Contacts of the helix formed by residues 124 - 137 (chain A) in PDB entry 2B4M
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 THR 124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A TRP* 1.3 78.9 - - - +
125A GLN* 1.3 60.0 + - - +
126A ASP* 3.4 17.9 + - - -
127A GLU* 3.0 29.2 + - - +
128A MET* 3.1 22.0 + - - +
248A MET* 3.4 13.8 - - - +
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Residues in contact with GLN 125 (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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73A THR* 3.2 35.8 - - - +
74A PRO* 3.5 27.6 - - + +
124A THR* 1.3 74.0 - - - +
126A ASP* 1.3 63.3 + - - +
128A MET* 3.5 5.1 + - - +
129A GLY* 3.0 21.1 + - - -
132A MET* 4.4 5.2 - - - +
248A MET* 3.6 24.5 - - + +
249A THR 5.0 2.5 - - - +
250A GLY 3.6 19.3 + - - -
251A VAL* 4.0 1.8 - - - +
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Residues in contact with ASP 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A THR* 3.7 18.1 + - - -
125A GLN* 1.3 75.0 + - - +
127A GLU* 1.3 66.9 + - - +
128A MET 3.3 0.2 - - - -
129A GLY* 3.6 3.6 - - - +
130A GLU* 2.9 26.2 + - - +
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Residues in contact with GLU 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A TRP* 3.2 8.8 - - + +
124A THR* 3.0 41.4 + - - +
126A ASP* 1.3 84.4 - - - +
128A MET* 1.3 58.1 + - - +
130A GLU* 3.1 24.2 - - - +
131A ILE 3.9 0.9 + - - -
148A TYR* 3.3 28.2 - - - +
152A HIS* 4.2 17.5 + - + -
155A GLN* 2.8 33.2 + - - -
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Residues in contact with MET 128 (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 PRO* 4.2 13.0 - - - -
99A ILE* 4.1 14.1 - - + -
123A TRP* 3.7 31.1 - - + +
124A THR 3.1 12.7 + - - +
125A GLN 3.7 8.3 - - - +
127A GLU* 1.3 77.2 - - - +
129A GLY* 1.3 55.8 + - - +
131A ILE* 3.0 9.0 + - - +
132A MET* 2.9 36.0 + - + +
180A SER* 3.4 44.6 - - - +
181A GLU* 4.4 2.0 - - - +
183A ALA* 3.7 14.8 - - + -
184A SER* 4.4 5.4 - - - -
248A MET* 3.8 20.2 - - + -
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Residues in contact with GLY 129 (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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76A TRP* 6.0 0.9 - - - -
79A SER* 5.9 0.9 - - - -
125A GLN 3.0 13.4 + - - -
126A ASP* 3.4 6.0 + - - -
128A MET* 1.3 71.1 - - - +
130A GLU* 1.3 65.4 + - - +
131A ILE 3.0 1.8 - - - -
132A MET* 3.7 19.2 - - - +
133A ILE* 2.9 43.2 + - - +
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Residues in contact with GLU 130 (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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126A ASP 2.9 13.2 + - - +
127A GLU* 3.1 16.3 - - - +
129A GLY* 1.3 74.8 - - - +
131A ILE* 1.3 57.6 + - - +
133A ILE* 4.8 2.3 - - - +
134A LYS* 3.9 29.0 + - - +
144A VAL* 4.5 2.2 - - - +
148A TYR* 3.0 17.2 - - + -
151A LYS* 3.2 33.4 + - - +
152A HIS* 2.2 43.3 + - - -
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Residues in contact with ILE 131 (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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123A TRP* 3.6 31.6 - - + -
127A GLU 4.4 0.4 - - - +
128A MET 3.0 9.0 + - - +
129A GLY 3.0 0.4 - - - -
130A GLU* 1.3 75.9 - - - +
132A MET* 1.3 66.2 + - - +
133A ILE 3.2 2.5 + - - -
134A LYS* 3.2 4.5 + - - +
135A VAL* 3.0 32.8 + - + +
141A PRO* 5.4 2.7 - - + +
144A VAL* 3.8 24.0 - - + -
145A ALA* 4.9 6.1 - - + +
148A TYR* 3.7 32.8 - - + -
182A ILE 5.3 0.2 - - - +
183A ALA* 3.8 24.9 - - + +
186A ASN* 6.2 1.6 - - + -
187A VAL* 4.0 15.9 - - + -
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Residues in contact with MET 132 (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 PRO* 3.9 5.4 - - + +
75A HIS* 3.6 43.1 - - - +
76A TRP* 3.8 19.5 - - + +
125A GLN 4.4 4.7 - - - +
128A MET* 2.9 30.9 + - + +
129A GLY* 3.7 26.0 - - - +
131A ILE* 1.3 73.0 - - - +
133A ILE* 1.3 57.6 + - - +
135A VAL* 3.5 6.4 + - - +
136A GLU* 3.1 28.9 + - - +
179A ASP* 3.7 26.4 - - + +
180A SER* 3.8 23.8 - - - -
183A ALA* 4.1 2.0 - - + -
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Residues in contact with ILE 133 (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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76A TRP* 4.0 22.0 - - + -
79A SER* 3.9 25.6 - - - +
129A GLY* 2.9 28.5 + - - +
130A GLU* 4.8 2.7 - - - +
132A MET* 1.3 73.0 - - - +
134A LYS* 1.3 62.9 + - + +
136A GLU* 3.4 5.2 + - - +
137A GLU* 2.9 50.4 + - + +
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Residues in contact with LYS 134 (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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130A GLU* 3.9 20.7 + - - +
131A ILE 3.2 8.1 + - - +
133A ILE* 1.3 80.0 - - + +
135A VAL* 1.3 59.4 + - - +
137A GLU* 3.4 17.1 - - + +
139A GLU* 3.0 53.1 + - + +
144A VAL* 3.8 21.5 - - + -
147A GLU* 4.4 15.2 + - - +
151A LYS* 5.0 11.9 - - - +
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Residues in contact with VAL 135 (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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131A ILE* 3.0 31.9 + - + +
132A MET* 3.9 7.0 - - - +
134A LYS* 1.3 74.8 - - - +
136A GLU* 1.3 59.9 + - - +
138A GLY* 2.8 22.0 + - - -
139A GLU 3.5 13.5 - - - +
141A PRO* 3.9 40.8 - - + -
144A VAL* 4.0 9.0 - - + -
179A ASP* 5.4 8.3 - - - +
182A ILE* 4.9 12.1 - - + -
183A ALA* 6.2 0.2 - - - -
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Residues in contact with GLU 136 (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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54A THR* 5.1 1.6 + - - -
76A TRP* 3.1 50.9 + - + +
80A ARG* 3.9 22.6 + - - +
132A MET 3.1 17.0 + - - +
133A ILE* 3.8 4.9 - - - +
135A VAL* 1.3 71.8 - - - +
137A GLU* 1.3 58.4 + - + +
138A GLY* 3.0 9.1 + - - -
179A ASP* 4.1 9.5 - - - +
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Residues in contact with GLU 137 (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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133A ILE* 2.9 43.0 + - + +
134A LYS* 3.4 15.9 - - - +
136A GLU* 1.3 73.8 - - - +
138A GLY* 1.3 58.5 + - - +
139A GLU* 3.5 8.2 + - - +
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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