Contacts of the helix formed by residues 167 - 178 (chain A) in PDB entry 6FBU
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 167 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A GLN* 3.0 26.6 + - - -
52A LYS* 4.0 0.2 - - - -
157A LEU 4.6 0.7 - - - +
158A LEU* 3.6 11.2 - - - +
166A LEU* 1.3 75.0 - - - +
168A ASN* 1.3 60.9 + - - -
170A LEU* 3.3 1.7 + - - +
171A ARG* 2.8 27.7 + - - +
428C G 3.4 14.8 - - - -
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Residues in contact with ASN 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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2A GLN* 3.7 1.6 - - - +
158A LEU* 3.6 7.8 - - + +
167A GLY* 1.3 67.6 - - - -
169A TYR* 1.3 68.7 + - - +
171A ARG* 2.8 45.8 + - - +
172A VAL* 3.0 16.8 + - - +
230A PHE* 4.6 4.3 - - - -
252A ARG* 3.8 12.5 - - - +
253A PRO* 2.7 34.4 + - - +
427C PED 2.8 31.1 + - - +
428C G 3.1 18.8 + - - +
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Residues in contact with TYR 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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2A GLN* 3.2 37.2 - - + -
4A PRO* 3.8 6.6 - - - +
5A GLU* 2.6 31.2 + - - -
167A GLY 3.5 0.2 - - - -
168A ASN* 1.3 76.9 - - - +
170A LEU* 1.3 84.3 + - + +
172A VAL* 3.1 5.2 - - - +
173A GLU* 2.9 26.4 + - + +
208A SER* 2.7 19.1 + - - -
212A ARG* 3.8 11.2 - - - -
225A PHE* 3.6 21.3 - + - -
227A PHE* 3.4 20.0 - + - -
230A PHE* 3.8 42.0 - + + -
302A SO4 4.0 5.8 - - - -
427C PED 3.4 9.9 + - - +
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Residues in contact with LEU 170 (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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2A GLN* 3.0 27.4 + - + +
4A PRO* 3.6 28.5 - - + -
165A GLY 3.9 9.6 - - - +
166A LEU* 4.1 7.4 - - + -
167A GLY 3.7 5.6 - - - +
169A TYR* 1.3 101.4 - - + +
171A ARG* 1.3 58.3 + - - +
173A GLU* 4.5 1.1 - - - +
174A ILE* 2.9 45.6 + - + +
204A ILE* 3.9 26.0 - - + +
205A PRO* 3.9 29.6 - - + -
208A SER* 4.7 1.1 - - - -
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Residues in contact with ARG 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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153A PHE 4.4 1.8 - - - -
154A ALA* 2.8 45.3 + - - +
157A LEU* 4.1 23.1 - - + +
158A LEU* 3.6 18.4 - - + +
166A LEU* 5.8 0.6 - - - +
167A GLY 2.8 14.8 + - - +
168A ASN* 2.8 35.5 + - - +
170A LEU* 1.3 76.4 - - - +
172A VAL* 1.3 62.0 + - - +
174A ILE* 4.0 1.3 - - - +
175A LEU* 3.1 39.8 + - + +
249A LEU* 3.5 21.0 + - - +
250A SER* 3.3 20.6 + - - -
252A ARG* 3.7 8.7 + - - +
253A PRO 3.3 15.4 + - - -
254A PHE* 4.0 19.2 - - + +
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Residues in contact with VAL 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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168A ASN* 3.0 18.4 + - - +
169A TYR 3.1 11.4 - - - +
171A ARG* 1.3 76.2 - - - +
173A GLU* 1.3 63.2 + - - +
175A LEU* 4.0 1.8 - - - +
176A TRP* 3.0 30.3 + - - +
229A VAL* 3.9 11.2 - - + +
230A PHE* 3.7 33.7 - - + -
253A PRO 4.7 0.7 - - - +
254A PHE* 3.5 36.1 - - + -
255A TYR* 3.7 27.6 - - + +
261A GLN* 4.8 0.9 + - - -
