Contacts of the helix formed by residues 87 - 102 (chain I) in PDB entry 6RAR
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 87 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18B C 5.0 0.2 - - - +
19B A 3.3 44.0 + - - +
20B A 4.9 0.5 + - - -
84I ARG* 3.8 33.0 - - + +
85I GLU 5.2 0.4 - - - -
86I LEU* 1.3 78.4 - - - +
88I GLY* 1.3 70.9 + - - +
89I HIS 3.2 0.3 + - - -
90I ALA* 3.0 13.8 + - - +
91I ALA* 2.9 14.8 + - - +
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Residues in contact with GLY 88 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B A 3.6 23.5 - - - -
20B A 4.8 3.6 - - - -
87I THR* 1.3 75.6 - - - +
89I HIS* 1.3 61.9 + - - -
91I ALA* 3.1 4.6 + - - +
92I ARG* 3.0 25.8 + - - +
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Residues in contact with HIS 89 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B A 3.2 59.0 + - - +
21B T 3.9 13.5 + - - -
88I GLY* 1.3 71.3 - - - -
90I ALA* 1.3 65.9 + - - +
92I ARG* 3.3 45.3 + - + +
93I ASP* 3.0 35.4 + - - +
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Residues in contact with ALA 90 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B A 4.6 1.4 + - - -
86I LEU* 3.8 23.4 - - + +
87I THR* 3.0 13.4 + - - +
89I HIS* 1.3 78.6 - - - +
91I ALA* 1.3 61.2 + - - +
93I ASP* 4.1 4.4 - - - +
94I ALA* 3.1 22.5 + - - +
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Residues in contact with ALA 91 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54I GLY 6.1 0.4 - - - +
55I VAL* 5.8 6.5 - - + -
81I LEU* 3.6 26.2 - - + -
86I LEU* 3.7 13.9 - - - +
87I THR* 2.9 19.8 + - - +
88I GLY 3.5 9.0 - - - +
90I ALA* 1.3 74.8 - - - +
92I ARG* 1.3 65.7 + - - +
94I ALA* 3.0 4.5 + - - +
95I ILE* 2.8 31.4 + - + +
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Residues in contact with ARG 92 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59I PRO* 6.2 4.0 - - + -
88I GLY 3.0 15.1 + - - +
89I HIS* 3.3 49.4 + - + +
91I ALA* 1.3 75.9 - - - +
93I ASP* 1.3 83.9 + - - +
95I ILE* 3.1 11.2 + - - +
96I LEU* 2.9 47.1 + - + +
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Residues in contact with ASP 93 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89I HIS* 3.0 23.1 + - - +
90I ALA* 4.1 4.8 - - - +
92I ARG* 1.3 103.2 + - - +
94I ALA* 1.3 58.4 + - - +
96I LEU* 3.3 14.6 + - - +
97I THR* 3.0 31.2 + - - -
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Residues in contact with ALA 94 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77I LEU* 3.7 24.6 - - + +
80I LYS* 5.7 1.3 - - - +
86I LEU* 3.9 18.6 - - + -
90I ALA 3.1 18.2 + - - +
91I ALA* 3.0 5.9 + - - +
93I ASP* 1.3 76.1 - - - +
95I ILE* 1.3 62.3 + - - +
97I THR* 3.4 7.8 + - - +
98I ALA* 3.2 21.8 + - - +
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Residues in contact with ILE 95 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55I VAL* 3.9 35.9 - - + -
57I ILE 5.8 0.4 - - - +
58I VAL* 4.1 15.9 - - + -
59I PRO* 4.6 11.9 - - + -
77I LEU* 4.5 10.8 - - + -
81I LEU* 4.1 24.7 - - + -
91I ALA* 2.8 24.6 + - + +
92I ARG* 3.6 7.6 - - - +
94I ALA* 1.3 76.0 - - - +
96I LEU* 1.3 64.0 + - - +
98I ALA* 3.5 0.5 + - - +
99I MET* 3.1 20.8 + - - +
107I TRP* 3.6 26.7 - - + -
115I LEU* 4.2 10.5 - - + -
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Residues in contact with LEU 96 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59I PRO* 3.9 28.0 - - + -
92I ARG* 2.9 34.7 + - + +
93I ASP* 3.6 23.3 - - - +
94I ALA 3.3 0.2 - - - -
95I ILE* 1.3 75.7 - - - +
97I THR* 1.3 65.1 + - - +
99I MET* 3.1 18.9 + - + +
100I GLU* 2.9 35.9 + - - +
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Residues in contact with THR 97 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93I ASP 3.0 16.0 + - - -
94I ALA* 3.4 8.7 + - - -
95I ILE 3.4 0.2 - - - -
96I LEU* 1.3 75.9 - - - +
98I ALA* 1.3 63.2 + - - +
100I GLU* 3.5 15.6 + - - +
101I SER* 3.3 26.0 + - - +
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Residues in contact with ALA 98 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69I PHE* 3.7 27.3 - - + -
77I LEU* 3.9 22.0 - - + -
94I ALA 3.2 13.1 + - - +
95I ILE 3.7 8.1 - - - +
97I THR* 1.3 77.9 - - - +
99I MET* 1.3 62.4 + - - +
101I SER* 3.2 3.6 + - - -
102I ALA* 3.0 24.6 + - - +
107I TRP* 3.9 11.9 - - + -
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Residues in contact with MET 99 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59I PRO* 3.8 15.7 - - + +
60I GLU 3.4 28.0 - - - +
61I LYS* 2.5 50.4 + - + +
95I ILE 3.1 14.3 + - - +
96I LEU* 3.1 30.9 + - + +
98I ALA* 1.3 76.7 - - - +
100I GLU* 1.3 56.4 + - + +
102I ALA* 3.2 6.1 + - - +
107I TRP* 3.3 45.7 - - + +
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Residues in contact with GLU 100 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61I LYS* 2.8 19.1 + - - +
65I LYS* 3.6 9.4 - - - +
66I SER* 4.0 3.8 - - - -
67I GLN* 4.2 6.4 + - + +
96I LEU* 2.9 29.4 + - + +
97I THR* 3.8 14.8 + - - +
98I ALA 3.3 0.2 - - - -
99I MET* 1.3 79.5 - - + +
101I SER* 1.3 59.9 + - - +
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Residues in contact with SER 101 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66I SER* 3.9 0.7 - - - -
67I GLN* 2.9 52.2 + - - +
68I ASN 4.9 0.9 - - - -
69I PHE* 3.7 23.6 + - - +
97I THR* 3.3 15.5 + - - +
98I ALA* 3.2 9.0 + - - -
100I GLU* 1.3 76.2 - - - +
102I ALA* 1.3 62.1 + - - +
103I THR* 4.0 0.7 + - - +
106I GLU* 4.9 0.2 - - - +
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Residues in contact with ALA 102 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61I LYS* 2.4 31.9 + - - -
65I LYS 3.8 3.6 - - - +
66I SER* 4.0 1.2 - - - -
69I PHE* 3.6 17.7 - - + +
98I ALA 3.0 16.9 + - - +
99I MET 3.2 5.3 + - - +
100I GLU 3.7 0.2 - - - +
101I SER* 1.3 80.2 - - - +
103I THR* 1.3 67.6 + - - +
106I GLU* 3.4 18.6 - - + +
107I TRP* 4.1 17.5 - - + -
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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