Contacts of the helix formed by residues 160 - 169 (chain O) in PDB entry 1FQV
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 HIS 160 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159O LEU* 1.3 77.2 - - - +
161O PRO* 1.3 87.7 - - + +
162O ASP* 2.8 54.0 + - + +
163O VAL* 2.9 28.6 + - + +
164O THR* 3.3 9.7 + - - +
184O GLN* 3.5 31.4 + - + +
185O PRO* 3.8 11.2 + - - +
186O LEU* 4.5 2.9 - - + +
159P TRP* 5.9 1.2 - - - +
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Residues in contact with PRO 161 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159O LEU 3.8 5.3 - - - +
160O HIS* 1.3 95.6 - - + +
162O ASP* 1.3 56.2 + - - +
164O THR* 2.8 27.0 + - + +
165O GLY* 2.9 13.7 + - - -
182O MET* 4.8 2.7 - - + -
184O GLN* 3.3 23.3 - - + +
185O PRO 2.9 28.5 - - - +
186O LEU 3.5 13.2 - - - +
188O GLU* 4.8 2.5 - - - +
190O PHE* 3.7 4.2 - - - -
209O THR* 3.3 28.5 - - + -
213O ILE* 5.1 1.6 - - + -
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Residues in contact with ASP 162 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160O HIS* 2.8 31.1 + - + +
161O PRO* 1.3 73.5 - - - +
163O VAL* 1.3 59.9 + - + +
166O ARG* 2.9 46.8 + - - +
186O LEU* 2.9 46.5 - - - +
190O PHE* 3.2 20.4 - - + -
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Residues in contact with VAL 163 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159O LEU* 4.0 12.6 - - + -
160O HIS* 2.9 23.5 + - + +
162O ASP* 1.3 79.9 - - + +
164O THR* 1.3 57.2 + - - +
166O ARG* 3.5 21.8 + - - +
167O LEU* 2.9 55.6 + - + +
159P TRP* 3.6 48.9 - - + +
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Residues in contact with THR 164 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159O LEU* 3.2 35.2 - - + -
160O HIS 3.8 5.2 - - - +
161O PRO* 2.8 19.9 + - - +
163O VAL* 1.3 76.7 - - - +
165O GLY* 1.3 56.6 + - - +
167O LEU* 3.8 5.5 - - - +
168O LEU* 2.9 37.9 + - - +
175O PHE* 4.7 12.1 - - + -
182O MET* 3.3 30.5 - - + -
213O ILE* 3.2 22.9 - - - +
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Residues in contact with GLY 165 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161O PRO 2.9 10.9 + - - -
164O THR* 1.3 76.4 + - - +
166O ARG* 1.3 58.2 + - - +
168O LEU* 3.2 0.6 + - - -
169O SER* 2.8 32.1 + - - -
188O GLU* 4.8 2.2 - - - -
190O PHE* 3.4 28.9 - - - -
193O PHE* 3.3 20.1 - - - -
213O ILE* 5.8 0.2 - - - -
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Residues in contact with ARG 166 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162O ASP* 2.9 37.9 + - - +
163O VAL* 3.9 22.1 - - - +
165O GLY* 1.3 75.8 - - - +
167O LEU* 1.3 64.1 + - + +
169O SER* 2.6 21.8 + - - +
170O GLN* 3.1 22.1 - - - +
190O PHE* 3.2 11.4 - - + -
155P LYS* 6.0 3.8 - - - +
156P GLU* 3.3 59.1 + - - +
159P TRP* 4.9 0.8 - - - +
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Residues in contact with LEU 167 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130O LEU* 5.7 1.6 - - + -
149O TRP* 3.6 29.8 - - + -
152O LEU* 3.9 17.5 - - + -
154O LEU* 3.8 26.5 - - + -
163O VAL* 2.9 44.0 + - + +
164O THR* 3.9 5.4 - - - +
166O ARG* 1.3 81.9 - - + +
168O LEU* 1.3 63.4 + - + +
169O SER 3.1 2.3 + - - -
170O GLN* 3.3 21.3 + - - +
172O VAL* 2.9 23.3 - - - +
175O PHE* 6.0 1.1 - - + -
159P TRP* 3.9 17.9 - - + +
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Residues in contact with LEU 168 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152O LEU* 6.2 0.4 - - + -
164O THR* 2.9 28.1 + - - +
165O GLY 3.2 0.2 + - - -
167O LEU* 1.3 77.2 - - + +
169O SER* 1.3 59.4 + - - +
170O GLN 3.2 1.9 + - - -
171O GLY* 3.6 9.3 + - - -
172O VAL* 4.0 15.7 + - + -
175O PHE* 3.5 39.5 - - + -
193O PHE* 3.3 53.9 - - + +
194O ARG 4.5 0.9 + - - -
195O VAL* 3.4 21.6 - - + +
198O MET* 3.8 18.4 - - + -
213O ILE* 3.8 13.7 - - + -
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Residues in contact with SER 169 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146O GLU* 5.2 1.9 - - - +
165O GLY 2.8 13.7 + - - -
166O ARG* 2.6 28.5 + - - +
168O LEU* 1.3 75.5 - - - +
170O GLN* 1.3 56.1 + - - +
171O GLY 3.1 9.0 + - - -
190O PHE* 4.9 9.3 - - - -
191O SER* 5.2 7.2 - - - -
192O PRO 5.3 2.9 - - - -
193O PHE* 3.8 13.9 - - - -
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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