Contacts of the helix formed by residues 93 - 106 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A VAL* 3.4 27.1 + - - -
91A TYR 3.3 4.6 - - - -
92A ASN* 1.3 80.3 + - - +
94A GLY* 1.3 64.6 + - - +
95A SER* 3.4 2.7 - - - -
96A LEU* 3.2 19.2 + - - +
97A ALA 3.3 2.6 + - - -
122A CYS* 4.5 0.7 - - - -
124A ILE* 3.1 28.3 - - - +
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Residues in contact with GLY 94 (chain A).
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* 4.7 2.3 - - - -
61A LEU* 3.8 15.7 - - - +
62A ARG 3.3 20.0 - - - -
63A MET* 3.8 8.7 - - - +
90A VAL 5.2 0.2 + - - -
92A ASN* 3.2 14.9 + - - +
93A GLY* 1.3 77.0 - - - +
95A SER* 1.3 62.9 + - - +
96A LEU 3.2 0.7 + - - -
97A ALA* 3.2 6.4 + - - +
98A TRP* 3.1 19.6 + - - +
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Residues in contact with SER 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ARG 4.3 0.6 + - - -
63A MET* 3.7 16.5 - - - +
64A LEU 5.8 1.1 - - - +
65A LYS* 4.2 13.9 - - - -
87A GLU* 3.4 22.1 + - - +
90A VAL 5.0 2.1 + - - -
92A ASN* 5.2 0.2 + - - -
93A GLY 4.8 1.0 - - - -
94A GLY* 1.3 74.8 + - - +
96A LEU* 1.3 66.9 + - - +
98A TRP* 3.6 3.5 - - - +
99A PHE* 3.0 32.4 + - - -
301A SAM 3.0 34.7 + - - -
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Residues in contact with LEU 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A GLU* 3.6 34.5 - - + -
90A VAL* 3.3 46.9 - - + -
93A GLY* 3.2 15.4 + - - +
94A GLY 3.1 0.6 - - - -
95A SER* 1.3 85.2 + - - +
97A ALA* 1.3 63.3 + - - +
99A PHE* 3.5 2.8 + - + +
100A ARG* 3.3 22.0 + - - +
112A VAL* 3.9 24.3 - - + +
113A ILE 4.1 6.3 - - - +
114A GLY* 4.5 5.6 - - - -
124A ILE* 3.9 12.3 - - + -
132A ILE* 3.7 19.9 - - + +
134A LEU* 4.8 5.4 - - + -
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Residues in contact with ALA 97 (chain A).
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* 4.3 9.2 - - + +
61A LEU* 3.5 32.8 - - + -
93A GLY 3.3 2.9 + - - +
94A GLY 3.2 4.3 + - - +
96A LEU* 1.3 78.1 - - - +
98A TRP* 1.3 57.7 + - - +
100A ARG* 3.2 7.3 + - - +
101A ASP* 2.8 41.5 + - - +
124A ILE* 4.3 6.7 - - + +
128A ASP* 5.2 6.1 - - - +
132A ILE* 4.2 11.8 - - + +
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Residues in contact with TRP 98 (chain A).
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* 3.4 48.8 - + + +
63A MET* 3.9 26.7 - - + -
65A LYS* 5.1 2.7 - - + -
70A GLN* 3.4 57.2 + - + -
73A TYR* 3.6 16.6 - + + -
74A HIS* 4.3 4.5 - - + -
77A LEU* 5.1 2.0 - - + -
94A GLY 3.1 12.8 + - - +
95A SER 3.6 6.3 - - - +
96A LEU 3.3 0.2 - - - -
97A ALA* 1.3 76.2 - - - +
99A PHE* 1.3 108.2 + + - +
101A ASP* 3.8 1.0 - - - +
102A LEU* 3.0 54.8 + - + +
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Residues in contact with PHE 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A LYS* 3.9 19.1 - - + -
73A TYR* 3.8 21.5 - + + -
77A LEU* 4.2 19.1 - - + +
85A ILE* 4.1 20.5 - - + +
87A GLU* 3.2 33.0 - - + -
95A SER* 3.0 25.6 + - - +
96A LEU* 3.8 6.7 - - + +
98A TRP* 1.3 102.2 - + - +
100A ARG* 1.3 52.4 + - - +
102A LEU* 4.0 3.1 - - - +
103A THR* 2.5 37.6 + - - +
112A VAL* 4.3 14.5 - - + +
158A ILE* 3.6 24.0 - - + -
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Residues in contact with ARG 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ARG* 4.2 1.6 - - - +
96A LEU 3.3 9.5 + - - +
97A ALA* 3.2 11.5 + - - +
99A PHE* 1.3 77.4 - - - +
101A ASP* 1.3 91.1 + - - +
103A THR* 2.6 21.2 + - - +
104A LYS* 3.0 35.1 + - + +
110A CYS 4.8 2.5 - - - +
112A VAL* 3.9 12.1 - - + +
128A ASP* 3.0 50.4 + - - -
130A GLU* 2.8 44.0 + - - +
131A ASN* 3.8 18.4 - - + +
132A ILE* 3.3 19.9 - - + +
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Residues in contact with ASP 101 (chain A).
