Contacts of the helix formed by residues 93 - 106 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90F VAL* 3.2 27.0 + - - -
91F TYR 3.4 0.8 + - - -
92F ASN* 1.3 78.1 - - - +
94F GLY* 1.3 64.6 + - - +
95F SER* 3.1 4.0 - - - -
96F LEU* 2.8 22.8 + - - +
97F ALA 3.0 10.0 + - - -
122F CYS* 4.6 1.8 - - - -
124F ILE* 3.5 19.3 - - - +
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Residues in contact with GLY 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58F TRP* 4.5 2.6 - - - -
61F LEU* 4.2 15.9 - - - +
62F ARG 3.5 18.2 - - - -
63F MET* 3.9 10.0 - - - +
92F ASN* 3.3 14.1 + - - +
93F GLY* 1.3 76.2 - - - +
95F SER* 1.3 61.5 + - - +
97F ALA* 3.1 6.8 + - - +
98F TRP* 2.9 23.4 + - - +
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Residues in contact with SER 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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62F ARG 4.7 0.6 + - - -
63F MET* 4.2 7.6 - - - +
64F LEU* 4.8 10.1 + - - +
65F LYS* 3.4 35.8 - - - +
87F GLU* 3.3 24.8 + - - -
90F VAL 5.8 2.2 + - - -
92F ASN* 5.3 0.8 - - - +
93F GLY 3.1 1.2 - - - -
94F GLY* 1.3 75.6 - - - +
96F LEU* 1.3 58.7 + - - +
98F TRP* 3.2 8.4 + - - +
99F PHE* 3.0 38.4 + - - -
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Residues in contact with LEU 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87F GLU* 3.6 37.9 - - + -
89F GLY 5.5 0.7 - - - +
90F VAL* 4.2 22.2 - - + -
93F GLY* 2.8 13.0 + - - +
95F SER* 1.3 82.0 - - - +
97F ALA* 1.3 60.7 + - - +
99F PHE* 3.6 1.0 + - + -
100F ARG* 3.2 23.6 + - - +
112F VAL* 3.7 29.9 - - + +
113F ILE 4.7 0.2 - - - +
114F GLY* 3.9 23.6 - - - +
122F CYS* 6.3 0.4 - - - -
124F ILE* 4.5 4.5 - - + -
132F ILE* 4.2 17.0 - - + +
134F LEU* 3.9 20.2 - - + -
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Residues in contact with ALA 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58F TRP* 3.4 7.6 + - + -
61F LEU* 4.0 26.0 - - + -
93F GLY 3.0 10.5 + - - +
94F GLY 3.1 7.4 + - - +
96F LEU* 1.3 74.8 - - - +
98F TRP* 1.3 58.3 + - - +
100F ARG* 3.4 22.1 + - - +
101F ASP* 3.1 34.5 + - - +
124F ILE* 4.3 10.2 - - + +
132F ILE* 5.1 0.4 - - - -
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Residues in contact with TRP 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58F TRP* 3.9 42.8 - + + +
63F MET* 4.2 20.6 - - + -
65F LYS* 6.0 2.9 - - + -
70F GLN* 3.4 55.5 - - + +
73F TYR* 3.6 27.4 - + + -
74F HIS* 4.1 2.5 - - + -
77F LEU* 5.6 0.4 - - + -
94F GLY 2.9 12.1 + - - +
95F SER* 3.4 10.5 - - - +
96F LEU 3.1 0.2 - - - -
97F ALA* 1.3 75.3 - - - +
99F PHE* 1.3 82.1 - + - +
100F ARG 3.1 1.1 - - - -
101F ASP* 3.0 1.9 + - - +
102F LEU* 2.8 73.3 + - + +
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Residues in contact with PHE 99 (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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65F LYS* 4.4 11.4 - - - -
73F TYR* 3.8 27.4 - + - -
77F LEU* 3.9 35.9 - - + -
85F ILE* 3.7 23.8 - - + -
87F GLU* 4.3 12.6 - - + -
95F SER* 3.0 27.1 + - - +
96F LEU* 4.0 3.6 - - - +
98F TRP* 1.3 90.5 - + - +
100F ARG* 1.3 58.3 + - - +
102F LEU* 4.1 2.6 - - - +
103F THR* 2.9 33.0 + - - +
112F VAL* 3.9 19.7 - - + +
156F ILE* 6.0 0.2 - - + -
158F ILE* 3.3 35.0 - - + -
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Residues in contact with ARG 100 (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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59F ARG* 4.3 7.1 - - - +
