Contacts of the helix formed by residues 142 - 157 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142D ASP* 4.6 2.0 - - - -
141E LEU* 1.3 75.6 - - - +
143E PHE* 1.3 88.2 + - - +
144E GLN 3.2 2.7 - - - +
145E GLN* 2.7 38.1 + - - +
146E TYR* 3.2 15.7 + - - -
139F THR 5.2 7.4 - - - +
141F LEU 4.0 11.3 - - - +
142F ASP* 5.1 2.9 - - - -
143F PHE* 5.2 2.8 + - - +
146F TYR* 3.8 23.7 + - - +
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Residues in contact with PHE 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D ASP* 4.6 7.4 + - - +
143D PHE* 4.1 29.8 - + + -
144D GLN* 3.2 29.8 - - + -
142E ASP* 1.3 84.0 + - - +
144E GLN* 1.3 58.3 + - - +
146E TYR* 3.0 25.8 + - - +
147E VAL* 3.1 34.6 + - + +
143F PHE* 3.8 35.4 - + + -
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Residues in contact with GLN 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E ASP* 3.2 3.8 + - - +
143E PHE* 1.3 79.3 - - - +
145E GLN* 1.3 61.9 + - - +
147E VAL* 3.2 19.5 - - + +
148E PHE* 2.9 27.5 + - - +
53F VAL* 3.7 12.5 - - - +
54F CYS 2.9 24.7 + - - +
55F LEU* 4.8 2.6 - - - +
143F PHE* 5.1 13.1 - - + -
146F TYR* 3.1 57.3 + - + +
147F VAL* 5.4 2.4 - - - +
149F ILE* 5.5 0.2 - - - +
150F ASN* 3.2 29.3 - - - +
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Residues in contact with GLN 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E LEU* 3.8 13.2 - - + +
142E ASP* 2.7 43.7 + - - +
144E GLN* 1.3 77.3 - - - +
146E TYR* 1.3 57.9 + - - +
148E PHE* 3.4 2.1 + - - +
149E ILE* 2.8 32.7 + - - +
346E LEU 5.3 1.8 - - - +
347E ILE* 4.2 22.9 - - + +
55F LEU* 4.0 30.4 - - + +
56F PRO* 5.9 0.2 - - - +
137F ARG 5.1 6.6 - - - +
139F THR* 3.5 25.8 + - - +
146F TYR* 3.6 23.6 + - - -
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Residues in contact with TYR 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D ASP* 3.3 24.9 + - - +
144D GLN* 3.5 43.3 - - + -
145D GLN* 4.5 9.7 + - - -
54E CYS 4.4 11.0 - - - +
55E LEU* 5.0 3.6 - - + -
56E PRO* 4.3 18.0 - - + +
138E LYS 4.5 3.1 + - - -
139E THR* 3.8 14.6 + - - -
141E LEU* 3.4 36.3 + - + +
142E ASP 3.2 28.4 + - - -
143E PHE* 3.0 12.5 + - - +
145E GLN* 1.3 75.2 - - - +
147E VAL* 1.3 61.9 + - - +
149E ILE* 3.3 12.0 - - + +
150E ASN* 3.0 32.9 + - - +
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Residues in contact with VAL 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D GLN* 5.1 2.5 - - - +
143E PHE* 3.1 41.4 + - + +
144E GLN* 3.2 32.5 - - + +
146E TYR* 1.3 76.7 - - + +
148E PHE* 1.3 57.2 + - - +
150E ASN* 2.8 22.9 - - - +
151E GLN* 3.0 19.9 + - - +
53F VAL* 3.9 12.7 - - + +
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Residues in contact with PHE 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144E GLN 2.9 17.4 + - - +
145E GLN 3.7 3.6 - - - +
147E VAL* 1.3 79.9 - - - +
149E ILE* 1.3 62.2 + - + +
151E GLN* 3.3 3.7 - - - +
152E MET* 2.9 53.9 + - + +
343E VAL* 4.0 9.9 - - + -
346E LEU* 3.6 29.2 - - + -
347E ILE* 4.7 6.7 - - + -
53F VAL* 3.6 38.4 - - + -
55F LEU* 3.5 28.9 - - + -
336F GLU* 6.1 1.3 - - + -
353F GLU* 5.0 8.7 - - + -
354F CYS* 4.6 2.9 - - - -
355F THR* 3.6 25.1 - - + -
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Residues in contact with ILE 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E CYS* 4.3 18.1 - - + +
55E LEU* 5.6 1.1 - - - +
56E PRO* 6.2 2.0 - - + -
141E LEU* 6.0 2.5 - - + -
145E GLN 2.8 16.2 + - - +
146E TYR* 3.2 26.4 + - + +
148E PHE* 1.3 80.3 - - + +
150E ASN* 1.3 61.5 + - - +
152E MET* 3.5 4.4 + - + +
153E CYS* 3.0 26.2 + - - +
341E PRO* 4.8 0.9 - - + -
343E VAL* 3.8 27.1 - - + +
347E ILE* 3.9 24.2 - - + -
349E TYR 6.1 0.2 - - - +
352E PHE* 3.5 35.7 - - + -
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Residues in contact with ASN 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D GLN* 4.3 14.5 - - - +
