Contacts of the helix formed by residues 93 - 105 (chain D) in PDB entry 3BRW
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 LEU 93 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10D GLY* 4.7 3.4 - - - -
11D SER 5.7 0.4 - - - +
80D LEU* 4.0 23.0 - - + +
81D VAL 3.6 22.0 - - - +
82D TYR* 3.6 22.4 - - + -
89D THR 3.9 7.6 - - - +
90D PHE* 3.5 20.2 - - + +
91D ASN 3.1 0.8 - - - -
92D ASP* 1.3 79.3 - - + +
94D GLN* 1.3 67.8 + - - +
96D LEU* 2.8 26.0 + - + +
97D ARG* 2.9 13.7 + - - +
113D LEU* 3.4 30.1 - - + -
134D LEU* 4.9 3.1 - - + -
138D TRP* 4.0 13.9 - - + -
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Residues in contact with GLN 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D PHE 4.6 0.6 + - - -
91D ASN* 3.6 11.9 + - - +
92D ASP 3.4 1.8 - - - -
93D LEU* 1.3 80.3 - - - +
95D ASP* 1.3 60.2 + - + +
97D ARG* 3.3 4.0 + - - +
98D GLU* 2.6 65.5 + - - +
134D LEU* 4.0 10.6 - - - +
137D GLN* 5.2 2.5 + - - -
138D TRP* 3.3 31.5 + - - +
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Residues in contact with ASP 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240B ARG* 6.0 0.3 + - - -
91D ASN 5.1 1.4 - - - +
92D ASP* 4.0 10.9 - - - +
94D GLN* 1.3 74.8 - - + +
96D LEU* 1.3 60.0 + - - +
98D GLU* 3.8 21.5 - - + +
99D GLN* 3.3 20.7 + - - +
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Residues in contact with LEU 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D LEU* 3.7 35.4 - - + -
10D GLY* 4.0 24.7 - - - +
62D GLU* 6.1 3.8 - - + -
68D ARG* 4.5 21.1 - - - +
72D MET* 5.7 1.3 - - + -
80D LEU* 4.9 2.5 - - + -
92D ASP* 3.9 12.6 - - + +
93D LEU* 2.8 21.6 + - + +
95D ASP* 1.3 81.4 + - - +
97D ARG* 1.3 65.2 + - - +
99D GLN* 3.2 20.2 + - - +
100D ILE* 3.0 27.9 + - + +
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Residues in contact with ARG 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D LEU* 3.8 15.7 - - + +
93D LEU 2.9 4.9 + - - -
94D GLN* 3.5 10.8 - - - +
96D LEU* 1.3 77.0 - - - +
98D GLU* 1.3 63.8 + - + +
100D ILE* 3.3 8.5 + - - +
101D LEU* 3.2 56.1 + - + +
107D ASP* 4.5 8.9 + - - +
109D VAL 5.6 1.2 + - - -
111D MET* 3.5 36.8 - - - +
138D TRP* 3.4 77.6 + - + +
139D ASN* 3.8 19.4 - - - +
141D CYS* 4.6 2.0 - - - +
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Residues in contact with GLU 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D GLN* 2.6 50.4 + - - +
95D ASP* 3.8 17.8 - - + +
97D ARG* 1.3 79.6 - - + +
99D GLN* 1.3 62.6 + - - +
101D LEU* 3.6 8.9 + - + +
102D ARG* 3.1 35.4 + - - +
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Residues in contact with GLN 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D ARG* 4.7 4.9 + - - +
69D ASP* 3.4 24.9 + - - +
72D MET* 3.3 35.7 - - - +
95D ASP 3.3 20.7 + - - +
96D LEU* 3.2 19.9 + - - +
98D GLU* 1.3 76.4 - - - +
100D ILE* 1.3 64.2 + - - +
102D ARG* 3.4 26.4 + - - +
103D VAL* 3.1 33.9 + - - +
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Residues in contact with ILE 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D LEU* 4.5 10.8 - - + -
72D MET* 3.6 34.5 - - + +
78D PHE* 3.7 44.2 - - + -
80D LEU* 4.9 4.5 - - + -
96D LEU 3.0 22.9 + - - +
97D ARG* 3.4 11.0 - - - +
99D GLN* 1.3 74.2 - - - +
101D LEU* 1.3 60.3 + - - +
103D VAL* 2.9 5.2 + - - +
104D LYS* 2.8 42.5 + - + +
109D VAL* 4.2 8.7 - - + -
111D MET* 4.2 16.8 - - + -
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Residues in contact with LEU 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D ARG* 3.2 55.5 + - + +
98D GLU* 4.0 7.6 - - + +
100D ILE* 1.3 78.3 - - - +
102D ARG* 1.3 53.9 + - - +
104D LYS* 4.6 0.9 - - - +
105D ASP* 2.8 34.3 + - - -
106D THR 3.4 13.3 - - - +
107D ASP* 3.7 32.3 - - + +
109D VAL* 4.2 8.7 - - + -
111D MET* 4.0 15.7 - - + -
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Residues in contact with ARG 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D ASP* 5.6 1.8 + - - -
98D GLU* 3.1 26.8 + - - +
99D GLN* 3.6 27.9 - - - +
101D LEU* 1.3 80.4 - - - +
103D VAL* 1.3 67.0 + - - +
105D ASP* 3.5 14.4 + - - +
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Residues in contact with VAL 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D ASP* 3.5 33.0 - - - +
72D MET* 3.7 24.2 - - + -
73D LYS* 3.8 30.4 - - + +
99D GLN* 3.1 25.0 + - + +
100D ILE 2.9 4.2 + - - +
102D ARG* 1.3 83.8 - - + +
104D LYS* 1.3 61.9 + - - +
105D ASP* 3.5 2.8 + - - +
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Residues in contact with LYS 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D MET* 3.2 18.2 - - + +
73D LYS* 2.6 23.6 + - - +
75D GLY 2.5 29.1 + - - -
76D GLN* 4.9 1.1 - - - +
78D PHE* 3.7 11.2 - - - -
100D ILE* 2.8 23.8 + - + +
103D VAL* 1.3 71.6 - - - +
105D ASP* 1.3 64.9 + - - +
106D THR* 3.1 16.2 + - - +
109D VAL* 3.7 38.4 - - + -
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Residues in contact with ASP 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D LEU 2.8 15.0 + - - -
102D ARG* 3.8 10.5 - - - +
103D VAL 3.2 5.0 - - - +
104D LYS* 1.3 77.2 - - - +
106D THR* 1.3 58.4 + - - +
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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