Contacts of the helix formed by residues 93 - 106 (chain D) in PDB entry 2BM9
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 93 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90D VAL* 3.2 28.8 + - - -
91D TYR 3.3 2.0 + - - -
92D ASN* 1.3 77.8 + - - +
94D GLY* 1.3 62.3 + - - +
95D SER 3.4 2.5 - - - -
96D LEU* 3.4 13.1 + - - +
97D ALA 3.4 6.4 + - - -
122D CYS* 4.5 3.6 - - - -
124D ILE* 2.9 31.9 - - - +
301D SAM 5.0 0.2 - - - -
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Residues in contact with GLY 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D TRP* 4.3 4.9 - - - -
61D LEU* 3.7 15.5 - - - -
62D ARG 3.6 21.5 - - - -
63D MET* 4.2 6.5 - - - +
92D ASN* 3.0 14.7 + - - -
93D GLY* 1.3 77.4 - - - +
95D SER* 1.3 60.6 - - - +
97D ALA* 3.4 5.7 + - - +
98D TRP* 3.2 19.4 + - - +
301D SAM 4.7 0.2 + - - -
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Residues in contact with SER 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D ARG 4.7 0.4 + - - -
63D MET* 4.1 10.1 - - - +
64D LEU 5.8 1.3 - - - -
65D LYS* 4.0 18.1 - - - -
87D GLU* 2.7 29.1 + - - +
92D ASN* 4.6 0.2 + - - -
93D GLY 3.4 0.2 - - - -
94D GLY* 1.3 73.4 - - - +
96D LEU* 1.3 62.1 + - - +
98D TRP* 3.5 10.8 - - - +
99D PHE* 3.1 32.3 + - - -
301D SAM 3.8 26.5 + - - -
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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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87D GLU* 3.5 35.9 - - + -
90D VAL* 3.7 31.2 - - + +
93D GLY* 3.4 16.6 + - - +
94D GLY 3.2 0.4 - - - -
95D SER* 1.3 79.3 + - - +
97D ALA* 1.3 64.6 + - - +
99D PHE* 3.3 2.6 + - - +
100D ARG* 3.0 24.4 + - - +
112D VAL* 3.6 26.4 - - + +
113D ILE 3.9 5.6 - - - +
114D GLY* 4.2 5.6 - - - -
122D CYS* 6.0 0.2 - - - -
124D ILE* 4.2 3.8 - - + -
132D ILE* 3.7 21.4 - - + +
133D THR 6.1 0.2 - - - +
134D LEU* 4.0 19.3 - - + -
301D SAM 6.2 0.2 - - - +
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Residues in contact with ALA 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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58D TRP* 4.1 10.8 - - + +
59D ARG* 5.7 3.4 - - + +
61D LEU* 3.8 23.6 - - + -
93D GLY 3.4 4.8 + - - +
94D GLY 3.4 10.1 + - - +
96D LEU* 1.3 78.6 - - - +
98D TRP* 1.3 56.4 + - - +
100D ARG* 3.3 14.8 + - - +
101D ASP* 2.9 36.1 + - - +
124D ILE* 4.2 8.5 - - + -
132D ILE* 4.0 11.0 - - - +
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Residues in contact with TRP 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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58D TRP* 3.5 49.0 - + + +
63D MET* 3.9 15.9 - - + -
65D LYS* 5.2 7.4 - - + -
70D GLN* 3.3 56.1 + - + +
73D TYR* 3.5 27.8 - + + -
74D HIS* 5.5 0.4 - - + -
77D LEU* 5.7 0.4 - - + -
94D GLY 3.2 11.3 + - - +
95D SER* 3.5 11.9 - - - +
96D LEU 3.1 0.4 - - - -
97D ALA* 1.3 74.9 - - - +
99D PHE* 1.3 103.2 + + - +
101D ASP* 3.0 3.5 + - - +
102D LEU* 3.0 54.5 + - + +
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Residues in contact with PHE 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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65D LYS* 4.0 7.6 - - - -
73D TYR* 3.9 33.9 - + + -
77D LEU* 4.2 10.1 - - + -
85D ILE* 3.6 30.7 - - + -
87D GLU* 3.7 20.9 - - + -
95D SER* 3.1 24.1 + - - +
96D LEU* 3.3 5.6 + - - +
98D TRP* 1.3 102.9 - + - +
100D ARG* 1.3 52.6 + - - +
102D LEU* 4.1 2.9 - - - +
103D THR* 2.7 39.7 + - - +
112D VAL* 4.0 16.8 - - + -
156D ILE* 6.0 0.4 - - + -
