Contacts of the helix formed by residues 142 - 157 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A ARG 5.7 0.2 - - - +
138A LYS* 5.1 6.0 - - - +
141A LEU 3.2 11.6 + - - +
142A ASP 5.3 0.3 - - - -
143A PHE* 5.4 1.1 + - - -
146A TYR* 3.2 31.1 + - + +
142E ASP* 5.1 1.8 - - - -
141F LEU* 1.3 74.5 - - - +
143F PHE* 1.3 86.7 + - - +
144F GLN 3.4 2.5 - - - +
145F GLN* 2.8 31.3 + - + +
146F TYR* 3.1 25.1 + - - -
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Residues in contact with PHE 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A PHE* 3.6 37.7 - + + -
142E ASP* 5.2 4.7 + - - +
143E PHE* 3.8 37.7 - + + -
144E GLN* 5.1 11.9 - - + -
142F ASP* 1.3 85.1 + - - +
144F GLN* 1.3 58.4 + - - +
146F TYR* 2.9 31.6 + + + +
147F VAL* 3.0 34.2 + - + -
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Residues in contact with GLN 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A VAL* 3.5 19.2 - - + +
54A CYS 3.2 13.5 + - - +
55A LEU* 5.0 2.0 - - - +
143A PHE* 4.8 14.3 - - + -
146A TYR* 3.1 57.4 + - + +
147A VAL* 5.0 3.0 - - - +
150A ASN* 3.1 32.5 - - - +
142F ASP* 3.4 3.2 + - - -
143F PHE* 1.3 78.8 - - - +
145F GLN* 1.3 60.8 + - - +
147F VAL* 3.2 17.0 - - + +
148F PHE* 2.9 28.6 + - - +
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Residues in contact with GLN 145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LEU* 4.4 28.0 - - + +
137A ARG* 3.1 23.7 + - - +
138A LYS 4.2 6.9 + - - -
139A THR* 4.7 4.8 + - - +
146A TYR* 4.3 12.3 + - + +
141F LEU* 3.3 28.0 - - + +
142F ASP* 2.8 40.3 + - + +
144F GLN* 1.3 77.0 - - - +
146F TYR* 1.3 58.6 + - - +
148F PHE* 3.4 4.2 + - - +
149F ILE* 2.9 30.9 + - - +
346F LEU 5.3 7.9 + - - +
347F ILE* 5.4 7.3 - - + +
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Residues in contact with TYR 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142E ASP* 3.8 23.8 + - - -
144E GLN* 3.1 47.0 + - + +
145E GLN* 3.6 12.8 + - - -
54F CYS 4.8 0.9 - - - -
55F LEU* 5.2 1.6 - - + -
56F PRO* 4.0 24.2 - - + -
139F THR* 3.4 28.9 + - - +
141F LEU* 3.5 27.1 + - + +
142F ASP 3.1 25.7 + - - -
143F PHE* 2.9 14.3 + + + +
145F GLN* 1.3 78.1 - - - +
147F VAL* 1.3 59.2 + - + +
149F ILE* 3.2 12.1 + - + +
150F ASN* 3.0 31.7 + - - +
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Residues in contact with VAL 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A VAL* 4.4 10.2 - - + +
144E GLN* 5.6 1.8 - - - +
143F PHE* 3.0 40.7 + - + +
144F GLN* 3.2 32.8 - - + +
146F TYR* 1.3 75.0 - - + +
148F PHE* 1.3 62.9 + - - +
150F ASN* 2.8 25.3 - - - +
151F GLN* 3.0 15.1 + - - +
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Residues in contact with PHE 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A VAL* 3.7 40.8 - - + -
54A CYS 5.3 0.2 - - - -
55A LEU* 3.6 24.0 - - + -
336A GLU* 6.2 0.4 - - - -
353A GLU* 5.1 7.9 - - + -
354A CYS 4.9 1.6 - - - -
355A THR* 3.6 25.7 - - + +
144F GLN 2.9 16.6 + - - +
145F GLN 3.6 4.7 - - - +
147F VAL* 1.3 79.7 - - - +
149F ILE* 1.3 66.0 + - + +
151F GLN* 3.3 3.3 + - - +
152F MET* 3.0 48.4 + - + +
343F VAL* 4.1 17.9 - - + -
346F LEU* 3.6 29.8 - - + -
347F ILE* 4.8 2.9 - - + -
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Residues in contact with ILE 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54F CYS* 4.5 16.3 - - + +
56F PRO* 6.0 4.9 - - + -
141F LEU* 5.7 3.8 - - + -
145F GLN 2.9 16.2 + - - +
146F TYR* 3.2 25.7 + - + +
148F PHE* 1.3 82.0 - - + +
150F ASN* 1.3 61.7 + - - +
152F MET* 3.4 5.2 + - + +
153F CYS* 2.9 26.2 + - - +
341F PRO* 4.3 4.4 - - + +
343F VAL* 3.8 19.1 - - + -
347F ILE* 3.7 33.0 - - + -
352F PHE* 3.5 31.5 - - + -
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Residues in contact with ASN 150 (chain F).
