Contacts of the helix formed by residues 75 - 85 (chain B) in PDB entry 6RZ5
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 THR 75 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B LEU 3.8 12.6 - - - +
72B CYS* 2.7 22.7 + - - -
74B CYS* 1.3 79.0 - - + +
76B LEU* 1.3 63.8 + - - +
77B PRO* 3.3 2.9 - - - -
78B LEU* 3.0 29.9 + - + +
79B ARG* 3.6 7.0 + - - +
95B LEU* 6.5 0.4 - - + -
98B LEU* 4.8 11.4 - - + +
99B SER* 4.0 26.8 + - - +
102B ALA* 3.6 25.7 - - + +
103B LEU 5.3 0.2 + - - -
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Residues in contact with LEU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B TYR* 3.7 32.3 - - + +
33B ILE* 3.8 32.3 - - + -
34B SER* 3.2 22.9 - - - +
72B CYS* 3.2 31.8 + - - +
73B VAL* 4.0 14.4 - - + +
75B THR* 1.3 76.1 + - - +
77B PRO* 1.4 62.8 - - + +
79B ARG* 3.0 36.9 + - - +
80B VAL* 3.1 14.0 + - - +
103B LEU* 5.3 2.2 - - + -
285B ALA* 4.7 9.9 - - + +
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Residues in contact with PRO 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B SER* 4.0 2.9 - - - +
73B VAL 3.1 20.2 - - - +
74B CYS 3.7 5.8 - - - +
75B THR 3.4 5.2 - - - -
76B LEU* 1.4 87.0 - - + +
78B LEU* 1.4 55.2 + - - +
80B VAL* 3.3 14.5 + - + +
81B VAL* 3.1 32.4 + - - +
2018B OLA 4.1 76.6 - - + +
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Residues in contact with LEU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B CYS 5.2 3.1 - - - +
75B THR* 3.0 21.1 + - + +
77B PRO* 1.4 72.8 - - - +
79B ARG* 1.4 65.0 + - - +
81B VAL* 3.3 5.6 + - + +
82B TYR* 3.1 23.0 + - - +
89B TRP* 3.7 26.3 - - + -
91B PHE* 3.7 34.1 - - + -
95B LEU* 4.3 27.1 - - + -
99B SER* 3.6 19.1 - - - +
2018B OLA 5.0 20.9 - - + -
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Residues in contact with ARG 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B TYR* 3.6 39.2 + - + -
75B THR* 3.6 8.3 + - - +
76B LEU* 3.0 35.2 + - - +
78B LEU* 1.4 75.3 - - - +
80B VAL* 1.4 58.7 + - - +
82B TYR* 3.4 3.1 + - - +
83B TYR* 2.9 35.7 + - + -
89B TRP* 4.6 0.2 - - - -
99B SER* 3.4 25.1 + - - -
100B THR* 3.8 9.1 + - - +
103B LEU* 3.7 27.5 - - - +
104B TYR* 5.9 1.8 - - - -
174B PHE* 3.3 64.0 - - + +
281B LEU* 4.3 11.3 - - - +
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Residues in contact with VAL 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B SER* 3.8 18.1 + - - +
30B TYR* 3.6 26.0 - - + -
31B SER* 3.4 29.8 - - - +
34B SER* 4.8 1.1 - - - +
76B LEU 3.1 14.7 + - - +
77B PRO* 3.4 14.1 - - + +
78B LEU 3.2 0.2 - - - -
79B ARG* 1.4 74.8 - - - +
81B VAL* 1.4 55.8 + - - +
83B TYR* 3.3 3.0 + - - -
84B VAL* 3.0 41.8 + - + +
2018B OLA 3.8 23.6 - - + +
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Residues in contact with VAL 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B PRO 3.1 15.0 + - - +
78B LEU* 3.3 8.5 + - + +
80B VAL* 1.4 74.2 - - - +
82B TYR* 1.3 58.9 + - - +
84B VAL* 3.7 7.3 + - + +
85B HIS* 3.2 37.5 + - + +
90B LEU* 4.5 10.7 - - + +
91B PHE* 3.5 29.8 - - + -
2018B OLA 4.0 29.2 - - + +
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Residues in contact with TYR 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B ARG* 6.2 0.9 - - - -
78B LEU 3.1 11.8 + - - +
79B ARG* 3.4 8.5 - - - +
81B VAL* 1.3 77.7 - - - +
83B TYR* 1.4 97.7 + + - +
85B HIS* 3.4 8.0 + - - +
87B GLY* 3.0 47.1 + - - -
88B ILE 3.5 26.2 + - - -
89B TRP* 3.5 35.4 - + + -
90B LEU* 6.5 0.2 - - - -
91B PHE* 5.2 1.1 - - - -
172B LYS* 3.3 26.1 + - - +
173B CYS* 3.1 37.4 + - + -
174B PHE* 4.0 5.2 - + - -
175B GLU* 3.7 6.7 + - - -
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Residues in contact with TYR 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B ARG* 4.6 14.7 + - + -
23B ASN* 3.1 56.3 - - - +
26B TYR* 3.5 54.4 - + + -
27B SER* 3.6 16.4 - - - +
30B TYR* 4.0 13.0 - + - -
79B ARG* 2.9 29.2 + - + +
80B VAL* 3.3 2.6 + - - +
82B TYR* 1.4 99.0 - + - +
84B VAL* 1.3 63.7 + - - +
85B HIS 3.2 1.3 - - - -
86B LYS* 3.5 4.8 + - - +
173B CYS 4.7 0.2 + - - -
174B PHE* 3.8 32.4 + + - +
281B LEU* 6.1 0.2 - - - +
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Residues in contact with VAL 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B SER* 3.6 17.5 - - - +
80B VAL* 3.0 28.2 + - + +
81B VAL* 3.9 7.6 - - + +
83B TYR* 1.3 76.8 - - - +
85B HIS* 1.4 70.4 + - + +
86B LYS* 3.3 9.1 + - - +
2018B OLA 5.4 3.8 - - - +
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Residues in contact with HIS 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B VAL* 3.2 31.2 + - + +
82B TYR 3.7 5.2 - - - +
83B TYR 3.2 0.6 - - - -
84B VAL* 1.4 86.7 - - + +
86B LYS* 1.4 66.3 + - - +
87B GLY 3.3 2.8 + - - -
88B ILE* 3.5 32.0 - - + +
90B LEU* 3.5 26.8 - - + +
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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