158D ILE* 3.5 33.4 - - + -
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Residues in contact with ARG 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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59D ARG* 4.0 15.8 - - - +
96D LEU 3.0 17.5 + - - +
97D ALA* 3.5 15.8 + - - +
99D PHE* 1.3 76.4 - - - +
101D ASP* 1.3 89.0 + - - +
103D THR* 2.8 17.3 + - - -
104D LYS* 3.2 26.5 + - - +
110D CYS 6.0 0.2 - - - +
112D VAL* 3.8 11.6 - - + +
124D ILE* 5.2 0.4 - - - +
128D ASP* 3.3 25.8 + - - +
129D MET* 3.6 2.6 - - - +
130D GLU* 3.1 56.7 + - - +
131D ASN* 4.2 16.2 - - + +
132D ILE* 4.1 10.4 - - + +
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Residues in contact with ASP 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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58D TRP* 3.2 28.2 + - + -
59D ARG* 2.9 32.0 + - - -
97D ALA* 2.9 18.1 + - - +
98D TRP 3.0 0.9 + - - +
100D ARG* 1.3 112.4 + - - +
102D LEU* 1.3 60.3 + - - +
104D LYS* 3.5 7.2 + - - +
105D ILE* 3.0 31.9 + - - +
105E ILE* 3.5 19.6 - - + +
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Residues in contact with LEU 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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58D TRP* 4.3 21.1 - - + -
74D HIS* 4.6 21.3 - - + -
77D LEU* 4.4 9.6 - - + -
98D TRP* 3.0 55.8 + - + +
99D PHE* 4.1 3.1 - - - +
101D ASP* 1.3 76.9 - - - +
103D THR* 1.3 60.3 + - - +
105D ILE* 3.2 5.1 + - + +
106D MET* 2.9 45.9 + - + +
58E TRP* 3.7 33.4 - - + -
105E ILE* 5.4 2.2 - - + -
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Residues in contact with THR 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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77D LEU* 3.5 24.0 - - + +
82D PRO* 5.0 1.1 - - + +
85D ILE* 4.3 3.4 - - + -
99D PHE 2.7 23.4 + - - +
100D ARG* 2.8 17.2 + - - +
102D LEU* 1.3 75.2 - - - +
104D LYS* 1.3 56.2 + - - +
106D MET* 3.4 4.3 + - - -
107D GLY 3.1 2.9 + - - -
108D ILE* 2.7 50.6 + - + +
110D CYS* 3.6 39.6 + - + +
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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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100D ARG* 3.2 34.1 + - - +
101D ASP* 3.5 8.7 - - - +
102D LEU 3.1 0.6 - - - -
103D THR* 1.3 76.8 + - - +
105D ILE* 1.3 58.6 + - + +
107D GLY* 3.0 19.1 + - - -
108D ILE 4.3 4.5 - - - -
130D GLU* 4.7 15.5 - - + +
131D ASN* 5.8 2.9 - - - +
105E ILE* 6.1 2.8 - - - +
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Residues in contact with ILE 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 ASP 3.0 16.7 + - - +
102D LEU* 3.5 9.2 - - + +
104D LYS* 1.3 77.1 - - + +
106D MET* 1.3 60.5 + - + +
107D GLY 3.2 1.1 + - - -
58E TRP* 4.3 15.3 - - + -
59E ARG* 2.8 55.1 + - - +
101E ASP* 4.1 19.7 - - + +
104E LYS* 5.4 5.4 - - + -
105E ILE* 3.3 37.9 - - + -
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Residues in contact with MET 106 (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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74D HIS* 3.4 26.0 - - + +
77D LEU* 3.8 11.0 - - - -
78D TRP* 3.2 65.5 - - + +
81D ARG* 3.2 22.2 + - - -
102D LEU* 2.9 35.3 + - + +
103D THR 3.4 1.3 + - - +
104D LYS 3.2 0.2 - - - -
105D ILE* 1.3 78.7 - - + +
107D GLY* 1.3 55.3 + - - +
108D ILE* 3.1 23.8 - - + -
58E TRP* 6.4 0.9 - - + -
59E ARG* 4.1 23.7 + - + +
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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