Contacts of the helix formed by residues 131 - 147 (chain A) in PDB entry 3L6B
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 SER 131 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A GLU* 2.9 6.9 + - - +
130A PRO* 1.3 75.7 - - - +
132A ASP* 1.3 64.5 + - - +
133A GLU* 3.6 9.2 + - - +
134A SER* 2.9 26.5 + - - -
135A ARG* 3.0 31.3 + - - +
232A PRO* 4.1 18.6 - - - -
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Residues in contact with ASP 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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131A SER* 1.3 72.9 - - - +
133A GLU* 1.3 58.4 + - - +
135A ARG* 3.3 11.3 + - - +
136A GLU* 2.9 40.4 + - + +
228A PRO* 5.4 0.9 - - - +
229A ASN* 5.0 3.3 - - - +
241A LYS 4.1 4.3 - - - +
242A SER* 3.4 24.1 + - - -
243A SER* 3.0 37.9 + - - -
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Residues in contact with GLU 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A SER* 3.2 8.3 + - - +
132A ASP* 1.3 79.3 - - - +
134A SER* 1.3 57.0 + - - +
136A GLU* 4.0 3.4 - - - +
137A ASN* 2.9 54.7 + - - +
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Residues in contact with SER 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A CYS* 3.3 5.9 - - - +
129A GLU* 2.9 50.8 + - - +
131A SER* 2.9 17.3 + - - -
133A GLU* 1.3 73.4 - - - +
135A ARG* 1.3 67.3 + - - +
137A ASN* 4.7 4.0 - - - +
138A VAL* 2.9 33.7 + - - +
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Residues in contact with ARG 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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82A HIS* 3.0 58.4 + - + +
83A SER* 3.5 3.8 - - - +
84A SER* 3.8 16.4 - - - +
105A VAL* 4.1 1.2 - - - +
107A PRO* 3.7 20.6 - - + +
128A CYS* 3.7 24.4 - - - -
131A SER 3.0 24.3 + - - +
132A ASP* 3.6 11.1 + - - +
134A SER* 1.3 77.1 - - - +
136A GLU* 1.3 61.9 + - - +
139A ALA* 3.0 26.7 + - - +
153A PRO* 3.8 2.2 - - - +
241A LYS* 5.7 3.6 - - - +
242A SER* 3.2 19.0 + - - +
348A MLI 2.9 42.2 + - - -
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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
----------------------------------------------------------
82A HIS* 2.9 29.7 + - + +
132A ASP* 2.9 26.2 + - + +
133A GLU* 4.0 4.0 - - - +
135A ARG* 1.3 76.4 - - - +
137A ASN* 1.3 62.7 + - - +
139A ALA* 3.4 2.4 + - - +
140A LYS* 3.0 28.2 + - - +
150A MET* 4.5 3.1 - - - +
152A HIS* 2.7 32.4 + - - -
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Residues in contact with ASN 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 GLU* 2.9 43.3 + - - +
134A SER* 4.2 2.9 - - - +
136A GLU* 1.3 80.1 - - - +
138A VAL* 1.3 65.7 + - + +
140A LYS* 3.3 11.9 + - - +
141A ARG* 3.0 22.5 + - - +
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Residues in contact with VAL 138 (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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105A VAL* 3.7 26.9 - - + -
126A VAL* 4.1 10.1 - - + -
127A TYR 5.0 1.6 - - - +
128A CYS* 3.9 15.7 - - + -
134A SER* 2.9 26.7 + - - +
137A ASN* 1.3 73.7 - - + +
139A ALA* 1.3 61.0 + - - +
141A ARG* 3.2 34.7 + - - +
142A VAL* 2.9 29.0 + - + +
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Residues in contact with ALA 139 (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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80A VAL* 3.8 4.0 - - + +
81A THR 4.3 3.8 - - - +
82A HIS* 3.7 24.7 - - + -
105A VAL* 3.8 14.5 - - + +
135A ARG 3.0 21.1 + - - +
136A GLU 3.9 2.5 - - - +
138A VAL* 1.3 75.8 - - - +
140A LYS* 1.3 57.9 + - - +
143A THR* 2.8 35.3 + - - -
150A MET* 3.9 19.3 - - + -
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Residues in contact with LYS 140 (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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136A GLU 3.0 17.4 + - - +
137A ASN* 3.5 11.4 - - - +
138A VAL 3.2 0.2 - - - -
139A ALA* 1.3 76.1 - - - +
141A ARG* 1.3 62.7 + - - +
143A THR* 3.3 6.7 + - - -
144A GLU* 3.1 45.7 + - + +
150A MET* 6.0 0.9 - - - -
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Residues in contact with ARG 141 (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 VAL* 4.1 10.3 - - - +
137A ASN 3.0 13.0 + - - +
138A VAL* 3.5 35.7 - - - +
140A LYS* 1.3 77.6 - - - +
142A VAL* 1.3 68.7 + - - +
144A GLU* 3.3 10.0 + - - +
145A GLU* 2.9 77.8 + - + +
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Residues in contact with VAL 142 (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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80A VAL* 3.9 11.0 - - + -
103A TYR* 3.8 32.5 - - + -
105A VAL* 4.0 16.8 - - + -
126A VAL* 4.4 13.5 - - + -
138A VAL* 2.9 24.5 + - + +
139A ALA 4.0 2.9 - - - +
141A ARG* 1.3 91.0 - - - +
143A THR* 1.3 62.6 + - - +
145A GLU* 3.9 7.8 - - - +
146A THR* 2.8 38.7 + - + +
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Residues in contact with THR 143 (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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80A VAL* 3.4 18.8 - - - +
139A ALA 2.8 25.9 + - - -
140A LYS* 3.6 6.9 - - - -
141A ARG 3.3 0.2 - - - -
142A VAL* 1.3 76.7 - - - +
144A GLU* 1.3 58.7 + - + +
146A THR* 3.9 4.5 - - - -
147A GLU* 3.0 25.8 + - - -
148A GLY 3.1 32.1 + - - +
150A MET* 3.8 25.9 - - + +
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Residues in contact with GLU 144 (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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140A LYS* 3.1 45.0 + - + +
141A ARG* 3.3 10.0 + - - +
143A THR* 1.3 78.4 - - + +
145A GLU* 1.3 64.3 + - + +
147A GLU* 3.3 17.8 + - - +
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Residues in contact with GLU 145 (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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141A ARG* 2.9 62.4 + - + +
142A VAL* 3.9 7.7 - - - +
144A GLU* 1.3 77.8 - - + +
146A THR* 1.3 62.6 + - + +
147A GLU* 3.6 4.0 + - - +
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Residues in contact with THR 146 (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 LYS* 4.1 12.6 - - - +
78A ALA* 4.4 5.0 - - - +
80A VAL* 3.6 12.1 - - - +
103A TYR* 3.7 49.6 - - + +
142A VAL* 2.8 25.9 + - + +
143A THR 3.4 0.7 + - - -
145A GLU* 1.3 78.9 - - + +
147A GLU* 1.3 68.8 + - - +
148A GLY* 3.2 13.4 + - - -
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Residues in contact with GLU 147 (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 LYS* 3.4 44.9 + - + +
143A THR 3.0 9.8 + - - -
144A GLU* 3.3 12.3 + - - +
145A GLU 3.3 4.4 - - - +
146A THR* 1.3 80.7 - - - +
148A GLY* 1.3 62.7 + - - +
149A ILE* 5.5 0.5 - - - +
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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