Contacts of the helix formed by residues 160 - 172 (chain M) in PDB entry 6FF7
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 PRO 160 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156M LEU 4.9 0.7 - - - +
159M HIS* 1.3 71.3 - - - +
161M LEU* 1.3 65.0 + - - +
162M PRO 3.5 0.7 - - - -
163M GLU* 3.2 10.4 + - + +
164M THR* 3.0 25.1 + - - -
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Residues in contact with LEU 161 (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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159M HIS* 3.2 11.8 - - + +
160M PRO* 1.3 78.2 - - - +
162M PRO* 1.3 59.1 - - - +
164M THR* 3.2 4.3 + - - -
165M ALA* 2.9 30.3 + - - +
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Residues in contact with PRO 162 (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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152M TYR* 4.3 4.9 - - - +
155M PHE* 4.1 36.1 - - + +
156M LEU* 4.6 0.4 - - - +
159M HIS* 4.5 3.6 - - + +
160M PRO 3.5 0.4 - - - -
161M LEU* 1.3 77.9 - - - +
163M GLU* 1.3 57.2 + - - +
165M ALA* 4.5 5.4 - - + -
166M VAL* 2.9 35.3 + - + +
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Residues in contact with GLU 163 (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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152M TYR* 4.5 7.4 - - - +
156M LEU* 3.6 29.8 - - + +
160M PRO* 3.2 12.8 + - + +
162M PRO* 1.3 78.6 - - - +
164M THR* 1.3 52.9 + - - +
167M ARG* 2.5 42.3 + - + +
187M LEU* 6.0 8.1 - - + -
195M GLU* 6.0 3.1 - - + -
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Residues in contact with THR 164 (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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160M PRO* 3.0 17.2 + - - -
161M LEU* 3.9 4.3 - - - -
163M GLU* 1.3 76.3 - - - +
165M ALA* 1.3 59.4 + - - +
167M ARG* 4.5 2.2 - - - -
168M GLY* 2.9 26.2 + - - -
195M GLU* 5.5 11.6 - - - +
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Residues in contact with ALA 165 (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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161M LEU 2.9 17.2 + - - +
162M PRO* 4.2 5.2 - - + +
164M THR* 1.3 77.7 - - - +
166M VAL* 1.3 57.8 + - - +
168M GLY* 4.2 0.2 - - - -
169M TYR* 2.9 33.1 + - - +
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Residues in contact with VAL 166 (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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152M TYR* 3.6 24.0 - - + -
162M PRO* 2.9 19.7 + - + +
165M ALA* 1.3 74.9 - - - +
167M ARG* 1.3 60.4 + - - +
169M TYR* 4.6 3.1 - - - -
170M ARG* 2.8 32.7 + - - +
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Residues in contact with ARG 167 (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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152M TYR* 5.5 0.8 - - - +
163M GLU* 2.5 25.0 + - + +
164M THR* 4.3 2.2 - - - +
166M VAL* 1.3 76.7 - - - +
168M GLY* 1.3 60.7 + - - +
170M ARG* 3.9 2.8 - - - +
171M ARG* 2.9 33.4 + - - +
183M TYR* 4.4 26.0 - - + +
187M LEU* 5.7 5.6 - - + -
195M GLU* 5.9 3.8 - - + -
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Residues in contact with GLY 168 (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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164M THR 2.9 19.0 + - - -
167M ARG* 1.3 77.8 - - - +
169M TYR* 1.3 59.5 + - - +
171M ARG* 4.6 3.0 - - - +
172M PHE* 3.2 27.7 + - - +
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Residues in contact with TYR 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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165M ALA 2.9 21.9 + - - +
166M VAL* 4.3 3.4 - - - +
168M GLY* 1.3 76.6 - - - +
170M ARG* 1.3 59.3 + - - +
172M PHE* 4.1 2.0 - - - -
173M LEU* 3.2 29.8 + - - +
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Residues in contact with ARG 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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166M VAL 2.8 22.9 + - - +
167M ARG* 3.3 3.8 + - - +
169M TYR* 1.3 76.8 - - - +
171M ARG* 1.3 63.2 + - - +
173M LEU* 3.3 18.1 + - - +
174M LYS* 5.3 1.2 - - - +
179M SER* 4.8 14.8 - - - +
183M TYR* 5.9 4.5 - - + -
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Residues in contact with ARG 171 (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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167M ARG 2.9 17.9 + - - +
168M GLY* 4.6 2.9 - - - +
170M ARG* 1.3 77.4 - - - +
172M PHE* 1.3 59.6 + - - +
173M LEU 3.4 3.2 + - - +
176M SER 5.5 2.6 - - - +
179M SER* 5.4 1.8 - - - -
180M ALA* 3.8 35.4 - - + +
183M TYR* 5.6 3.3 - - + +
199M ARG* 5.8 5.6 - - + -
202M THR* 5.9 7.4 - - - -
1030U LYS* 5.8 0.2 - - - +
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Residues in contact with PHE 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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168M GLY 3.2 21.2 + - - +
169M TYR* 4.7 1.8 - - - +
170M ARG 3.3 0.2 - - - -
171M ARG* 1.3 75.6 - - - +
173M LEU* 1.3 58.7 + - - +
1029U VAL 5.7 1.6 - - - +
1030U LYS* 3.3 39.6 - - + +
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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