Contacts of the helix formed by residues 93 - 107 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B LEU* 5.1 0.2 - - - -
90B VAL* 2.9 27.7 + - - -
91B TYR 3.4 0.8 + - - -
92B ASN* 1.3 77.4 + - - +
94B GLY* 1.3 58.2 + - - +
95B SER* 3.4 2.7 - - - -
96B LEU* 2.9 25.8 + - - +
97B ALA* 2.9 13.3 + - - +
122B CYS* 4.6 0.9 - - - -
124B ILE* 3.3 19.9 - - - +
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Residues in contact with GLY 94 (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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58B TRP* 4.8 3.4 - - - -
61B LEU* 4.3 19.7 - - - -
62B ARG 3.6 18.6 - - - -
63B MET* 3.5 10.3 - - - +
92B ASN* 3.2 11.1 + - - -
93B GLY* 1.3 73.4 - - - +
95B SER* 1.3 66.0 + - - +
97B ALA* 3.8 0.5 - - - +
98B TRP* 2.9 26.5 + - - +
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Residues in contact with SER 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ARG 4.7 1.0 + - - -
63B MET* 3.8 12.9 - - - +
64B LEU* 5.2 3.8 + - - +
65B LYS* 4.0 14.0 + - - +
87B GLU* 3.1 27.8 - - - -
90B VAL 5.0 1.4 + - - -
92B ASN* 5.0 0.9 + - - -
93B GLY 5.0 1.0 - - - -
94B GLY* 1.3 73.5 + - - +
96B LEU* 1.3 63.1 + - - +
98B TRP* 3.7 2.2 - - - +
99B PHE* 3.0 33.5 + - - -
301B SAM 2.6 30.7 + - - -
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Residues in contact with LEU 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B GLU* 3.6 34.5 - - + -
89B GLY 5.2 1.3 - - - +
90B VAL* 3.8 28.9 - - + -
93B GLY* 2.9 18.4 + - - +
95B SER* 1.3 83.2 - - - +
97B ALA* 1.3 58.0 + - - +
99B PHE* 3.1 10.4 + - - +
100B ARG* 3.2 14.2 + - - +
112B VAL* 3.7 20.7 - - + +
114B GLY* 4.1 18.8 - - - +
122B CYS* 5.9 0.4 - - - -
124B ILE* 3.9 8.7 - - + -
132B ILE* 3.7 27.6 - - + -
134B LEU* 4.5 11.2 - - + -
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Residues in contact with ALA 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B TRP* 4.3 4.0 - - + -
59B ARG* 4.6 6.1 - - - +
61B LEU* 4.0 22.7 - - + -
93B GLY 2.9 15.0 + - - +
94B GLY 4.4 0.9 - - - +
96B LEU* 1.3 70.1 - - - +
98B TRP* 1.3 61.9 + - - +
100B ARG* 3.9 17.6 + - - +
101B ASP* 3.0 34.3 + - - +
124B ILE* 4.1 13.0 - - + +
128B ASP* 5.1 0.7 - - - +
132B ILE* 4.1 9.6 - - + -
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Residues in contact with TRP 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B TRP* 3.5 45.3 - + + +
63B MET* 3.8 22.7 - - + -
65B LYS* 5.5 3.8 - - + -
70B GLN* 3.4 57.8 + - + -
73B TYR* 3.7 15.0 - + + -
74B HIS* 5.2 0.2 - - + -
77B LEU* 5.9 0.2 - - + -
94B GLY 2.9 20.2 + - - +
95B SER* 3.7 3.1 - - - +
97B ALA* 1.3 76.5 - - - +
99B PHE* 1.3 111.5 + + - +
101B ASP* 3.0 11.8 + - - +
102B LEU* 3.0 51.1 + - + +
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Residues in contact with PHE 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B LYS* 4.0 8.3 - - - -
73B TYR* 3.8 33.2 - + - -
77B LEU* 4.0 17.3 - - + +
85B ILE* 3.4 31.6 - - + +
87B GLU* 3.6 18.8 - - + -
95B SER* 3.0 27.6 + - - +
96B LEU* 3.7 4.3 - - - +
98B TRP* 1.3 101.0 - + - +
100B ARG* 1.3 52.6 + - - +
102B LEU* 4.2 2.7 - - - +
103B THR* 2.7 38.6 + - - +
112B VAL* 3.9 16.6 - - + +
156B ILE* 6.0 0.9 - - + -
158B ILE* 3.4 31.0 - - + -
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Residues in contact with ARG 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ARG* 3.6 6.7 - - - +
96B LEU 3.2 14.0 + - - +
97B ALA* 3.9 8.8 - - - +
