Contacts of the helix formed by residues 93 - 107 (chain L) in PDB entry 2BM8
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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90L VAL* 3.1 27.2 + - - -
91L TYR 3.3 1.0 - - - -
92L ASN* 1.3 79.4 + - - +
94L GLY* 1.3 64.9 + - - +
95L SER* 3.3 3.6 - - - -
96L LEU* 3.1 11.4 + - - +
97L ALA* 3.1 18.4 + - - +
122L CYS* 4.2 0.9 - - - -
124L ILE* 3.5 21.4 - - - +
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Residues in contact with GLY 94 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58L TRP* 4.6 4.2 - - - +
61L LEU* 4.1 15.3 - - - -
62L ARG 3.4 21.3 - - - -
63L MET* 3.8 8.9 - - - +
90L VAL 4.8 0.2 + - - -
92L ASN* 3.2 14.2 + - - -
93L GLY* 1.3 77.9 - - - +
95L SER* 1.3 57.3 + - - +
97L ALA* 3.3 3.5 + - - +
98L TRP* 3.0 26.2 + - - +
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Residues in contact with SER 95 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62L ARG 4.7 0.4 + - - -
63L MET* 4.0 11.8 - - - +
64L LEU 6.0 2.0 - - - +
65L LYS* 3.9 31.4 + - - -
87L GLU* 3.5 17.8 + - - -
90L VAL 5.1 5.0 + - - -
92L ASN* 5.0 0.2 + - - -
93L GLY 5.0 0.7 - - - -
94L GLY* 1.3 73.0 + - - +
96L LEU* 1.3 70.9 + - - +
98L TRP* 3.5 9.0 - - - +
99L PHE* 2.9 33.5 + - - -
160L ASN* 5.4 0.3 + - - -
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Residues in contact with LEU 96 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87L GLU* 3.5 37.2 - - + -
90L VAL* 3.6 41.7 - - + +
93L GLY* 3.1 12.7 + - - +
95L SER* 1.3 85.7 + - - +
97L ALA* 1.3 60.6 + - - +
99L PHE* 3.5 1.1 + - + -
100L ARG* 3.2 23.7 + - - +
112L VAL* 3.7 29.7 - - + +
114L GLY* 4.1 13.0 - - - -
122L CYS* 5.5 0.2 - - - -
124L ILE* 4.3 8.3 - - + -
132L ILE* 4.1 9.3 - - + +
134L LEU* 4.5 14.6 - - + -
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Residues in contact with ALA 97 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58L TRP* 4.4 3.1 - - + -
61L LEU* 3.9 22.4 - - + -
93L GLY 3.1 11.5 + - - +
94L GLY 3.7 7.4 - - - +
96L LEU* 1.3 74.3 - - - +
98L TRP* 1.3 59.6 + - - +
100L ARG* 3.5 14.9 + - - +
101L ASP* 2.9 40.1 + - - +
124L ILE* 4.3 12.1 - - + -
128L ASP* 5.6 0.9 - - - +
132L ILE* 4.1 10.1 - - + -
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Residues in contact with TRP 98 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58L TRP* 3.5 50.3 - + + +
63L MET* 3.9 21.1 - - + -
65L LYS* 5.4 2.2 - - + -
70L GLN* 3.5 54.5 + - + -
73L TYR* 3.6 16.8 - + + -
74L HIS* 5.2 0.7 - - + -
77L LEU* 5.3 0.2 - - + -
94L GLY 3.0 16.7 + - - +
95L SER* 3.2 6.9 + - - +
97L ALA* 1.3 74.2 - - - +
99L PHE* 1.3 107.9 + + - +
101L ASP* 3.3 2.8 + - - +
102L LEU* 2.9 65.3 + - + +
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Residues in contact with PHE 99 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65L LYS* 4.1 13.0 - - - -
73L TYR* 3.9 24.7 - + + -
77L LEU* 4.2 12.3 - - + -
85L ILE* 3.9 28.3 - - + -
87L GLU* 3.7 19.7 - - + -
95L SER* 2.9 29.4 + - - +
96L LEU* 3.8 5.6 - - - +
98L TRP* 1.3 101.5 - + - +
100L ARG* 1.3 61.2 + - - +
102L LEU* 3.8 3.0 - - - +
103L THR* 2.9 32.4 + - - +
112L VAL* 4.0 15.5 - - + -
156L ILE* 6.0 0.2 - - + -
158L ILE* 3.6 32.3 - - + -
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Residues in contact with ARG 100 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59L ARG* 4.0 0.8 - - - +
