Contacts of the helix formed by residues 165 - 177 (chain A) in PDB entry 2FQ6
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 ASP 165 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A PRO 4.5 3.6 + - - -
135A LEU* 5.6 2.5 - - - +
137A GLY* 4.5 11.6 - - - -
163A VAL 3.8 0.8 + - - -
164A HIS* 1.3 68.4 - - - +
166A VAL* 1.3 63.1 + - - +
167A PRO* 3.5 1.3 - - - +
168A ALA* 3.3 29.2 + - + +
169A ILE* 3.1 28.4 + - - +
299A PHE* 3.4 43.1 - - + -
302A ARG* 2.9 22.8 + - - -
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Residues in contact with VAL 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A LEU* 4.1 15.9 - - + -
155A SER* 4.8 3.4 - - - -
164A HIS* 3.4 24.1 + - + +
165A ASP* 1.3 70.0 - - - +
167A PRO* 1.3 73.4 - - + +
169A ILE* 3.1 7.1 + - - +
170A VAL* 2.8 32.8 + - + +
184A ILE* 4.6 5.8 - - + -
194A PHE* 3.7 26.0 - - + -
199A PHE* 3.8 20.4 - - + -
201A ILE* 3.7 23.6 - - + -
303A ASP* 4.5 1.0 + - - +
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Residues in contact with PRO 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A ASP* 3.5 3.4 - - - +
166A VAL* 1.3 93.1 - - + +
168A ALA* 1.3 60.2 + - - +
170A VAL* 4.0 5.3 - - + +
171A ALA* 3.0 25.6 + - - +
199A PHE* 3.7 26.7 - - + +
302A ARG* 3.4 28.0 - - - +
303A ASP* 3.5 10.5 - - - +
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Residues in contact with ALA 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A GLY* 4.2 1.8 - - - -
138A ALA* 3.8 30.1 - - + +
165A ASP* 3.2 31.9 + - - +
167A PRO* 1.3 78.4 - - - +
169A ILE* 1.3 63.2 + - - +
171A ALA* 3.6 5.4 + - - +
172A ALA* 3.2 23.4 + - - +
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Residues in contact with ILE 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A PHE* 4.0 24.5 - - + -
134A PRO 4.6 2.2 - - - +
136A ILE* 4.6 2.7 - - + -
137A GLY* 3.7 31.4 - - - +
140A ILE* 3.8 22.1 - - + +
151A VAL* 4.6 1.1 - - + -
153A LEU* 4.0 27.4 - - + -
164A HIS* 4.2 19.5 - - + +
165A ASP 3.1 14.5 + - - +
166A VAL* 3.1 9.1 + - - +
168A ALA* 1.3 77.0 - - - +
170A VAL* 1.3 59.4 - - + +
172A ALA* 3.2 3.5 + - - +
173A VAL* 2.9 35.1 + - + +
182A ILE* 5.6 1.1 - - + -
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Residues in contact with VAL 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A LEU* 5.1 2.7 - - + -
166A VAL* 2.8 36.1 + - + +
167A PRO* 4.0 4.3 - - + +
169A ILE* 1.3 71.9 - - - +
171A ALA* 1.3 65.3 + - - +
173A VAL* 3.4 1.0 + - - +
174A ARG* 2.9 37.7 + - + +
182A ILE* 4.0 24.9 - - + -
199A PHE 3.6 26.0 - - - +
200A GLY* 4.1 15.3 - - - +
201A ILE* 4.1 12.1 - - + -
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Residues in contact with ALA 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A PRO 3.0 18.4 + - - +
168A ALA* 4.0 5.6 - - - +
169A ILE 3.3 0.2 - - - -
170A VAL* 1.3 79.0 - - - +
172A ALA* 1.3 63.9 + - - +
174A ARG* 4.0 4.9 - - - +
175A SER* 3.1 23.9 + - - -
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Residues in contact with ALA 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A ALA* 3.9 11.2 - - + +
140A ILE* 3.7 14.8 - - + -
141A VAL* 3.6 25.4 - - + -
144A LEU* 4.4 3.4 - - - -
168A ALA 3.2 17.1 + - - +
169A ILE 3.2 5.4 + - - +
171A ALA* 1.3 73.6 - - - +
173A VAL* 1.3 67.0 - - - +
175A SER* 2.7 25.0 + - - -
176A VAL* 3.2 9.2 + - - +
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Residues in contact with VAL 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A ILE* 4.6 4.0 - - + -
144A LEU* 3.9 17.0 - - + +
151A VAL* 3.9 23.8 - - + -
169A ILE* 2.9 35.2 + - + +
170A VAL 3.8 3.6 - - - +
172A ALA* 1.3 74.2 - - - +
174A ARG* 1.3 60.4 + - - +
176A VAL 3.1 0.7 + - - -
177A VAL* 2.8 54.3 + - + +
180A ALA* 4.0 9.2 - - + -
182A ILE* 3.8 26.9 - - + -
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Residues in contact with ARG 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A VAL* 2.9 32.6 + - + +
171A ALA* 4.0 5.4 - - - +
173A VAL* 1.3 74.3 - - - +
175A SER* 1.3 61.0 + - - +
176A VAL 3.4 0.5 + - - -
177A VAL 4.7 2.0 + - - -
178A PRO* 3.5 43.6 + - + +
180A ALA 3.1 24.7 + - - -
182A ILE* 3.6 19.0 - - - +
200A GLY* 3.1 24.2 + - - -
202A ASP* 2.7 31.7 + - - -
228A ARG* 3.5 6.0 - - - +
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Residues in contact with SER 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A VAL* 4.9 1.6 - - - +
171A ALA 3.1 13.8 + - - -
172A ALA* 2.7 23.0 + - - -
174A ARG* 1.3 76.5 - - - +
176A VAL* 1.3 69.5 + - - +
178A PRO* 4.9 2.3 - - - +
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Residues in contact with VAL 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A VAL* 4.1 23.3 - - + +
144A LEU* 3.8 33.4 - - + +
145A GLN 6.1 0.7 - - - -
172A ALA 3.2 3.8 + - - +
173A VAL 3.1 1.6 + - - -
175A SER* 1.3 95.4 + - - +
177A VAL* 1.3 70.0 + - + +
178A PRO* 3.5 8.2 - - - +
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Residues in contact with VAL 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A LEU* 4.0 22.2 - - + -
145A GLN 3.4 26.2 - - - +
146A PRO* 4.5 9.4 - - + +
148A THR* 4.1 17.9 - - - +
173A VAL* 2.8 38.6 + - + +
174A ARG* 4.7 0.3 + - - -
176A VAL* 1.3 84.9 - - + +
178A PRO* 1.4 66.2 - - - +
179A ASP* 3.1 3.4 - - + +
180A ALA* 3.0 22.4 + - + +
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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