Contacts of the helix formed by residues 142 - 157 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142B ASP* 5.1 1.3 - - - -
141C LEU* 1.3 74.4 - - - +
143C PHE* 1.3 87.2 + - - +
144C GLN 3.4 2.2 - - - +
145C GLN* 2.8 30.8 + - + +
146C TYR* 3.1 25.8 + - - -
137D ARG 5.7 0.2 - - - +
138D LYS* 5.1 6.3 - - - +
141D LEU 3.2 11.4 - - - +
142D ASP 5.3 0.5 - - - -
143D PHE* 5.4 0.9 + - - -
146D TYR* 3.2 32.4 + - + +
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Residues in contact with PHE 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B ASP* 5.2 4.5 + - - +
143B PHE* 3.8 37.0 - + + -
144B GLN* 5.1 11.2 - - + -
142C ASP* 1.3 85.3 + - - +
144C GLN* 1.3 59.2 + - - +
146C TYR* 2.9 31.1 + + + +
147C VAL* 3.0 36.3 + - + +
143D PHE* 3.6 38.1 - + + -
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Residues in contact with GLN 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C ASP* 3.4 3.2 + - - -
143C PHE* 1.3 78.4 - - - +
145C GLN* 1.3 60.6 + - - +
147C VAL* 3.2 16.7 - - + +
148C PHE* 2.9 28.8 + - - +
53D VAL* 3.5 19.7 - - + +
54D CYS 3.2 13.3 + - - +
55D LEU* 5.0 2.2 - - - +
143D PHE* 4.8 14.5 - - + -
146D TYR* 3.1 55.3 + - + +
147D VAL* 5.0 3.2 - - - +
149D ILE* 5.3 0.2 - - - +
150D ASN* 3.1 32.3 - - - +
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Residues in contact with GLN 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C LEU* 3.3 27.3 - - + +
142C ASP* 2.8 41.4 + - + +
144C GLN* 1.3 78.4 - - - +
146C TYR* 1.3 57.2 + - - +
148C PHE* 3.4 4.0 + - - +
149C ILE* 2.9 30.8 + - - +
346C LEU 5.3 7.9 + - - +
347C ILE* 5.4 6.8 - - + +
55D LEU* 4.4 27.6 - - + +
137D ARG* 3.1 24.2 + - - +
138D LYS 4.2 7.1 + - - -
139D THR* 4.7 4.6 + - - +
146D TYR* 4.3 13.0 + - + +
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Residues in contact with TYR 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B ASP* 3.8 23.6 + - - +
144B GLN* 3.1 49.3 + - + +
145B GLN* 3.6 14.0 + - - -
54C CYS 4.8 0.7 - - - -
55C LEU* 5.2 1.3 - - + -
56C PRO* 4.0 24.5 - - + -
139C THR* 3.4 29.8 + - - +
141C LEU* 3.5 27.8 + - + +
142C ASP 3.1 25.6 + - - -
143C PHE* 2.9 14.0 + + + +
145C GLN* 1.3 76.5 - - - +
147C VAL* 1.3 59.0 + - + +
149C ILE* 3.2 12.8 + - + +
150C ASN* 3.0 31.5 + - - +
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Residues in contact with VAL 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B GLN* 5.6 1.6 - - - +
143C PHE* 3.0 40.9 + - + +
144C GLN* 3.2 33.2 - - + +
146C TYR* 1.3 75.3 - - + +
148C PHE* 1.3 64.1 + - - +
150C ASN* 2.8 23.9 - - - +
151C GLN* 3.0 15.1 + - - +
53D VAL* 4.4 9.8 - - + +
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Residues in contact with PHE 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C GLN 2.9 17.6 + - - +
145C GLN 3.6 4.5 - - - +
147C VAL* 1.3 79.5 - - - +
149C ILE* 1.3 65.6 + - + +
151C GLN* 3.3 3.3 + - - +
152C MET* 3.0 48.5 + - + +
343C VAL* 4.1 17.7 - - + -
346C LEU* 3.6 30.5 - - + -
347C ILE* 4.8 2.2 - - + -
53D VAL* 3.7 42.0 - - + -
55D LEU* 3.6 24.9 - - + -
336D GLU* 6.2 0.4 - - + -
353D GLU* 5.1 7.6 - - + -
354D CYS 4.9 2.2 - - - -
355D THR* 3.6 25.1 - - + +
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Residues in contact with ILE 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C CYS* 4.5 16.2 - - + +
56C PRO* 6.0 4.5 - - + -
141C LEU* 5.7 4.0 - - + -
145C GLN 2.9 17.3 + - - +
146C TYR* 3.2 26.0 + - + +
148C PHE* 1.3 80.3 - - + +
150C ASN* 1.3 62.8 + - - +
152C MET* 3.4 5.0 + - + +
153C CYS* 2.9 26.7 + - - +
341C PRO* 4.3 4.0 - - + +
343C VAL* 3.8 19.1 - - + -
347C ILE* 3.7 32.5 - - + -
352C PHE* 3.5 32.2 - - + -
