Contacts of the helix formed by residues 142 - 155 (chain A) in PDB entry 6M04
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 ASP 142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A ASN* 4.3 1.0 + - - -
141A LEU* 1.3 73.5 - - - +
143A PHE* 1.3 88.6 + - - +
144A GLN* 3.2 5.2 - - - -
145A GLN* 3.0 35.1 + - - +
146A TYR* 3.2 13.4 + - - -
138B LYS* 5.2 6.6 + - - +
141B LEU 4.0 13.0 + - - +
142B ASP* 4.6 2.9 - - - -
143B PHE* 4.6 6.9 + - - +
146B TYR* 3.3 31.2 + - - +
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Residues in contact with PHE 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 LEU 4.0 0.2 + - - -
142A ASP* 1.3 85.3 + - - +
144A GLN* 1.3 59.1 + - - +
146A TYR* 3.0 24.9 + + + +
147A VAL* 3.1 37.7 + - + +
143B PHE* 4.1 31.9 - + + -
142F ASP* 5.4 1.0 + - - -
143F PHE* 3.6 40.2 - + + -
144F GLN* 4.8 19.3 - - + -
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Residues in contact with GLN 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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142A ASP* 3.2 3.8 + - - +
143A PHE* 1.3 80.3 - - - +
145A GLN* 1.3 59.6 + - - +
147A VAL* 3.2 28.9 - - - +
148A PHE* 3.0 24.8 + - - +
53B VAL* 3.5 17.6 - - - +
54B CYS 4.5 7.8 + - - +
55B LEU* 5.3 1.1 - - + -
143B PHE* 3.2 32.8 - - + -
146B TYR* 3.5 53.6 - - + +
147B VAL* 5.1 2.4 - - - +
150B ASN* 4.3 13.7 - - - +
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Residues in contact with GLN 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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140A ASN 4.5 0.2 + - - -
141A LEU* 3.4 30.0 - - + +
142A ASP* 3.0 48.0 - - - +
144A GLN* 1.3 75.4 + - - +
146A TYR* 1.3 60.8 + - - +
148A PHE* 3.7 7.5 - - - +
149A ILE* 2.9 31.5 + - - +
347A ILE* 3.9 17.6 - - + +
55B LEU* 3.8 21.1 - - + -
137B ARG 3.9 18.6 + - - -
138B LYS* 4.8 5.0 + - - +
146B TYR* 4.5 9.2 + - - -
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Residues in contact with TYR 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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54A CYS 4.9 2.0 - - - -
55A LEU* 5.3 4.5 - - + -
56A PRO* 4.7 15.4 - - + +
138A LYS 4.3 3.3 + - - -
139A THR* 3.6 13.7 + - - -
141A LEU* 3.2 45.3 + - + +
142A ASP 3.2 17.9 + - - -
143A PHE* 3.0 18.8 + + + +
145A GLN* 1.3 78.3 - - - +
147A VAL* 1.3 60.7 + - + +
149A ILE* 3.2 12.9 + - + +
150A ASN* 3.0 29.8 + - - +
142F ASP* 3.2 30.7 + - + -
144F GLN* 3.1 44.6 + - + +
145F GLN* 4.3 13.3 + - + -
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Residues in contact with VAL 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 PHE* 3.1 37.7 + - + +
144A GLN* 3.2 41.5 - - - +
146A TYR* 1.3 74.3 - - + +
148A PHE* 1.3 64.3 + - - +
150A ASN* 2.8 26.3 - - - +
151A GLN* 3.0 14.0 + - - +
53B VAL* 4.5 6.2 - - + +
144F GLN* 5.3 2.5 - - - +
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Residues in contact with PHE 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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144A GLN 3.0 16.5 + - - +
145A GLN 3.7 2.0 - - - +
147A VAL* 1.3 78.8 - - - +
149A ILE* 1.3 59.7 + - - +
151A GLN* 3.3 2.3 + - - +
152A MET* 2.9 49.8 + - + +
343A VAL* 4.2 11.7 - - + -
346A LEU* 3.6 31.6 - - + -
347A ILE* 4.0 11.9 - - + -
53B VAL* 3.8 40.4 - - + -
55B LEU* 3.5 29.4 - - + -
336B GLU* 6.1 1.1 - - + -
353B GLU* 5.1 5.4 - - + -
354B CYS 4.8 2.2 - - - -
355B THR* 3.7 25.4 - - + -
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Residues in contact with ILE 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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54A CYS* 4.5 16.8 - - + +