51E GLN* 6.0 0.2 - - - +
52E VAL* 3.1 37.1 + - + +
53E VAL* 3.8 6.7 - - - +
54E CYS* 3.9 17.0 - - + +
146E TYR 3.0 16.1 + - - +
147E VAL* 2.8 33.9 - - - +
149E ILE* 1.3 75.3 - - - +
151E GLN* 1.3 62.8 + - - +
153E CYS* 4.2 5.4 - - - -
154E TYR* 2.9 32.2 + - - +
354E CYS* 4.1 1.3 - - - -
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Residues in contact with GLN 151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147E VAL 3.0 15.5 + - - +
148E PHE* 3.3 9.2 - - - +
150E ASN* 1.3 83.0 + - - +
152E MET* 1.3 60.7 + - - +
154E TYR* 3.8 7.9 - - - +
155E HIS* 3.0 36.7 + - - +
51F GLN* 5.1 9.6 + - - +
53F VAL* 3.8 11.9 - - + +
335F PHE* 5.4 0.9 - - + -
355F THR* 3.7 24.7 - - + -
356F HIS 4.5 0.6 + - - -
357F ASN* 3.0 54.5 - - - +
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Residues in contact with MET 152 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148E PHE* 2.9 47.7 + - + +
149E ILE* 3.8 7.6 - - + +
151E GLN* 1.3 76.3 - - - +
153E CYS* 1.3 58.6 + - - +
155E HIS* 3.4 1.6 + - - +
156E LEU* 2.9 58.4 + - + +
341E PRO* 4.2 17.0 - - + -
342E LYS* 6.2 1.1 - - - -
343E VAL* 4.0 15.7 - - + -
335F PHE* 3.6 30.7 - - + -
336F GLU* 3.3 28.0 - - + +
355F THR* 4.7 3.3 - - - +
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Residues in contact with CYS 153 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E VAL* 5.6 0.2 - - - -
54E CYS* 3.6 18.6 - - - -
149E ILE 3.0 17.2 + - - +
150E ASN 4.0 0.9 - - - +
152E MET* 1.3 77.9 - - - +
154E TYR* 1.3 57.7 + - - +
156E LEU 3.0 1.2 + - - -
157E ALA* 2.6 42.6 + - - +
158E LEU* 3.7 4.0 + - - -
337E HIS* 5.1 2.7 - - - -
339E CYS* 3.6 33.0 - - - -
341E PRO* 6.0 0.6 - - + +
352E PHE* 5.2 2.5 - - + -
354E CYS* 3.5 27.8 - - - -
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Residues in contact with TYR 154 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46E GLN* 4.7 2.8 + - - -
50E ASP* 2.9 34.5 + - - -
51E GLN* 6.2 0.9 - - - -
52E VAL* 3.7 23.3 - - + +
150E ASN 2.9 20.3 + - - +
151E GLN* 3.8 7.0 - - - +
153E CYS* 1.3 77.2 - - - +
155E HIS* 1.3 81.9 + + - +
156E LEU 3.8 0.2 + - - -
158E LEU* 3.7 31.0 - - + +
163E LYS* 3.1 47.0 + - + +
164E TYR* 5.8 1.2 - - - -
356E HIS* 4.7 6.5 - + - -
49F LYS* 3.9 18.0 + - + -
357F ASN* 4.7 10.1 - - - -
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Residues in contact with HIS 155 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151E GLN* 3.0 18.2 + - - +
152E MET 3.6 0.7 - - - +
154E TYR* 1.3 97.3 - + - +
156E LEU* 1.3 66.7 + - - +
158E LEU 5.1 0.7 - - - -
163E LYS* 3.5 23.7 + - - +
164E TYR* 5.7 0.2 - - - -
49F LYS* 6.0 0.8 + - - -
335F PHE* 3.2 38.5 - + + -
356F HIS 4.2 0.9 - - - -
357F ASN* 3.1 53.1 + - - -
359F ALA 4.9 2.5 - - - -
360F TYR* 3.9 28.8 - + + +
361F MET 6.1 0.6 + - - -
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Residues in contact with LEU 156 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152E MET* 2.9 46.9 + - + +
153E CYS* 4.2 1.8 - - - +
155E HIS* 1.3 88.5 - - + +
157E ALA* 1.3 60.4 + - - +
158E LEU 3.5 8.6 + - - +
339E CYS* 4.8 7.4 - - - -
341E PRO* 4.5 16.4 - - + -
342E LYS* 5.3 10.1 - - + +
335F PHE* 5.2 4.0 - - + -
336F GLU* 5.8 0.4 - - - +
360F TYR* 4.2 15.5 - - + +
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Residues in contact with ALA 157 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153E CYS* 2.6 38.9 + - - -
156E LEU* 1.3 72.2 - - - +
158E LEU* 1.3 67.0 + - - +
159E PRO* 4.1 0.3 - - - +
337E HIS* 4.0 25.9 - - + +
338E VAL 4.7 4.9 - - - +
339E CYS* 3.6 23.1 - - + -
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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
------------------------------------------------------------
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