0 2.8 - - - -
104H VAL* 5.4 3.1 - - + +
107H VAL* 3.6 34.3 - - + +
201J TYR 4.6 11.2 - - - -
202J ASP* 3.7 20.7 - - - +
205J ASN* 3.2 41.7 - - + +
333L LYS* 3.7 49.1 - - + -
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Residues in contact with SER 87 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51H LEU* 3.3 16.9 - - - +
52H PHE* 3.7 20.8 - - - -
83H VAL* 3.4 10.3 + - - -
85H LEU 3.3 0.6 - - - -
86H TRP* 1.3 78.6 - - - +
88H SER* 1.3 62.4 + - - +
90H THR* 3.4 17.5 + - - -
91H LEU* 4.2 3.3 + - - +
205J ASN* 4.6 7.8 + - - -
206J LEU* 6.0 3.7 - - - +
209J LEU* 3.3 40.1 - - - +
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Residues in contact with SER 88 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47H ALA* 3.6 27.0 - - - +
48H VAL* 3.4 24.2 - - - -
51H LEU* 3.7 22.3 - - - +
52H PHE* 3.2 26.7 - - - -
84H LYS 3.2 10.4 + - - -
85H LEU 3.7 3.4 + - - -
86H TRP 3.5 0.4 - - - -
87H SER* 1.3 78.4 - - - +
89H LEU* 1.3 63.4 + - - +
90H THR 3.5 0.5 + - - -
91H LEU* 3.9 8.7 + - - +
93H GLY* 4.9 2.8 + - - -
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Residues in contact with LEU 89 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43H LEU* 4.5 14.1 - - + -
44H LEU* 3.8 31.9 - - + +
47H ALA* 3.8 25.1 - - + -
48H VAL* 5.9 0.7 - - + -
75H LEU* 4.9 1.1 - - + -
85H LEU* 3.4 36.5 + - + +
86H TRP 4.3 1.3 - - - +
87H SER 3.4 0.4 - - - -
88H SER* 1.3 75.2 - - - +
90H THR* 1.3 63.0 + - - +
91H LEU 3.4 1.1 - - - -
92H LEU* 4.0 7.3 + - - +
93H GLY 5.0 4.8 + - - +
102H PHE* 3.3 67.1 - - + +
198J ARG* 4.4 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