55A LEU* 5.9 1.3 - - - -
56A PRO* 6.2 2.0 - - + -
141A LEU* 5.9 2.9 - - + -
145A GLN 2.9 16.4 + - - +
146A TYR* 3.2 26.4 + - + +
148A PHE* 1.3 78.5 - - + +
150A ASN* 1.3 62.6 + - + +
152A MET* 3.5 3.9 + - + +
153A CYS* 3.0 27.5 + - - +
343A VAL* 4.0 19.3 - - + +
347A ILE* 3.8 31.9 - - + -
348A GLY 5.6 1.3 - - - +
352A PHE* 3.5 39.2 - - + -
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Residues in contact with ASN 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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51A GLN* 6.1 0.2 - - - +
52A VAL* 3.1 33.0 + - + +
53A VAL* 3.9 0.2 - - - +
54A CYS* 3.9 21.1 - - + +
146A TYR 3.0 13.2 + - - +
147A VAL* 2.8 35.3 - - - +
149A ILE* 1.3 76.6 - - - +
151A GLN* 1.3 62.0 + - - +
153A CYS* 3.8 5.6 - - - +
154A TYR* 2.9 30.0 + - - +
354A CYS* 4.2 1.6 - - - -
144F GLN* 3.1 24.8 - - - +
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Residues in contact with GLN 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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147A VAL 3.0 15.4 + - - +
148A PHE* 3.4 7.6 - - - +
150A ASN* 1.3 82.4 + - - +
152A MET* 1.3 63.3 + - - +
154A TYR* 3.0 20.1 + - - +
155A HIS* 3.1 26.0 + - - +
51B GLN* 5.3 5.2 + - - +
53B VAL* 4.2 8.9 - - + +
335B PHE* 5.1 2.4 - - + -
355B THR* 3.7 24.7 - - + +
356B HIS 4.9 1.0 - - - -
357B ASN* 3.0 54.1 - - - +
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Residues in contact with MET 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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148A PHE* 2.9 47.9 + - + +
149A ILE* 3.8 7.2 - - + +
151A GLN* 1.3 76.9 - - - +
153A CYS* 1.3 62.0 + - - +
155A HIS* 3.5 1.9 + - - +
156A LEU* 3.3 45.6 + - + +
341A PRO* 4.1 15.5 - - + -
342A LYS* 5.1 3.6 - - - -
343A VAL* 4.1 16.8 - - + -
335B PHE* 3.9 26.0 - - + -
336B GLU* 3.3 30.3 - - + +
355B THR* 4.7 4.3 - - - -
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Residues in contact with CYS 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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54A CYS* 3.5 30.3 - - - -
149A ILE 3.0 18.7 + - - +
150A ASN 4.1 0.7 - - - +
152A MET* 1.3 78.2 - - - +
154A TYR* 1.3 58.7 + - - +
156A LEU 3.0 1.8 + - - +
157A ALA* 2.8 38.1 + - - -
158A LEU* 3.7 5.3 - - - +
337A HIS* 5.0 1.3 - - - -
339A CYS* 3.6 33.9 - - - -
352A PHE* 4.1 7.4 - - + -
354A CYS* 3.6 15.9 - - - -
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Residues in contact with TYR 154 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A GLN* 4.4 1.0 + - - -
50A ASP* 2.7 28.3 + - - -
52A VAL* 3.7 27.6 - - + +
150A ASN 2.9 19.5 + - - +
151A GLN* 3.0 13.7 + - - +
153A CYS* 1.3 76.4 - - - +
155A HIS* 1.3 97.3 + + - +
156A LEU 3.7 0.5 + - - -
158A LEU* 3.7 26.9 - - + +
163A LYS* 3.5 32.3 + - + +
356A HIS* 4.2 18.4 - + - -
49B LYS* 4.1 16.4 + - + -
357B ASN* 4.9 4.7 - - - -
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Residues in contact with HIS 155 (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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151A GLN* 3.1 13.3 + - - +
152A MET 3.5 0.9 + - - +
153A CYS 3.2 0.2 - - - -
154A TYR* 1.3 109.1 - + - +
156A LEU* 1.3 71.1 + - - +
158A LEU 5.2 0.2 - - - -
163A LYS* 5.2 14.1 - - + +
164A TYR* 6.2 0.4 - - - -
49B LYS* 6.1 0.2 + - - -
335B PHE* 3.2 38.9 - + + -
357B ASN* 3.3 41.0 + - - -
359B ALA 5.2 1.1 - - - -
360B TYR* 3.7 33.3 + + + +
361B MET 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