Contacts of the helix formed by residues 85 - 96 (chain F) in PDB entry 2R6C
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 GLY 85 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80F LEU* 3.7 21.0 - - - +
81F GLU* 4.9 6.3 - - - -
83F ILE* 5.0 1.2 - - - +
84F GLY* 1.3 77.6 + - - -
86F VAL* 1.3 60.9 + - - -
87F SER* 2.9 14.7 - - - +
88F TYR* 3.8 10.4 + - - +
89F LEU* 3.9 11.6 + - - +
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Residues in contact with VAL 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E GLU* 3.3 38.4 - - - +
67F LEU* 5.3 2.1 - - + +
71F THR* 4.0 11.9 - - + -
80F LEU* 3.8 19.4 - - + +
85F GLY* 1.3 73.2 - - - -
87F SER* 1.3 57.4 + - - +
89F LEU* 3.1 9.4 + - - +
90F SER* 2.7 38.2 + - - +
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Residues in contact with SER 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85F GLY* 4.3 9.8 - - - -
86F VAL* 1.3 83.5 + - - +
88F TYR* 1.3 52.1 + - - +
90F SER* 3.3 7.3 + - - -
91F GLU* 2.7 44.4 + - - +
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Residues in contact with TYR 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F GLN* 3.1 29.2 + - - +
45F ARG* 3.9 11.6 + - - -
47F ALA* 5.2 2.0 - - + -
48F HIS* 2.6 40.2 + + - -
51F ILE* 4.4 1.8 - - + -
83F ILE* 4.0 20.4 - - + -
84F GLY* 3.4 25.4 - - - +
85F GLY 3.8 3.6 - - - +
86F VAL 3.4 0.2 - - - -
87F SER* 1.3 78.1 - - - +
89F LEU* 1.3 56.7 + - - +
91F GLU* 3.2 26.3 + - + +
92F LEU* 2.8 61.3 + - + +
456I LEU* 5.2 0.7 - - + -
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Residues in contact with LEU 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F PHE* 3.6 32.6 - - + -
51F ILE* 3.8 34.3 - - + -
67F LEU* 3.6 13.3 - - + +
70F VAL* 4.3 3.4 - - + -
71F THR* 3.3 33.9 - - + +
74F LEU* 3.6 25.1 - - + -
80F LEU* 5.0 2.0 - - + -
83F ILE* 4.9 3.8 - - + -
85F GLY 3.9 13.0 + - - +
86F VAL* 3.1 11.4 + - - +
88F TYR* 1.3 77.9 - - - +
90F SER* 1.3 57.1 + - - +
92F LEU* 3.6 2.5 + - + -
93F ALA* 3.1 25.1 + - - +
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Residues in contact with SER 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67F LEU* 3.5 20.4 - - - +
86F VAL* 2.7 21.0 + - - +
87F SER* 3.6 6.1 - - - -
89F LEU* 1.3 71.0 - - - +
91F GLU* 1.3 67.9 + - - +
93F ALA* 2.9 7.2 + - - -
94F ASP* 2.7 41.9 + - - +
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Residues in contact with GLU 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87F SER* 2.7 25.4 + - - +
88F TYR* 3.2 28.6 + - + +
90F SER* 1.3 71.2 - - - +
92F LEU* 1.3 56.6 + - - +
94F ASP* 4.1 3.7 - - - +
95F ALA* 2.9 33.4 + - - +
456I LEU* 3.6 40.6 + - + +
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Residues in contact with LEU 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F GLN* 3.6 46.0 - - + +
21F LEU* 4.1 16.4 - - + -
22F GLY* 3.5 23.8 - - - +
25F PHE* 4.5 4.9 - - + -
51F ILE* 4.0 17.3 - - + -
88F TYR* 2.8 59.4 + - + +
89F LEU* 3.8 11.0 - - + +
91F GLU* 1.3 72.9 - - - +
93F ALA* 1.3 64.6 + - - +
95F ALA* 3.9 0.8 - - - +
96F VAL* 3.5 16.5 + - - +
456I LEU* 4.3 7.0 - - + -
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Residues in contact with ALA 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F GLY 4.5 4.1 - - - +
25F PHE* 3.9 28.7 - - + -
26F LEU* 5.2 6.6 - - - +
67F LEU* 4.5 10.8 - - + -
89F LEU 3.1 12.7 + - - +
90F SER* 2.9 11.7 + - - +
92F LEU* 1.3 81.4 - - - +
94F ASP* 1.3 66.2 + - - +
95F ALA 3.4 0.2 + - - -
96F VAL* 3.7 14.6 + - - +
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Residues in contact with ASP 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90F SER* 2.7 37.6 + - - +
91F GLU* 4.1 3.3 - - - +
93F ALA* 1.3 74.0 - - - +
95F ALA* 1.3 60.2 + - - +
96F VAL 4.6 0.4 - - - -
457I LEU 4.4 1.1 - - - -
458I PRO* 3.7 6.1 - - + +
459I ALA* 2.9 28.9 + - - +
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Residues in contact with ALA 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F GLU 2.9 18.5 + - - +
92F LEU* 3.9 3.6 - - - +
94F ASP* 1.3 76.7 - - - +
96F VAL* 1.3 69.3 + - + +
97F PRO 3.4 1.0 - - - -
456I LEU* 3.7 28.3 - - + +
457I LEU 3.1 19.3 - - - +
459I ALA* 3.3 9.2 - - - -
462I ASN* 2.9 24.3 + - - +
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Residues in contact with VAL 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F GLN 4.1 2.9 - - - +
19F ALA* 3.9 26.0 - - + +
22F GLY* 3.7 24.9 - - - +
23F ALA* 4.1 17.3 - - + +
26F LEU* 4.3 12.3 - - + +
92F LEU 3.5 9.4 + - - +
93F ALA 3.7 10.4 + - - +
94F ASP 3.5 0.2 - - - -
95F ALA* 1.3 82.4 - - + +
97F PRO* 1.4 68.3 - - + +
98F THR* 3.2 30.1 - - - +
459I ALA* 3.6 9.8 - - - +
551I HIS* 4.9 0.5 - - - -
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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