96F LEU 3.2 17.7 + - - +
97F ALA* 3.4 32.9 + - - +
98F TRP 3.1 1.0 - - - -
99F PHE* 1.3 73.0 - - - +
101F ASP* 1.3 90.5 + - - +
102F LEU 2.9 3.5 + - - -
103F THR* 3.3 5.8 + - - -
104F LYS* 3.1 35.9 + - + +
110F CYS 6.1 0.4 - - - -
112F VAL* 3.9 7.7 - - + +
124F ILE* 5.9 1.6 - - - +
128F ASP* 2.6 52.3 + - - +
130F GLU* 2.8 34.1 + - - +
131F ASN* 4.1 19.7 - - + +
132F ILE* 4.7 7.0 - - + +
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Residues in contact with ASP 101 (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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105C ILE* 4.5 11.8 - - + +
58F TRP* 3.3 33.0 + - + +
59F ARG* 3.1 29.4 + - - -
97F ALA* 3.1 19.5 + - - +
98F TRP 3.0 4.0 + - - +
100F ARG* 1.3 109.5 + - - +
102F LEU* 1.3 57.0 + - - +
104F LYS* 3.6 15.6 - - - +
105F ILE* 3.1 27.0 - - - +
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Residues in contact with LEU 102 (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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58C TRP* 3.4 36.8 - - + -
59C ARG* 6.2 0.2 - - - -
58F TRP* 6.4 2.5 - - + -
74F HIS* 4.6 15.7 - - + -
77F LEU* 4.5 9.6 - - + -
98F TRP* 2.8 64.4 + - + +
99F PHE* 4.1 3.4 - - - +
100F ARG 2.9 1.4 + - - -
101F ASP* 1.3 78.0 - - - +
103F THR* 1.3 65.3 + - - +
104F LYS 3.0 1.7 + - - -
105F ILE* 3.3 8.7 + - + -
106F MET* 3.1 42.3 + - + +
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Residues in contact with THR 103 (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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77F LEU* 3.7 24.2 - - + -
82F PRO* 4.8 1.6 - - + +
85F ILE* 5.0 2.2 - - + -
99F PHE 2.9 20.7 + - - +
100F ARG* 3.3 9.7 + - - -
102F LEU* 1.3 76.2 - - - +
104F LYS* 1.3 58.9 + - - +
106F MET* 3.2 8.0 + - - -
107F GLY 3.2 3.3 + - - -
108F ILE* 2.9 47.6 + - + +
110F CYS* 3.3 44.3 + - + +
112F VAL* 5.0 0.2 - - - +
131F ASN* 5.9 0.3 + - - -
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Residues in contact with LYS 104 (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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105C ILE* 6.0 5.8 - - + -
100F ARG* 3.1 31.6 + - + +
101F ASP* 3.6 14.6 - - - +
102F LEU 3.0 0.4 - - - -
103F THR* 1.3 76.5 + - - +
105F ILE* 1.3 57.4 + - + +
107F GLY* 2.9 20.8 + - - -
108F ILE 4.4 4.0 - - - -
130F GLU* 3.4 31.9 + - - +
131F ASN* 5.2 11.5 - - - +
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Residues in contact with ILE 105 (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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58C TRP* 4.4 16.4 - - + -
59C ARG* 3.0 36.3 + - - +
101C ASP* 3.7 39.7 - - + +
104C LYS* 5.4 7.4 - - + -
105C ILE* 3.5 45.1 - - + -
101F ASP 3.1 16.6 - - - +
102F LEU* 3.3 7.8 + - + +
104F LYS* 1.3 74.3 - - + +
106F MET* 1.3 56.9 + - - +
107F GLY 3.2 1.9 + - - -
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Residues in contact with MET 106 (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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59C ARG* 4.0 14.8 - - + +
74F HIS* 3.1 50.7 - - + +
77F LEU* 4.0 15.3 - - + -
78F TRP* 3.8 45.0 - - + -
81F ARG* 3.3 17.2 + - - -
102F LEU* 3.1 32.6 + - + +
103F THR 3.6 5.6 - - - +
104F LYS 3.1 0.8 - - - -
105F ILE* 1.3 78.8 - - - +
107F GLY* 1.3 55.2 + - - +
108F ILE* 3.0 24.0 + - + -
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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