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* 3.2 23.2 - - - +
52F VAL* 3.2 35.6 + - + +
53F VAL* 3.9 1.2 - - - +
54F CYS* 4.0 17.9 - - + +
146F TYR 3.0 15.6 + - - +
147F VAL* 2.8 34.6 - - - +
149F ILE* 1.3 74.6 - - - +
151F GLN* 1.3 63.1 + - - +
153F CYS* 4.2 5.4 - - - +
154F TYR* 2.9 30.3 + - - +
354F CYS* 4.0 2.2 - - - -
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Residues in contact with GLN 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A GLN* 5.2 5.3 + - - +
53A VAL* 4.6 7.6 - - + +
335A PHE* 5.2 1.7 - - + -
355A THR* 4.1 23.1 - - + +
356A HIS 5.5 0.4 - - - +
357A ASN* 3.0 45.8 - - - +
147F VAL 3.0 14.8 + - - +
148F PHE* 3.4 8.7 - - - +
149F ILE 3.3 0.2 - - - -
150F ASN* 1.3 83.1 + - - +
152F MET* 1.3 63.1 + - - +
154F TYR* 3.2 9.9 + - - +
155F HIS* 3.1 45.1 + - - +
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Residues in contact with MET 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A PHE* 4.0 19.3 - - + -
336A GLU* 3.4 24.2 - - + +
355A THR* 4.9 4.0 - - + +
148F PHE* 3.0 46.1 + - + +
149F ILE* 3.7 12.1 - - + +
151F GLN* 1.3 76.9 - - - +
153F CYS* 1.3 57.6 + - - +
155F HIS* 3.4 2.4 + - - -
156F LEU* 2.9 56.6 + - + +
339F CYS* 5.4 0.2 - - - -
341F PRO* 3.9 27.1 - - + -
342F LYS* 6.1 2.2 - - - -
343F VAL* 4.2 13.0 - - + -
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Residues in contact with CYS 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52F VAL* 5.2 0.2 - - - -
54F CYS* 3.6 18.2 - - - -
149F ILE 2.9 17.4 + - - +
150F ASN 3.5 1.1 + - - +
152F MET* 1.3 76.1 - - - +
154F TYR* 1.3 60.2 + - - +
156F LEU 4.5 0.2 - - - +
157F ALA* 3.0 33.3 + - - +
158F LEU* 3.6 7.9 - - - +
337F HIS* 4.9 4.5 - - - -
339F CYS* 3.6 31.4 - - + -
341F PRO* 5.9 1.5 - - + +
352F PHE* 5.2 3.1 - - + -
354F CYS* 3.6 30.7 - - - -
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Residues in contact with TYR 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LYS* 4.6 13.2 + - - -
357A ASN* 5.7 1.1 - - - -
46F GLN* 4.6 0.9 + - - -
50F ASP* 2.7 35.0 + - - -
51F GLN* 5.8 0.4 - - - -
52F VAL* 3.7 30.5 - - + +
150F ASN 2.9 19.1 + - - +
151F GLN* 3.7 10.3 - - - +
153F CYS* 1.3 77.3 - - - +
155F HIS* 1.3 95.9 + + - +
158F LEU* 4.0 26.9 + - + +
163F LYS* 3.9 33.8 + - + +
164F TYR* 5.7 0.7 - - - -
356F HIS* 4.4 15.3 - + - -
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Residues in contact with HIS 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335A PHE* 3.2 42.5 - + + -
357A ASN* 3.2 42.0 + - - -
359A ALA 5.4 2.2 - - - -
360A TYR* 3.3 42.6 - + + +
151F GLN* 3.1 19.7 + - - +
152F MET 4.4 0.9 - - - +
154F TYR* 1.3 110.4 - + - +
156F LEU* 1.3 60.4 + - - +
157F ALA 3.7 0.4 - - - -
158F LEU 5.1 3.2 - - - +
163F LYS* 5.7 7.3 + - - +
164F TYR* 5.9 2.2 + - - -
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Residues in contact with LEU 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335A PHE* 5.0 8.3 - - + -
336A GLU* 5.3 2.7 - - - +
360A TYR* 3.6 21.3 - - + +
152F MET* 2.9 42.1 + - + +
153F CYS 4.0 0.2 - - - -
155F HIS* 1.3 89.8 - - + +
157F ALA* 1.3 60.3 - - - +
158F LEU 3.9 0.7 - - - -
339F CYS* 4.3 10.1 - - - -
341F PRO* 5.9 6.3 - - + -
342F LYS* 6.0 8.7 - - + +
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Residues in contact with ALA 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153F CYS* 3.0 21.3 + - - +
156F LEU* 1.3 80.3 - - - +
158F LEU* 1.3 72.5 + - + +
159F PRO* 4.0 4.6 - - - +
337F HIS* 4.5 11.4 - - + +
338F VAL 4.9 4.7 - - - +
339F CYS* 3.7 32.3 - - + -
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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