Contacts of the helix formed by residues 141 - 154 (chain C) in PDB entry 6AH0
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 GLY 141 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139C HIS 3.0 7.4 + - - -
140C HIS* 1.3 79.3 - - - +
142C LYS* 1.3 66.1 + - - +
143C THR 3.3 2.5 - - - -
144C CYS* 3.4 1.0 + - - -
145C PHE* 3.0 21.1 + - - -
312C SER* 5.7 2.3 - - - -
1500C GTP 3.3 35.5 + - - -
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Residues in contact with LYS 142 (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 HIS 3.7 2.4 + - - -
141C GLY* 1.3 75.7 - - - +
143C THR* 1.3 64.3 + - - +
145C PHE* 3.2 2.6 + - - +
146C VAL* 2.9 20.8 + - - -
1500C GTP 3.0 8.8 + - - -
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Residues in contact with THR 143 (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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142C LYS* 1.3 73.4 - - - +
144C CYS* 1.3 55.1 + - - +
146C VAL* 3.2 2.9 + - - +
147C ASP* 3.0 24.9 + - - -
1500C GTP 2.3 30.1 + - - -
1501C MG 3.8 8.8 - - - -
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Residues in contact with CYS 144 (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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141C GLY 3.9 0.4 - - - -
143C THR* 1.3 68.0 - - - +
145C PHE* 1.3 65.3 + - - +
147C ASP* 3.2 2.4 + - - +
148C CYS* 2.9 21.5 + - - -
312C SER* 5.4 5.8 - - - +
1500C GTP 2.4 32.1 + - - -
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Residues in contact with PHE 145 (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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141C GLY 3.0 15.4 + - - -
142C LYS* 3.7 3.6 - - - +
144C CYS* 1.3 76.6 - - - +
146C VAL* 1.3 62.5 + - - +
148C CYS* 3.2 2.3 + - - +
149C LEU* 2.9 20.1 + - - -
312C SER* 5.0 15.3 - - - +
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Residues in contact with VAL 146 (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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142C LYS 2.9 13.6 + - - -
143C THR* 3.7 2.7 - - - +
145C PHE* 1.3 74.8 - - - +
147C ASP* 1.3 63.6 + - - +
149C LEU* 3.2 2.6 + - - +
150C ILE* 2.9 20.8 + - - -
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Residues in contact with ASP 147 (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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143C THR 3.0 13.8 + - - -
144C CYS* 3.2 4.0 + - - +
146C VAL* 1.3 76.3 - - - +
148C CYS* 1.3 60.8 + - - +
150C ILE* 3.2 2.9 + - - +
151C GLU* 3.0 19.8 + - - -
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Residues in contact with CYS 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 CYS 2.9 15.3 + - - -
145C PHE* 3.7 2.9 - - - +
147C ASP* 1.3 75.1 - - - +
149C LEU* 1.3 62.4 + - - +
151C GLU* 3.2 3.1 + - - +
152C GLN* 3.0 19.4 + - - -
312C SER 6.1 0.9 - - - -
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Residues in contact with LEU 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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145C PHE 2.9 14.5 + - - -
146C VAL* 3.6 3.8 - - - +
148C CYS* 1.3 76.5 - - - +
150C ILE* 1.3 60.6 + - - +
152C GLN* 3.2 2.9 + - - +
153C THR* 3.1 20.3 + - - -
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Residues in contact with ILE 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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146C VAL 2.9 14.6 + - - -
147C ASP* 3.6 3.4 - - - +
149C LEU* 1.3 74.6 - - - +
151C GLU* 1.3 54.7 + - - +
153C THR* 3.2 1.9 + - - +
154C HIS* 2.7 35.6 + - - +
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Residues in contact with GLU 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 ASP 3.0 14.2 + - - -
148C CYS* 3.2 4.4 + - - +
150C ILE* 1.3 76.9 - - - +
152C GLN* 1.3 63.2 + - - +
154C HIS 3.4 6.2 - - - -
155C PRO* 3.4 24.5 - - - +
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Residues in contact with GLN 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 CYS 3.0 13.8 + - - -
149C LEU* 3.2 4.0 + - - +
151C GLU* 1.3 77.6 - - - +
153C THR* 1.3 60.3 + - - +
155C PRO* 4.7 2.1 - - - +
426C GLU 6.2 0.4 - - - -
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Residues in contact with THR 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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149C LEU 3.1 12.0 + - - -
150C ILE* 3.6 3.4 - - - +
152C GLN* 1.3 79.7 - - - +
154C HIS* 1.3 56.6 + - - +
155C PRO 4.0 1.0 - - - -
189C VAL 5.4 7.9 - - - -
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Residues in contact with HIS 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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150C ILE 2.7 17.8 + - - +
151C GLU* 3.4 11.2 - - - +
153C THR* 1.3 74.1 - - - +
155C PRO* 1.3 59.2 - - - +
156C GLU* 3.0 19.0 + - - +
157C ILE* 4.2 1.6 + - - -
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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