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* 3.4 28.1 + - + -
59A ARG* 3.2 18.4 + - - -
97A ALA* 2.8 20.0 + - - +
98A TRP 3.9 0.4 - - - +
100A ARG* 1.3 108.7 + - - +
102A LEU* 1.3 61.5 + - - +
104A LYS* 3.5 8.7 + - - +
105A ILE* 3.2 29.3 + - - +
128A ASP* 4.8 0.3 - - - +
105B ILE* 3.2 29.8 - - + +
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Residues in contact with LEU 102 (chain A).
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* 5.2 6.0 - - + -
74A HIS* 3.7 19.3 - - + -
77A LEU* 4.2 15.7 - - + -
98A TRP* 3.0 59.5 + - + +
99A PHE* 4.0 3.6 - - - +
101A ASP* 1.3 73.6 - - - +
103A THR* 1.3 59.3 + - - +
104A LYS 3.1 2.4 + - - -
105A ILE* 3.3 7.3 + - + +
106A MET* 2.8 76.1 + - + +
58B TRP* 4.8 17.5 - - + -
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Residues in contact with THR 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A LEU* 4.5 13.7 - - + +
82A PRO* 4.8 1.6 - - + +
85A ILE* 4.5 3.8 - - + -
99A PHE 2.5 25.1 + - - +
100A ARG* 2.6 20.0 + - - +
102A LEU* 1.3 76.6 - - - +
104A LYS* 1.3 54.6 + - - +
106A MET* 3.9 1.6 - - - -
108A ILE* 2.7 70.1 + - + +
110A CYS* 3.5 35.6 + - + +
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Residues in contact with LYS 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A ARG* 3.0 37.1 + - + +
101A ASP* 3.8 8.7 - - - +
102A LEU 3.1 0.2 - - - -
103A THR* 1.3 74.5 - - - +
105A ILE* 1.3 63.3 + - + +
107A GLY* 2.9 21.5 + - - -
108A ILE 4.8 1.8 - - - +
130A GLU* 3.9 22.8 + - + +
131A ASN* 5.8 4.9 - - - +
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Residues in contact with ILE 105 (chain A).
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* 5.6 0.7 - - + -
101A ASP 3.2 13.6 + - - +
102A LEU* 3.6 11.0 - - + +
104A LYS* 1.3 81.1 - - + +
106A MET* 1.3 62.7 + - + +
107A GLY* 3.1 0.9 + - - -
58B TRP* 4.0 28.0 - - + -
59B ARG* 3.2 43.9 + - + +
101B ASP* 4.2 14.1 - - + +
104B LYS* 5.2 9.9 - - - +
105B ILE* 3.0 46.0 - - + -
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Residues in contact with MET 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A HIS* 3.3 45.3 - - + +
77A LEU* 3.9 11.4 - - - -
78A TRP* 3.8 35.2 - - + +
81A ARG* 3.4 17.7 + - - -
102A LEU* 2.8 49.6 + - + +
104A LYS 3.2 0.2 - - - -
105A ILE* 1.3 77.4 - - + +
107A GLY* 1.3 56.7 + - - +
108A ILE* 3.4 30.5 - - + -
59B ARG* 4.1 15.7 - - + +
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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