Contacts of the helix formed by residues 141 - 153 (chain A) in PDB entry 3EQ6
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 LYS 141 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139A GLN 4.1 2.9 - - - +
140A MET* 1.3 81.8 - - - +
142A SER* 1.3 69.2 + - - +
143A THR 3.3 0.4 - - - +
144A ASP* 2.8 20.2 + - - +
145A ILE* 3.1 12.6 + - - +
166A GLU* 3.5 20.6 + - - +
532A LYS 3.2 23.5 + - - -
533A SER* 3.6 16.2 + - - +
534A VAL 3.5 19.5 - - - +
535A THR 3.6 27.4 - - - +
537A PRO* 4.5 9.6 - - - -
911A BCO 4.2 21.0 + - - -
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Residues in contact with SER 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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141A LYS* 1.3 74.0 - - - +
143A THR* 1.3 62.4 + - - +
145A ILE* 3.1 6.5 + - - +
146A LEU* 2.8 27.9 + - - +
166A GLU* 3.0 39.6 + - - +
169A THR* 4.3 11.2 - - - +
170A VAL* 3.8 18.0 - - - +
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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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141A LYS* 3.3 1.4 - - - +
142A SER* 1.3 78.1 + - - +
144A ASP* 1.3 67.7 + - - +
146A LEU* 3.7 13.4 - - + +
147A TYR* 3.0 26.0 + - + +
170A VAL* 5.6 0.4 - - - -
484A GLU* 5.9 2.9 - - - +
534A VAL* 4.2 17.5 + - - +
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Residues in contact with ASP 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 MET* 3.5 19.1 - - + -
141A LYS* 2.8 27.3 + - - +
143A THR* 1.3 77.7 - - - +
145A ILE* 1.3 60.9 + - - +
147A TYR* 3.4 3.6 + - - +
148A ARG* 3.1 48.7 + - - +
534A VAL 4.4 0.7 - - - +
535A THR* 2.7 27.6 + - - -
536A ALA* 2.9 21.0 + - - -
539A LYS* 4.1 6.8 + - - -
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Residues in contact with ILE 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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112A VAL* 5.1 3.6 - - + -
140A MET* 3.9 29.2 - - + -
141A LYS 3.6 11.2 - - - +
142A SER* 3.1 9.3 + - - +
144A ASP* 1.3 74.0 - - - +
146A LEU* 1.3 66.8 + - - +
148A ARG* 3.2 7.1 + - - +
149A LEU* 3.0 44.1 + - + +
157A ILE* 4.5 5.2 - - + -
163A VAL* 4.0 26.0 - - + -
166A GLU* 4.3 11.4 - - + -
167A VAL* 3.8 31.6 - - + +
170A VAL* 4.4 6.7 - - + -
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Residues in contact with LEU 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A SER 2.8 19.6 + - - +
143A THR* 3.7 13.7 - - + +
145A ILE* 1.3 74.4 - - - +
147A TYR* 1.3 63.7 + - - +
149A LEU* 3.3 2.6 + - - +
150A GLN* 2.9 67.4 + - + +
170A VAL* 4.1 21.7 - - + +
173A GLU* 3.7 32.5 - - + +
174A CYS* 3.7 15.9 - - - -
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Residues in contact with TYR 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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143A THR* 3.0 21.0 + - + +
144A ASP* 3.4 6.1 - - - +
145A ILE 3.2 0.2 - - - -
146A LEU* 1.3 76.6 - - - +
148A ARG* 1.3 75.8 + - + +
150A GLN* 4.3 4.4 - - - +
151A MET* 3.0 64.3 + - + +
220A PHE* 4.2 7.2 - + - -
227A LEU* 3.4 43.4 + - + +
228A PRO* 2.6 39.4 + - + -
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Residues in contact with ARG 148 (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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134A MET* 5.5 3.1 - - + -
136A GLY* 5.9 2.2 - - - -
140A MET* 3.6 30.4 - - - +
144A ASP* 3.1 39.8 + - - +
145A ILE* 3.2 7.9 + - - +
147A TYR* 1.3 87.9 - - + +
149A LEU* 1.3 56.0 + - + +
152A SER* 2.5 42.5 + - - -
220A PHE* 3.7 53.7 + - + +
228A PRO* 4.1 21.5 - - - +
477A GLU* 5.6 0.4 + - - -
538A TYR* 5.5 4.4 + - - -
539A LYS* 5.4 6.9 - - - +
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Residues in contact with LEU 149 (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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110A ALA* 4.1 20.2 - - + -
134A MET* 5.5 0.2 - - + -
145A ILE* 3.0 39.2 + - + +
146A LEU 3.9 0.4 - - - +
148A ARG* 1.3 75.9 - - + +
150A GLN* 1.3 55.9 + - - +
152A SER* 3.7 3.4 - - - -
153A LYS* 2.7 35.5 + - - -
154A ALA* 3.3 24.6 + - + +
157A ILE* 4.2 16.8 - - + -
167A VAL* 5.2 4.3 - - + -
170A VAL* 4.6 7.0 - - + -
171A ALA* 5.6 0.4 - - - -
174A CYS* 3.7 31.9 - - + +
177A LEU* 4.5 20.4 - - + -
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Residues in contact with GLN 150 (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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146A LEU* 2.9 51.5 + - + +
147A TYR* 4.3 4.1 - - - +
149A LEU* 1.3 78.3 - - - +
151A MET* 1.3 63.9 + - + +
153A LYS* 3.3 16.2 + - - +
173A GLU* 3.0 32.7 + - - +
174A CYS* 4.2 7.4 - - - +
175A PRO* 5.6 3.1 - - + +
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Residues in contact with MET 151 (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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108A ARG* 4.8 1.0 + - - -
147A TYR* 3.0 52.2 + - + +
148A ARG 3.8 2.9 - - - +
150A GLN* 1.3 77.6 - - + +
152A SER* 1.3 60.9 + - - +
153A LYS* 4.6 4.2 - - - +
220A PHE* 3.6 20.2 - - + -
228A PRO 3.6 23.1 - - - +
229A LYS* 4.8 1.8 - - - -
230A MET* 3.7 37.4 - - + +
428A ASP* 4.5 6.6 - - - +
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Residues in contact with SER 152 (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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108A ARG* 2.7 30.5 + - - +
134A MET* 3.4 35.0 - - - +
148A ARG 2.5 24.0 + - - -
149A LEU* 3.4 2.1 + - - -
151A MET* 1.3 76.5 - - - +
153A LYS* 1.3 69.9 + - - +
154A ALA 3.2 10.4 + - - -
220A PHE* 4.2 2.7 - - - -
230A MET* 3.8 18.6 - - - -
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Residues in contact with LYS 153 (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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108A ARG* 5.0 4.9 + - - +
149A LEU 2.7 15.0 + - - -
150A GLN 3.3 12.2 + - - +
151A MET 4.6 4.0 - - - +
152A SER* 1.3 80.3 - - - +
154A ALA* 1.3 65.3 + - - +
155A LYS* 3.4 9.9 + - - +
176A SER* 3.7 30.9 - - - +
428A ASP* 6.1 0.4 - - - -
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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
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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