Contacts of the helix formed by residues 76 - 86 (chain N) in PDB entry 6C6U
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 ASN 76 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38N LEU* 4.5 24.1 - - + +
74N VAL* 3.8 6.2 + - - +
75N MET* 1.3 84.5 - - - +
77N ASP* 1.3 63.1 + - - +
78N ALA* 4.1 10.8 - - + +
79N SER* 2.8 27.6 + - - +
80N TRP* 2.9 15.2 + - - +
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Residues in contact with ASP 77 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375I PRO* 3.5 33.3 - - - +
376I PRO 4.5 5.4 - - - +
377I THR* 3.6 21.1 - - + +
75N MET* 5.2 5.5 - - - +
76N ASN* 1.3 74.1 - - - +
78N ALA* 1.3 55.3 + - - +
80N TRP* 3.6 9.1 - - - +
81N HIS* 2.7 42.1 + - + +
98N ASP 4.8 2.8 - - - +
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Residues in contact with ALA 78 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377I THR* 5.0 6.5 + - + +
35N MET* 3.8 26.6 - - + +
38N LEU* 6.3 0.7 - - + -
76N ASN* 3.2 7.7 - - + +
77N ASP* 1.3 77.6 - - - +
79N SER* 1.3 57.8 + - - +
81N HIS* 3.3 7.5 + - - +
82N LEU* 2.9 26.4 + - - +
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Residues in contact with SER 79 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35N MET* 4.6 5.1 - - - -
38N LEU* 4.7 19.1 - - - -
39N PHE* 4.3 20.4 - - - -
73N MET* 4.8 3.5 - - - +
74N VAL* 3.3 15.9 + - - -
75N MET* 4.3 1.4 - - - -
76N ASN* 2.8 32.5 + - - +
78N ALA* 1.3 76.3 - - - +
80N TRP* 1.3 60.7 + - - +
82N LEU* 3.2 8.7 + - - +
83N VAL* 3.0 33.9 + - - +
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Residues in contact with TRP 80 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374I GLU* 3.5 35.7 - - + -
375I PRO* 3.5 35.7 - - + -
73N MET* 5.7 0.2 - - - -
75N MET* 4.0 11.2 - - + -
76N ASN 2.9 16.1 + - - +
77N ASP* 3.6 7.6 - - - +
78N ALA 3.2 0.2 - - - -
79N SER* 1.3 75.3 + - - +
81N HIS* 1.3 93.0 + + - +
83N VAL* 3.4 2.1 + - - +
84N ARG* 3.0 59.4 + - - +
92N PHE* 3.4 42.6 - + - +
97N SER* 3.9 20.8 + - - -
98N ASP 5.8 0.4 - - - -
100N PRO* 4.4 13.2 - - + +
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Residues in contact with HIS 81 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367I TYR* 3.5 21.9 + - - -
375I PRO 3.2 21.5 + - - -
377I THR* 3.2 28.7 + - - -
380I ALA* 3.7 19.8 - - + +
77N ASP* 2.7 30.2 + - + +
78N ALA* 3.7 6.7 - - - +
80N TRP* 1.3 94.2 - + - +
82N LEU* 1.3 55.5 + - - +
84N ARG* 3.7 4.7 - - + +
85N SER* 2.8 33.0 + - - -
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Residues in contact with LEU 82 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26N LEU* 5.9 1.1 - - + -
29N HIS* 4.2 24.2 - - + +
30N ILE* 4.8 6.3 - - + -
33N HIS* 3.5 36.8 - - + -
35N MET* 4.3 21.3 - - + -
39N PHE* 3.6 31.2 - - + -
78N ALA 2.9 14.7 + - - +
79N SER* 3.3 8.5 - - - +
80N TRP 3.2 0.4 - - - -
81N HIS* 1.3 76.4 - - - +
83N VAL* 1.3 61.8 + - + +
85N SER* 2.8 22.7 + - - +
86N VAL* 3.1 16.3 + - + +
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Residues in contact with VAL 83 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12N VAL* 4.3 19.7 - - + -
26N LEU* 4.3 16.2 - - + -
39N PHE* 3.7 31.4 - - + -
71N VAL* 5.4 1.6 - - + -
73N MET* 3.8 11.9 - - - -
79N SER 3.0 16.3 + - - +
80N TRP 3.4 1.1 + - - +
82N LEU* 1.3 75.5 - - - +
84N ARG* 1.3 61.7 + - - +
86N VAL* 3.3 22.1 - - + +
89N VAL* 3.7 11.7 - - + +
92N PHE* 3.5 30.7 - - + -
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Residues in contact with ARG 84 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371I ARG* 5.6 7.5 - - - +
374I GLU* 4.4 13.3 + - - -
80N TRP* 3.0 59.0 + - + +
81N HIS* 3.7 5.2 - - + +
83N VAL* 1.3 80.7 - - + +
85N SER* 1.3 57.7 + - - +
86N VAL 3.4 5.9 - - - +
89N VAL* 4.6 13.3 - - + +
90N MET 3.0 26.2 + - - +
91N GLY* 3.4 24.2 - - - -
92N PHE* 4.6 4.1 - - + +
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Residues in contact with SER 85 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62I TYR* 5.8 0.7 + - - -
29N HIS* 4.4 11.7 + - - -
33N HIS* 5.7 1.7 + - - -
81N HIS 2.8 16.3 + - - -
82N LEU* 2.8 29.3 + - - +
84N ARG* 1.3 75.2 - - - +
86N VAL* 1.3 65.4 + - - +
87N PRO* 3.4 6.2 - - - +
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Residues in contact with VAL 86 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22N VAL 4.3 7.9 - - - +
25N SER* 4.4 2.2 - - - -
26N LEU* 3.7 46.4 - - + +
29N HIS* 3.8 24.4 + - + -
82N LEU* 3.1 16.4 + - + +
83N VAL 3.3 11.0 - - - +
84N ARG 3.4 5.2 - - - +
85N SER* 1.3 77.6 - - - +
87N PRO* 1.3 82.4 - - + +
89N VAL* 3.5 27.7 + - + +
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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