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Residues in contact with GLU 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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169A TYR* 2.9 25.2 + - + +
170A LEU* 4.1 3.1 - - - +
172A VAL* 1.3 78.8 - - + +
174A ILE* 1.3 57.2 + - - +
176A TRP* 4.0 4.7 - - - +
177A GLN* 3.0 28.1 + - - +
204A ILE* 3.5 19.7 - - + +
225A PHE* 4.5 6.5 - - + -
226A ARG 3.8 2.6 - - - +
227A PHE* 3.4 22.4 - - + -
228A LYS* 2.5 40.2 + - - +
229A VAL* 2.8 11.4 + - - +
230A PHE* 2.8 33.4 + - - +
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Residues in contact with ILE 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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157A LEU* 4.0 12.1 - - + -
166A LEU* 3.9 30.3 - - + -
170A LEU* 2.9 31.6 + - + +
171A ARG 4.0 2.2 - - - +
173A GLU* 1.3 74.3 - - - +
175A LEU* 1.3 66.1 + - - +
177A GLN* 3.2 11.3 + - - +
178A VAL* 3.2 14.7 + - - +
197A LEU* 3.9 27.1 - - + -
200A ALA* 3.8 31.6 - - + +
201A LEU* 4.1 13.0 - - + -
204A ILE* 3.6 19.7 - - + -
205A PRO* 4.3 4.9 - - + -
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Residues in contact with LEU 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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153A PHE* 4.0 30.1 - - + +
157A LEU* 4.0 13.7 - - + -
171A ARG* 3.1 36.6 + - + +
172A VAL* 4.1 2.2 - - - +
174A ILE* 1.3 77.3 - - - +
176A TRP* 1.3 55.8 + - - +
178A VAL* 3.3 6.5 + - + +
179A GLY 2.9 22.9 + - - -
180A LEU* 3.0 32.9 + - + +
181A THR 3.8 13.9 - - - +
182A GLY* 4.0 23.1 - - - -
197A LEU* 5.2 3.6 - - + -
254A PHE* 4.0 13.7 - - + -
261A GLN* 4.0 4.3 - - - +
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Residues in contact with TRP 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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172A VAL 3.0 19.1 + - - +
173A GLU* 4.0 4.9 - - - +
175A LEU* 1.3 75.6 - - - +
177A GLN* 1.3 78.7 + - + +
179A GLY 3.0 3.1 + - - -
228A LYS* 3.5 50.7 - - + -
229A VAL* 3.2 27.7 - - + +
237A CYS* 3.5 23.6 - - - -
238A GLU* 4.4 8.5 - - + -
239A ARG* 2.6 81.6 + - + -
257A CYS* 4.1 5.6 - - + -
260A CYS* 3.6 5.5 - - - -
261A GLN* 3.1 34.6 - - + +
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Residues in contact with GLN 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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173A GLU 3.0 19.8 + - - +
174A ILE 3.2 6.9 + - - +
176A TRP* 1.3 97.9 - - + +
178A VAL* 1.3 66.4 + - + +
200A ALA* 4.4 5.8 - - + -
204A ILE* 3.5 21.1 - - + +
228A LYS* 4.3 9.2 + - - +
239A ARG* 3.4 13.7 + - - +
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Residues in contact with VAL 178 (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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174A ILE 3.2 10.7 + - - +
175A LEU* 3.6 10.1 - - + +
176A TRP 3.2 0.4 - - - -
177A GLN* 1.3 80.7 - - + +
179A GLY* 1.3 61.2 + - - +
180A LEU* 3.4 30.9 + - + +
193A GLN* 5.3 6.1 + - - +
196A ALA* 3.6 43.3 - - + +
197A LEU* 4.0 15.0 - - + +
200A ALA* 3.7 18.2 - - + -
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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