Contacts of the helix formed by residues 50 - 66 (chain B) in PDB entry 1R6O
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 50 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48B SER 3.6 4.2 + - - -
49B VAL* 1.3 73.5 - - - +
51B LEU* 1.3 56.4 + - - +
52B VAL* 3.2 20.8 + - - +
53B ALA* 3.2 24.5 + - + +
54B LEU* 3.1 26.9 + - - +
127B HIS* 4.1 11.6 + - + +
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Residues in contact with LEU 51 (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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35B LEU* 4.0 26.4 - - + +
41B ARG* 4.0 18.6 - - + +
44B LEU* 4.0 34.1 - - + -
45B GLU* 4.0 28.9 - - + +
49B VAL* 3.0 25.5 + - + +
50B ASP* 1.3 70.0 + - - +
52B VAL* 1.3 65.7 + - + +
54B LEU* 4.0 3.1 - - + -
55B ARG* 3.1 24.9 + - - +
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Residues in contact with VAL 52 (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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50B ASP* 3.2 9.3 + - - +
51B LEU* 1.3 78.4 - - + +
53B ALA* 1.3 62.7 + - - +
55B ARG* 3.3 25.7 + - - +
56B GLN* 3.0 43.6 + - - +
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Residues in contact with ALA 53 (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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50B ASP* 3.2 29.2 + - + +
52B VAL* 1.3 77.0 - - - +
54B LEU* 1.3 60.1 + - - +
56B GLN* 3.3 15.1 + - - +
57B GLU* 2.9 41.9 + - - +
127B HIS* 4.2 10.5 - - + -
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Residues in contact with LEU 54 (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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31B LEU* 4.5 6.3 - - + -
35B LEU* 3.8 22.7 - - + -
44B LEU* 4.6 3.8 - - + -
49B VAL* 4.0 20.2 - - + -
50B ASP 3.1 17.6 + - - +
51B LEU* 4.2 5.4 - - + +
52B VAL 3.4 0.2 - - - -
53B ALA* 1.3 75.2 - - - +
55B ARG* 1.3 63.4 + - - +
57B GLU* 3.3 6.3 + - - +
58B LEU* 3.0 43.4 + - + +
123B LEU* 3.8 34.5 - - + -
124B LEU* 4.4 20.0 - - + -
127B HIS* 3.9 18.1 - - + +
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Residues in contact with ARG 55 (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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32B LEU* 3.6 21.9 - - + +
35B LEU* 3.7 16.3 - - + +
51B LEU 3.1 19.1 + - - +
52B VAL* 3.4 45.9 + - - +
54B LEU* 1.3 76.5 - - - +
56B GLN* 1.3 74.9 + - - +
58B LEU* 3.3 2.4 + - - +
59B GLU* 3.0 52.9 + - - +
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Residues in contact with GLN 56 (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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52B VAL* 3.0 33.8 + - - +
53B ALA* 3.3 15.2 + - - +
55B ARG* 1.3 93.3 - - - +
57B GLU* 1.3 59.7 + - + +
59B GLU* 3.4 9.4 + - - +
60B ALA* 3.0 30.7 + - - +
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Residues in contact with GLU 57 (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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53B ALA* 2.9 27.7 + - - +
54B LEU* 3.7 5.2 - - - +
56B GLN* 1.3 76.8 - - + +
58B LEU* 1.3 63.7 + - - +
60B ALA* 3.6 5.4 + - - +
61B PHE* 3.1 24.3 + - - +
119B GLN* 5.5 0.7 + - - -
123B LEU* 3.9 27.8 - - + +
126B LYS* 3.2 24.6 + - - -
127B HIS* 2.7 33.5 + - - -
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Residues in contact with LEU 58 (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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28B GLU* 3.8 35.7 - - + +
31B LEU* 3.8 35.2 - - + -
32B LEU* 3.9 28.3 - - + +
35B LEU* 4.3 5.8 - - + -
54B LEU* 3.0 32.9 + - + +