96L LEU 3.2 15.8 + - - +
97L ALA* 3.7 14.1 + - - +
99L PHE* 1.3 78.9 - - - +
101L ASP* 1.3 93.6 + - - +
103L THR* 2.9 19.6 + - - -
104L LYS* 3.1 22.5 + - - +
110L CYS 5.2 1.8 - - - +
112L VAL* 3.8 11.8 - - + +
128L ASP* 3.0 47.5 + - - +
130L GLU* 2.9 53.8 + - - +
131L ASN* 4.2 15.5 - - + +
132L ILE* 3.5 17.7 - - + +
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Residues in contact with ASP 101 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105I ILE* 4.1 14.6 - - + +
58L TRP* 3.1 35.2 + - + +
59L ARG* 2.9 31.1 + - - +
97L ALA* 2.9 20.0 + - - +
98L TRP 3.7 3.6 - - - +
100L ARG* 1.3 104.6 + - - +
102L LEU* 1.3 62.5 + - - +
104L LYS* 3.3 6.9 + - - +
105L ILE* 3.1 28.8 + - - +
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Residues in contact with LEU 102 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58I TRP* 3.8 35.7 - - + -
58L TRP* 5.2 6.7 - - + -
74L HIS* 4.0 20.2 - - + -
77L LEU* 3.9 18.8 - - + -
98L TRP* 2.9 60.3 + - + +
99L PHE* 3.8 4.0 - - - +
101L ASP* 1.3 76.9 - - - +
103L THR* 1.3 57.2 + - - +
105L ILE* 3.2 9.2 + - + +
106L MET* 3.0 44.8 + - + +
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Residues in contact with THR 103 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77L LEU* 3.8 24.5 - - + -
82L PRO* 4.8 1.6 - - + +
85L ILE* 4.4 2.2 - - + -
99L PHE 2.9 21.0 + - - +
100L ARG* 2.9 15.8 + - - -
102L LEU* 1.3 75.2 - - - +
104L LYS* 1.3 59.4 + - - +
106L MET* 3.4 4.8 + - - -
107L GLY 3.1 3.3 + - - -
108L ILE* 2.8 49.1 + - + +
110L CYS* 3.7 42.8 + - + +
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Residues in contact with LYS 104 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105I ILE* 6.0 4.9 - - + -
100L ARG* 3.1 25.3 + - - +
101L ASP* 3.6 8.1 - - - +
102L LEU 3.2 0.2 - - - -
103L THR* 1.3 76.3 + - - +
105L ILE* 1.3 64.9 + - + +
107L GLY* 3.2 12.4 + - - -
108L ILE 4.5 3.6 - - - -
130L GLU* 4.7 22.8 + - - +
131L ASN* 5.7 4.7 - - - +
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Residues in contact with ILE 105 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58I TRP* 4.2 20.4 - - + -
59I ARG* 2.9 44.3 + - - +
101I ASP* 4.0 27.6 - - + +
102I LEU* 5.7 0.9 - - + -
105I ILE* 3.5 34.8 - - + -
58L TRP* 5.1 6.1 - - + -
101L ASP* 3.1 21.4 + - + +
102L LEU* 3.2 10.3 + - + +
104L LYS* 1.3 79.5 - - + +
106L MET* 1.3 60.5 + - + +
107L GLY* 3.4 0.5 + - - -
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Residues in contact with MET 106 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58I TRP* 6.3 0.7 - - + -
59I ARG* 4.4 15.4 + - + +
74L HIS* 3.2 57.9 - - + +
77L LEU* 4.0 13.7 - - + -
78L TRP* 3.9 33.3 - - + +
81L ARG* 3.7 13.9 + - - -
102L LEU* 3.0 34.8 + - + +
103L THR 3.9 1.6 - - - +
104L LYS 3.3 0.4 - - - -
105L ILE* 1.3 76.5 - - + +
107L GLY* 1.3 61.2 + - - +
108L ILE* 3.6 29.3 + - + -
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Residues in contact with GLY 107 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81L ARG* 3.3 13.7 + - - -
103L THR 3.1 3.0 + - - -
104L LYS 3.2 8.6 + - - -
105L ILE 3.2 4.8 + - - -
106L MET* 1.3 78.9 - - - +
108L ILE* 1.3 60.4 + - - +
109L ASP 3.9 1.4 + - - -
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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
------------------------------------------------------------
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