Contacts of the helix formed by residues 178 - 188 (chain A) in PDB entry 5F3K
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 SER 178 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A THR* 2.7 31.9 + - - +
175A ILE* 2.9 15.5 + - - -
177A ARG* 1.3 79.9 + - - +
179A GLY* 1.3 64.7 + - - +
180A SER 3.3 2.7 - - - -
181A LYS* 3.2 30.4 + - - +
182A ALA* 2.9 21.2 + - - +
197A ILE* 5.0 0.5 - - - +
203A VAL* 4.3 16.5 - - - +
206A TYR* 4.3 1.1 - - - -
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Residues in contact with GLY 179 (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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177A ARG 3.5 3.2 - - - -
178A SER* 1.3 76.8 - - - +
180A SER* 1.3 56.7 + - - +
182A ALA* 3.2 1.7 + - - +
183A PHE* 2.9 34.3 + - - -
206A TYR* 3.3 40.2 + - - -
93B GLU* 3.9 10.3 - - - -
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Residues in contact with SER 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A SER 3.3 0.4 - - - -
179A GLY* 1.3 74.2 - - - +
181A LYS* 1.3 58.9 + - - +
183A PHE* 3.3 7.4 + - - +
184A LEU* 2.9 30.7 + - - +
93B GLU* 4.3 4.0 + - - -
96B LYS* 2.7 42.1 + - - +
97B LEU* 3.8 17.9 + - - +
100B ILE* 3.5 24.0 - - - +
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Residues in contact with LYS 181 (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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177A ARG 5.5 0.9 - - - +
178A SER* 3.2 33.7 + - - +
180A SER* 1.3 78.9 - - - +
182A ALA* 1.3 57.3 + - - +
184A LEU* 3.4 6.7 + - - +
185A ASP* 2.9 31.1 + - - +
203A VAL* 4.7 11.8 - - + +
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Residues in contact with ALA 182 (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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178A SER* 2.9 12.8 + - - +
179A GLY 3.5 7.2 - - - +
181A LYS* 1.3 75.7 - - - +
183A PHE* 1.3 59.5 + - + +
185A ASP* 3.4 3.3 + - - +
186A ALA* 2.9 29.1 + - - +
203A VAL* 3.3 38.9 - - + +
204A GLY* 5.1 2.8 - - - -
206A TYR* 3.5 22.4 - - + -
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Residues in contact with PHE 183 (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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101A VAL* 5.8 0.2 - - + -
105A LEU* 3.5 30.5 - - + +
179A GLY 2.9 26.3 + - - +
180A SER* 3.7 6.7 - - - +
182A ALA* 1.3 75.1 - - + +
184A LEU* 1.3 65.8 + - - +
186A ALA* 3.2 7.2 + - - +
187A LEU* 3.1 27.6 + - + +
206A TYR* 4.1 9.9 - + - -
210A MET* 3.7 31.4 - - + -
90B PHE* 3.8 17.5 - + - -
93B GLU* 3.3 41.3 - - + -
94B THR* 3.8 20.4 - - - -
97B LEU* 3.9 16.2 - - + -
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Residues in contact with LEU 184 (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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180A SER 2.9 17.8 + - - +
181A LYS* 3.8 5.6 - - - +
183A PHE* 1.3 75.6 - - - +
185A ASP* 1.3 64.4 + - - +
187A LEU* 3.1 4.9 + - + +
188A GLN* 3.0 56.4 + - - +
97B LEU* 3.8 19.7 - - + +
101B VAL* 4.6 7.0 - - + -
187B LEU* 3.9 30.5 - - + +
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Residues in contact with ASP 185 (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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181A LYS 2.9 18.2 + - - +
182A ALA 3.6 6.0 - - - +
184A LEU* 1.3 77.1 - - - +
186A ALA* 1.3 65.5 + - - +
188A GLN* 3.2 23.4 + - - +
203A VAL* 4.2 21.7 - - + +
204A GLY* 5.1 6.6 - - - -
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Residues in contact with ALA 186 (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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105A LEU* 4.5 20.4 - - + +
182A ALA 2.9 17.7 + - - +
183A PHE* 3.2 7.6 + - - +
185A ASP* 1.3 80.1 + - - +
187A LEU* 1.3 62.2 + - - +
188A GLN 4.3 3.5 - - - +
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Residues in contact with LEU 187 (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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101A VAL* 3.9 32.1 - - + +
104A SER* 6.2 1.1 - - - +
105A LEU* 4.1 23.1 - - + -
183A PHE 3.1 15.0 + - - +
184A LEU* 3.1 8.8 + - + +
186A ALA* 1.3 78.4 - - - +
188A GLN* 1.3 66.9 + - + +
97B LEU* 3.7 24.7 - - + -
184B LEU* 6.0 0.4 - - + -
187B LEU* 4.0 29.2 - - + -
188B GLN* 3.3 41.9 + - + +
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Residues in contact with GLN 188 (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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184A LEU* 3.0 39.9 + - + +
185A ASP* 3.2 15.9 + - - +
186A ALA 4.3 2.6 - - - +
187A LEU* 1.3 82.4 - - - +
186B ALA 4.4 1.0 - - - +
187B LEU 3.0 27.6 - - - +
188B GLN 3.7 17.0 - - - +
189B ASN* 2.7 28.8 + - + +
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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