99B PHE* 1.3 77.5 - - - +
101B ASP* 1.3 83.9 + - - +
103B THR* 2.6 19.0 + - - +
104B LYS* 2.9 35.9 + - - +
110B CYS 5.5 2.0 - - - +
112B VAL* 3.7 14.5 - - + +
128B ASP* 2.9 47.9 + - - -
130B GLU* 2.9 46.2 + - - +
131B ASN* 4.5 10.5 - - + +
132B ILE* 3.5 21.0 - - + +
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Residues in contact with ASP 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ILE* 4.2 12.5 - - + +
58B TRP* 2.9 35.2 + - + -
59B ARG* 2.7 33.9 + - - -
97B ALA 3.0 18.9 + - - +
98B TRP 3.0 5.9 + - - +
100B ARG* 1.3 102.8 + - - +
102B LEU* 1.3 62.6 + - - +
104B LYS* 3.0 26.6 + - - +
105B ILE* 3.2 18.8 + - - +
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Residues in contact with LEU 102 (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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58A TRP* 4.8 13.0 - - + -
58B TRP* 4.3 14.1 - - + -
74B HIS* 4.2 28.5 - - + +
77B LEU* 4.1 15.9 - - + -
98B TRP* 3.0 69.5 + - + +
99B PHE* 4.2 1.1 - - - +
101B ASP* 1.3 75.8 - - - +
103B THR* 1.3 64.6 + - - +
105B ILE* 3.1 16.7 + - + +
106B MET* 3.0 34.8 + - - +
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Residues in contact with THR 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LEU* 3.6 21.3 - - + -
82B PRO* 4.8 1.1 - - + +
85B ILE* 4.4 1.3 - - + -
99B PHE 2.7 18.1 + - - +
100B ARG* 2.6 24.6 + - - +
102B LEU* 1.3 78.0 - - - +
104B LYS* 1.3 60.7 + - - +
106B MET* 3.2 5.4 + - - -
108B ILE* 3.1 48.1 + - + +
110B CYS* 3.6 43.5 + - + +
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Residues in contact with LYS 104 (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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105A ILE* 5.2 10.3 - - - +
59B ARG* 5.6 4.2 - - - +
100B ARG* 2.9 28.0 + - - +
101B ASP* 3.0 32.0 + - - +
103B THR* 1.3 78.7 - - - +
105B ILE* 1.3 61.5 + - + +
107B GLY* 3.4 9.7 + - - -
108B ILE 5.0 2.5 - - - -
128B ASP* 5.6 1.8 + - - -
130B GLU* 4.1 21.0 + - - +
131B ASN* 5.9 3.8 - - - +
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Residues in contact with ILE 105 (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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58A TRP* 3.9 24.7 - - + -
59A ARG* 3.1 31.9 + - - +
101A ASP* 3.2 36.6 - - + +
105A ILE* 3.0 39.7 - - + -
101B ASP 3.4 13.0 - - - +
102B LEU* 3.1 19.0 + - + +
104B LYS* 1.3 76.9 - - + +
106B MET* 1.3 59.1 + - + +
107B GLY 3.3 1.0 + - - -
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Residues in contact with MET 106 (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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59A ARG* 4.0 19.5 + - + +
74B HIS* 4.1 14.8 - - + +
77B LEU* 3.6 17.5 - - + +
78B TRP* 3.0 64.0 - - + +
81B ARG* 3.0 23.7 + - - +
102B LEU* 3.0 37.6 + - - +
103B THR* 3.2 1.1 + - - -
104B LYS 3.2 0.4 - - - -
105B ILE* 1.3 79.4 - - + +
107B GLY* 1.3 59.9 + - - +
108B ILE* 3.3 23.6 - - + -
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Residues in contact with GLY 107 (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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81B ARG* 3.7 9.3 + - - -
103B THR 3.3 2.6 + - - -
104B LYS 3.4 8.4 + - - -
105B ILE 3.3 4.4 + - - -
106B MET* 1.3 78.4 - - - +
108B ILE* 1.3 60.7 + - - +
109B ASP 3.9 1.6 + - - -
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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