Contacts of the helix formed by residues 146 - 158 (chain C) in PDB entry 6E07
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 VAL 146 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112C TYR* 3.8 31.2 - - + -
142C LEU* 4.3 11.0 - - + -
143C PRO* 3.2 16.3 + - + +
144C PRO 3.0 0.8 - - - -
145C THR* 1.3 89.0 - - - +
147C TYR* 1.3 64.7 + - - +
148C GLU 3.1 4.2 + - - -
149C ALA* 3.1 12.2 + - + +
150C VAL* 3.0 38.7 + - + +
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Residues in contact with TYR 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C LEU* 3.7 29.1 + - + -
142C LEU* 3.6 31.4 + - + -
143C PRO 4.0 2.7 - - - -
144C PRO* 3.2 32.9 + - + +
146C VAL* 1.3 76.7 - - - +
148C GLU* 1.3 56.1 + - - +
150C VAL* 4.6 4.0 - - + +
151C THR* 2.7 41.9 + - + +
169C VAL* 3.6 22.7 - - + -
170C GLU* 3.6 12.4 + - - +
171C LYS* 3.2 46.0 + - - +
183C LEU* 4.1 26.2 - - + -
187C ILE* 5.1 4.5 - - + -
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Residues in contact with GLU 148 (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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144C PRO 4.8 0.8 + - - -
145C THR 5.2 2.6 + - - +
146C VAL 3.1 1.7 + - - -
147C TYR* 1.3 78.3 - - - +
149C ALA* 1.3 62.1 + - - +
151C THR* 3.1 8.7 + - - -
152C LYS* 3.2 7.3 + - - +
182C ARG* 2.3 46.4 + - - -
183C LEU* 4.0 11.7 - - + +
186C HIS* 3.0 52.4 + - + +
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Residues in contact with ALA 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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112C TYR* 3.9 9.2 - - + +
113C ASP* 3.8 32.5 - - + +
146C VAL* 3.1 15.6 + - + +
148C GLU* 1.3 79.5 - - - +
150C VAL* 1.3 64.1 + - + +
152C LYS* 3.5 9.4 + - - +
153C ASN* 3.1 31.1 + - - +
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Residues in contact with VAL 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C MET* 3.8 15.7 - - + -
112C TYR* 4.0 8.5 - - + -
118C TYR* 3.4 19.1 - - - +
140C LEU* 3.8 17.7 - - + -
142C LEU* 3.7 15.5 - - + -
146C VAL* 3.0 36.4 + - + +
147C TYR* 4.0 4.7 - - - +
149C ALA* 1.3 74.0 - - - +
151C THR* 1.3 60.2 + - - +
153C ASN* 3.3 1.7 + - - +
154C ILE* 2.9 49.7 + - + +
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Residues in contact with THR 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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140C LEU* 4.1 24.0 - - + -
147C TYR* 2.7 25.5 + - - +
148C GLU 3.1 10.0 + - - -
150C VAL* 1.3 77.0 - - - +
152C LYS* 1.3 59.9 + - - -
154C ILE* 4.0 5.1 - - + +
155C HIS* 3.1 26.5 + - - +
167C ILE* 4.4 16.6 - - + -
186C HIS* 3.2 17.6 + - - -
187C ILE* 4.1 23.9 - - + +
190C LEU* 4.0 3.8 - - - -
191C PHE* 3.6 14.6 - - + -
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Residues in contact with LYS 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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113C ASP* 3.5 24.9 + - - -
148C GLU 3.2 17.2 + - - +
149C ALA* 3.7 6.5 - - - +
150C VAL 3.3 0.2 - - - -
151C THR* 1.3 77.0 + - - +
153C ASN* 1.3 76.5 + - - +
155C HIS* 3.4 3.1 + - - +
156C GLU* 3.2 32.0 + - + +
186C HIS* 4.1 13.9 - - + -
190C LEU* 3.8 16.8 - - + +
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Residues in contact with ASN 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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112C TYR 3.4 17.4 + - - -
113C ASP* 3.4 22.8 + - - +
115C ALA* 4.1 16.2 + - - +
118C TYR* 3.4 38.5 - - + -
149C ALA 3.1 22.5 + - - +
152C LYS* 1.3 85.1 + - - +
154C ILE* 1.3 65.8 + - - +
156C GLU* 4.2 13.1 - - - +
157C SER* 3.1 32.4 + - - -
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Residues in contact with ILE 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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37C MET* 4.1 5.8 - - + -
118C TYR* 4.2 11.9 - - + -
121C LEU* 5.8 0.2 - - + -
138C PHE* 3.6 57.4 - - + -
140C LEU* 4.1 13.7 - - + -
150C VAL* 2.9 40.8 + - + +
151C THR* 4.0 6.7 - - + +
153C ASN* 1.3 75.0 - - - +
155C HIS* 1.3 60.0 + - - +
158C CYS* 3.0 33.3 + - + -
159C MET* 3.6 10.1 - - - +
167C ILE* 4.7 3.6 - - + -
191C PHE* 4.2 15.0 - - + -
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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 THR 3.1 18.1 + - - +
152C LYS 4.0 3.5 + - - +
154C ILE* 1.3 77.0 - - - +
156C GLU* 1.3 61.0 + - - +
159C MET* 3.8 35.2 - - + +
190C LEU* 3.1 55.2 + - + +
191C PHE* 3.8 13.2 - + + -
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Residues in contact with GLU 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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115C ALA* 5.0 9.0 - - - +
152C LYS* 3.2 26.2 + - + +
153C ASN* 3.9 16.9 - - - +
154C ILE 3.2 0.4 - - - -
155C HIS* 1.3 80.6 - - - +
157C SER* 1.3 64.9 + - - +
158C CYS 3.9 0.4 - - - -
159C MET* 5.9 0.2 - - - -
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Residues in contact with SER 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C ALA* 4.6 6.4 + - - +
118C TYR* 3.8 30.4 - - - +
119C GLN* 4.3 13.0 + - - +
122C ASN* 3.0 26.7 + - - +
153C ASN* 3.1 17.1 + - - -
156C GLU* 1.3 90.3 + - - +
158C CYS* 1.3 60.0 + - - +
159C MET 3.9 2.1 + - - +
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Residues in contact with CYS 158 (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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118C TYR* 3.4 39.7 - - - -
121C LEU* 4.2 19.7 - - - -
122C ASN* 3.7 11.7 - - - -
125C MET* 4.1 4.7 - - + -
136C ARG* 2.8 28.9 + - - -
138C PHE* 3.6 23.9 - - + -
154C ILE* 3.0 17.7 + - - +
157C SER* 1.3 83.8 - - - +
159C MET* 1.3 61.2 + - - +
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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