55B ARG 3.7 3.4 - - - +
57B GLU* 1.3 77.8 - - - +
59B GLU* 1.3 57.8 + - - +
61B PHE* 3.3 4.1 + - - +
62B ILE* 2.8 36.7 + - + +
120B ALA* 4.6 1.6 - - - -
123B LEU* 3.8 21.8 - - + -
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Residues in contact with GLU 59 (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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32B LEU* 3.7 22.6 - - + +
55B ARG* 3.0 51.8 + - - +
56B GLN* 3.8 8.3 - - - +
58B LEU* 1.3 76.5 - - - +
60B ALA* 1.3 62.4 + - - +
62B ILE* 3.4 7.1 + - + +
63B GLU* 3.0 34.6 + - + +
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Residues in contact with ALA 60 (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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56B GLN 3.0 18.9 + - - +
57B GLU* 3.9 6.3 - - - +
59B GLU* 1.3 76.5 - - - +
61B PHE* 1.3 62.0 + - - +
63B GLU* 4.0 3.9 - - - +
64B GLN* 3.1 38.4 + - - +
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Residues in contact with PHE 61 (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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26B THR* 6.3 0.4 - - + -
28B GLU* 3.7 31.6 - - + -
57B GLU 3.1 18.1 + - - +
58B LEU* 3.6 4.3 - - - +
60B ALA* 1.3 77.9 - - - +
62B ILE* 1.3 61.8 + - - +
64B GLN* 4.3 5.6 - - + -
65B THR* 2.5 66.1 + - + +
66B THR* 5.8 0.4 - - - -
119B GLN* 3.5 54.5 - - + +
25D PRO* 6.3 0.7 - - + -
27D MET* 6.1 1.1 - - - -
77D THR* 3.7 22.7 - - + -
79D GLU* 5.2 1.6 - - - -
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Residues in contact with ILE 62 (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 HIS* 4.0 1.9 - - - +
26B THR* 4.5 2.2 - - - +
28B GLU* 3.8 22.2 - - + +
29B HIS* 3.5 53.6 - - + +
32B LEU* 3.9 25.4 - - + -
58B LEU 2.8 26.4 + - - +
59B GLU* 3.7 5.4 - - - +
61B PHE* 1.3 75.4 - - + +
63B GLU* 1.3 74.9 + - - +
66B THR* 2.7 45.7 + - - +
412B ZN 3.9 3.4 - - - -
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Residues in contact with GLU 63 (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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20B HIS* 3.3 15.5 + - + -
22B HIS* 3.3 10.8 + - - -
59B GLU* 3.0 24.8 + - + +
60B ALA* 4.2 2.7 - - - +
62B ILE* 1.3 86.2 - - - +
64B GLN* 1.3 61.5 + - - +
66B THR 4.6 6.6 + - - +
412B ZN 2.0 37.0 - - - -
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Residues in contact with GLN 64 (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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60B ALA* 3.1 32.6 + - - +
61B PHE* 4.0 3.4 - - + +
63B GLU* 1.3 78.2 - - + +
65B THR* 1.3 70.9 + - + +
66B THR 3.9 0.2 - - - -
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Residues in contact with THR 65 (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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61B PHE* 2.5 58.1 + - + +
62B ILE 4.3 0.3 + - - -
64B GLN* 1.3 93.4 - - + +
66B THR* 1.3 61.9 + - - +
67B PRO* 3.4 11.6 - - - +
27D MET* 5.2 10.8 - - + -
76D PHE* 6.0 1.2 - - - +
77D THR* 3.5 27.1 + - + +
80D VAL* 4.7 4.4 - - - +
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Residues in contact with THR 66 (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 HIS* 3.5 33.2 + - + +
24B PHE* 3.6 28.3 - - + +
26B THR* 4.4 14.9 - - + +
29B HIS* 4.2 6.0 - - + -
61B PHE* 5.8 0.5 - - - -
62B ILE* 2.7 36.7 + - - +
63B GLU 4.6 4.9 - - - +
64B GLN 3.9 0.4 - - - -
65B THR* 1.3 78.2 + - - +
67B PRO* 1.3 74.7 - - + +
68B VAL* 3.6 4.9 + - - +
80D VAL* 5.3 1.8 - - + -
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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