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Residues in contact with ASN 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B GLN* 3.2 22.2 - - - +
52C VAL* 3.2 38.8 + - + +
53C VAL* 3.9 1.4 - - - +
54C CYS* 4.0 17.5 - - + +
146C TYR 3.0 14.6 + - - +
147C VAL* 2.8 35.3 - - - +
149C ILE* 1.3 77.0 - - - +
151C GLN* 1.3 64.0 + - - +
153C CYS* 4.2 5.4 - - - +
154C TYR* 2.9 29.6 + - - +
354C CYS* 4.0 2.2 - - - -
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Residues in contact with GLN 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C VAL 3.0 15.0 + - - +
148C PHE* 3.4 8.5 - - - +
150C ASN* 1.3 83.1 + - - +
152C MET* 1.3 62.2 + - - +
154C TYR* 3.2 10.8 + - - +
155C HIS* 3.1 44.5 + - - +
51D GLN* 5.2 5.7 + - - +
53D VAL* 4.6 6.9 - - + +
335D PHE* 5.2 1.7 - - + -
355D THR* 4.1 23.6 - - + +
356D HIS 5.1 1.5 + - - +
357D ASN* 3.0 46.8 + - - +
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Residues in contact with MET 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C PHE* 3.0 46.8 + - + +
149C ILE* 3.7 11.9 - - + +
150C ASN 3.3 0.2 - - - -
151C GLN* 1.3 77.5 - - - +
153C CYS* 1.3 58.7 + - - +
155C HIS* 3.4 2.5 + - - +
156C LEU* 2.9 56.8 + - + +
339C CYS* 5.4 0.4 - - - -
341C PRO* 3.9 25.8 - - + -
342C LYS* 5.8 2.9 - - + -
343C VAL* 4.2 11.7 - - + -
335D PHE* 4.0 19.3 - - + -
336D GLU* 3.4 24.7 - - + +
355D THR* 4.9 3.4 - - + -
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Residues in contact with CYS 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C VAL* 5.2 0.2 - - - -
54C CYS* 3.6 17.9 - - - -
149C ILE 2.9 17.6 + - - +
150C ASN 4.0 0.4 - - - +
151C GLN 3.3 0.2 - - - -
152C MET* 1.3 75.9 - - - +
154C TYR* 1.3 59.5 + - - +
156C LEU 4.5 0.2 - - - +
157C ALA* 3.0 33.6 + - - +
158C LEU* 3.6 7.9 - - - +
337C HIS* 4.9 3.8 - - - -
339C CYS* 3.6 31.9 - - + -
341C PRO* 5.9 1.3 - - + +
352C PHE* 5.2 2.7 - - + -
354C CYS* 3.6 31.0 - - - -
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Residues in contact with TYR 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C GLN* 4.6 0.7 + - - -
50C ASP* 2.7 35.2 + - - -
51C GLN* 5.8 0.7 - - - -
52C VAL* 3.7 28.9 - - + +
150C ASN 2.9 18.4 + - - +
151C GLN* 3.7 10.3 - - - +
153C CYS* 1.3 76.7 - - - +
155C HIS* 1.3 95.0 + + - +
158C LEU* 4.0 26.6 + - + +
163C LYS* 3.9 32.7 + - + +
164C TYR* 5.7 0.7 - - - -
356C HIS* 4.4 14.8 - + - -
49D LYS* 4.6 12.9 + - - -
357D ASN* 5.7 1.1 - - - -
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Residues in contact with HIS 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C GLN* 3.1 19.5 + - - +
152C MET 4.4 1.3 - - - +
154C TYR* 1.3 111.2 - + - +
156C LEU* 1.3 61.3 + - + +
157C ALA 3.7 0.9 - - - -
158C LEU 5.1 2.4 - - - +
163C LYS* 5.7 6.6 + - - +
164C TYR* 5.9 2.0 + - - -
335D PHE* 3.2 42.0 - + + -
357D ASN* 3.2 42.2 + - - -
359D ALA 5.4 2.0 - - - -
360D TYR* 3.3 42.9 - + + +
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Residues in contact with LEU 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C MET* 2.9 42.2 + - + +
153C CYS 4.0 0.4 - - - -
155C HIS* 1.3 87.6 - - + +
157C ALA* 1.3 61.7 + - - +
158C LEU 3.9 0.7 - - - -
339C CYS* 4.3 8.9 - - - -
341C PRO* 5.9 5.8 - - + -
342C LYS* 6.0 8.7 - - + +
335D PHE* 5.0 9.0 - - + -
336D GLU* 5.3 2.9 - - - +
360D TYR* 3.6 21.3 - - + +
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Residues in contact with ALA 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C CYS* 3.0 20.9 + - - +
156C LEU* 1.3 80.5 - - - +
158C LEU* 1.3 72.6 + - + +
159C PRO* 4.0 4.3 - - - +
337C HIS* 4.5 12.7 - - + +
338C VAL 4.9 4.3 - - - +
339C CYS* 3.7 32.8 - - + -
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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