Contacts of the helix formed by residues 168 - 183 (chain M) in PDB entry 6O81
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 ASN 168 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165M LEU 5.2 1.7 - - - +
166M ASP 3.7 1.0 - - - -
167M LEU* 1.3 82.3 + - - +
169M GLU* 1.3 64.4 + - - +
170M ASP* 3.5 2.7 - - + +
171M GLU* 3.8 23.3 - - + +
172M ARG* 3.8 18.0 + - - +
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Residues in contact with GLU 169 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168M ASN* 1.3 76.3 - - - +
170M ASP* 1.3 60.1 + - - +
172M ARG* 4.4 2.1 + - - +
173M GLU* 4.1 15.1 + - - +
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Residues in contact with ASP 170 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168M ASN* 4.2 2.7 - - + +
169M GLU* 1.3 77.8 - - + +
171M GLU* 1.3 59.9 + - - +
172M ARG 3.3 0.9 - - - -
173M GLU* 3.4 7.1 + - - +
174M VAL* 2.9 29.6 + - - +
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Residues in contact with GLU 171 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114M VAL* 5.5 1.6 - - - +
118M LEU* 5.6 11.0 - - + -
129M LEU* 5.0 13.0 - - + -
167M LEU* 4.3 11.4 - - + -
168M ASN* 3.8 26.3 - - + +
169M GLU 3.6 0.6 - - - -
170M ASP* 1.3 75.6 - - - +
172M ARG* 1.3 60.9 + - - +
174M VAL* 3.4 6.4 + - - +
175M LEU* 2.9 29.8 + - - +
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Residues in contact with ARG 172 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162M LEU* 4.2 23.1 - - + +
163M ASP* 5.9 1.1 - - - -
165M LEU* 4.8 12.6 - - + +
167M LEU* 5.3 3.5 - - + +
168M ASN 3.8 17.7 + - - +
169M GLU 4.8 2.7 - - - +
170M ASP 3.3 0.2 - - - -
171M GLU* 1.3 78.9 - - - +
173M GLU* 1.3 57.5 + - - +
175M LEU* 3.4 6.2 + - - +
176M ILE* 2.9 29.9 + - - +
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Residues in contact with GLU 173 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169M GLU 4.1 12.0 + - - +
170M ASP* 3.4 10.5 + - - +
171M GLU 3.3 0.2 - - - -
172M ARG* 1.3 77.0 - - - +
174M VAL* 1.3 59.5 + - - +
176M ILE* 3.4 6.0 + - - +
177M ASN* 2.9 30.1 + - - +
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Residues in contact with VAL 174 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114M VAL* 4.6 13.1 - - + +
117M VAL* 4.7 19.5 - - + -
118M LEU* 5.7 3.4 - - + +
170M ASP 2.9 17.3 + - - +
171M GLU* 3.8 7.0 - - - +
172M ARG 3.3 0.2 - - - -
173M GLU* 1.3 76.2 - - - +
175M LEU* 1.3 58.2 + - - +
177M ASN* 3.4 6.0 + - - +
178M ASN* 2.9 30.0 + - - +
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Residues in contact with LEU 175 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111M LEU* 6.4 2.5 - - + -
114M VAL* 4.4 16.0 - - + +
152M PHE* 6.2 4.3 - - + -
162M LEU* 6.3 1.8 - - + -
171M GLU 2.9 18.3 + - - +
172M ARG* 3.7 6.7 - - - +
174M VAL* 1.3 74.4 - - - +
176M ILE* 1.3 59.3 + - - +
178M ASN* 3.4 3.3 + - - +
179M ILE* 2.9 30.2 + - - +
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Residues in contact with ILE 176 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155M ALA 6.0 2.2 - - - +
159M PRO* 5.5 9.0 - - + -
162M LEU* 4.9 15.2 - - + +
172M ARG 2.9 17.6 + - - +
173M GLU* 3.8 7.2 - - - +
174M VAL 3.3 0.2 - - - -
175M LEU* 1.3 75.7 - - - +
177M ASN* 1.3 58.7 + - - +
179M ILE* 3.4 6.3 + - - +
180M ASN* 2.9 30.7 + - - +
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Residues in contact with ASN 177 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173M GLU 2.9 18.3 + - - +
174M VAL* 3.8 7.0 - - - +
176M ILE* 1.3 77.0 - - - +
178M ASN* 1.3 56.9 + - - +
180M ASN* 3.4 5.0 + - - +
181M ARG* 2.9 32.1 + - - +
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Residues in contact with ASN 178 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110M ILE* 4.1 26.2 - - + +
113M HIS* 4.9 7.9 - - + -
114M VAL* 4.7 7.9 - - + +
174M VAL 2.9 18.3 + - - +
175M LEU* 3.8 6.7 - - - +
177M ASN* 1.3 75.7 - - - +
179M ILE* 1.3 57.4 + - - +
181M ARG* 3.8 4.3 - - - +
182M ARG* 2.9 34.5 + - - +
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Residues in contact with ILE 179 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110M ILE* 5.4 6.2 - - + +
152M PHE* 4.7 29.6 - - + +
155M ALA* 5.6 4.0 - - + -
156M VAL* 4.3 10.6 - - + +
175M LEU 2.9 17.9 + - - +
176M ILE* 3.8 6.7 - - - +
178M ASN* 1.3 77.3 - - - +
180M ASN* 1.3 55.8 + - - +
182M ARG* 4.8 1.3 - - - -
183M LEU* 2.9 35.7 + - + +
184M THR* 3.7 2.9 + - - -
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Residues in contact with ASN 180 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156M VAL* 4.9 12.0 - - - +
176M ILE 2.9 17.7 + - - +
177M ASN* 4.0 5.2 - - - +
179M ILE* 1.3 77.1 - - - +
181M ARG* 1.3 58.6 + - - +
184M THR* 3.4 30.7 + - - +
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Residues in contact with ARG 181 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177M ASN 2.9 18.3 + - - +
178M ASN* 4.0 5.4 - - - +
179M ILE 3.2 0.2 - - - -
180M ASN* 1.3 79.4 - - - +
182M ARG* 1.3 58.5 + - - +
184M THR 4.9 1.5 - - - -
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Residues in contact with ARG 182 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106M THR 5.9 0.9 - - - +
110M ILE* 4.9 15.7 - - + -
178M ASN* 2.9 18.0 + - + +
179M ILE* 4.4 1.6 - - - +
181M ARG* 1.3 79.3 - - + +
183M LEU* 1.3 61.7 + - + +
184M THR 3.6 1.3 + - - -
185M PRO* 5.0 8.2 - - - +
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Residues in contact with LEU 183 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149M TYR* 5.3 16.4 - - + -
152M PHE* 5.3 9.6 - - + +
153M LYS* 5.6 8.3 - - + +
156M VAL* 4.6 11.1 - - + +
179M ILE* 2.9 16.4 + - + +
182M ARG* 1.3 76.7 - - + +
184M THR* 1.3 59.1 + - - +
185M PRO* 3.6 3.8 - - - -
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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
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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