Contacts of the helix formed by residues 178 - 189 (chain A) in PDB entry 1F4J
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 178 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169A LYS 4.3 1.6 + - - -
171A ASN* 3.1 27.2 + - + -
176A LEU 3.1 6.3 + - - +
177A LYS* 1.3 74.9 - - - +
179A PRO* 1.3 63.6 - - - +
180A ASP* 3.0 25.1 + - - +
181A MET* 3.0 54.3 + - + +
182A VAL* 3.1 18.8 + - - +
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Residues in contact with PRO 179 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A LYS 3.6 9.6 - - - +
178A ASP* 1.3 86.2 - - - +
180A ASP* 1.3 64.8 + - - +
182A VAL* 3.8 9.6 - - + -
183A TRP* 3.1 28.9 + - - +
466A HIS* 4.4 18.2 - - + +
469A ASP* 3.5 47.3 - - + +
470A ALA* 4.0 3.8 - - + +
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Residues in contact with ASP 180 (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 ASP* 3.0 16.1 + - - +
179A PRO* 1.3 77.8 - - - +
181A MET* 1.3 56.3 + - + +
184A ASP* 2.6 40.6 + - - +
469A ASP 4.2 2.8 - - - +
470A ALA* 3.3 5.4 - - - -
471A GLN* 2.9 58.5 + - - +
474A ILE* 3.4 14.3 - - + +
404B TYR* 4.6 0.7 - - - +
409B PHE* 4.8 8.5 - - + -
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Residues in contact with MET 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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166A HIS 4.2 6.3 - - - +
167A SER* 3.1 30.1 - - - +
169A LYS 3.1 27.8 - - - +
170A ARG 3.7 2.5 - - - +
171A ASN* 3.6 25.4 - - - +
172A PRO* 4.2 11.4 - - - -
178A ASP* 3.0 37.4 + - + +
180A ASP* 1.3 79.5 - - + +
182A VAL* 1.3 63.3 + - - +
185A PHE* 3.5 11.1 + - - +
402B PRO* 6.3 0.4 - - - -
403B ASN* 4.2 16.8 - - - -
404B TYR* 3.9 25.6 - - + +
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Residues in contact with VAL 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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167A SER* 3.5 18.1 + - - +
168A GLN* 3.6 23.2 + - - +
169A LYS 6.1 0.2 - - - +
177A LYS* 6.5 1.1 - - + -
178A ASP 3.1 20.3 + - - +
179A PRO* 3.7 9.0 - - + +
181A MET* 1.3 79.7 - - - +
183A TRP* 1.3 63.0 + - + +
185A PHE* 3.9 2.4 - - - +
186A TRP* 3.3 54.5 + - + -
466A HIS* 4.0 23.1 - - + +
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Residues in contact with TRP 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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179A PRO 3.1 23.4 + - - +
182A VAL* 1.3 73.9 - - + +
184A ASP* 1.3 63.9 + - - +
185A PHE 3.1 1.8 - - - -
186A TRP* 3.5 46.0 - + + +
187A SER* 2.7 31.2 + - - -
196A VAL* 4.4 7.2 - - + -
200A PHE* 3.8 20.6 - + - -
463A ILE* 4.0 20.2 - - + -
466A HIS* 2.8 34.4 + + - -
467A LEU* 3.4 42.2 - - + +
470A ALA* 4.2 4.0 - - + -
474A ILE* 3.3 21.6 - - + +
478A ALA* 4.4 7.9 - - + -
482A PHE* 4.2 20.6 - + - -
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Residues in contact with ASP 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 ASP 2.6 25.0 + - - +
183A TRP* 1.3 73.0 - - - +
185A PHE* 1.3 61.7 + - - +
187A SER* 3.0 18.1 + - - -
188A LEU* 3.1 22.7 - - - +
473A PHE* 4.3 5.9 - - - -
474A ILE* 3.7 15.4 - - + +
477A LYS* 5.7 0.7 + - - -
404B TYR* 2.7 32.4 + - + +
407B ASN* 3.2 1.0 - - - -
408B SER* 2.6 49.4 + - - -
409B PHE* 3.7 5.7 - - + -
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Residues in contact with PHE 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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155A ILE* 4.2 14.4 - - + -
160A LEU* 4.0 21.3 - - + -
163A SER* 4.0 9.9 - - - -
164A PHE* 3.6 39.9 - + + -
167A SER* 3.8 13.0 - - - +
181A MET 3.5 17.6 + - - +
182A VAL 3.9 2.0 - - - +
183A TRP 3.1 0.2 - - - -
184A ASP* 1.3 77.9 - - - +
186A TRP* 1.3 75.8 + + - +
188A LEU* 3.3 2.0 + - - +
189A ARG* 3.0 38.1 + - + +
404B TYR* 4.0 20.8 - + + -
405B TYR 3.4 26.5 - - - -
406B PRO* 4.2 13.2 - - + -
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Residues in contact with TRP 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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154A PHE* 3.5 30.2 - + + -
164A PHE* 3.2 19.8 - + - -
168A GLN* 3.3 26.9 - - - -
182A VAL* 3.3 28.4 + - + +
183A TRP* 3.5 39.5 + + + -
185A PHE* 1.3 94.3 - + - +
187A SER* 1.3 61.2 + - - +
189A ARG 3.0 20.5 - - - +
190A PRO* 3.6 3.5 - - - +
192A SER* 3.3 27.0 + - - +
196A VAL* 3.9 11.4 - - + -
199A LEU* 4.0 10.5 - - + -
200A PHE* 3.6 34.8 - + - -
481A ASN* 4.3 1.7 + - - -
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Residues in contact with SER 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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183A TRP* 2.7 23.4 + - - -
184A ASP* 3.0 14.0 + - - -
186A TRP* 1.3 73.3 - - - +
188A LEU* 1.3 67.4 + - - +
189A ARG 3.1 2.2 + - - -
190A PRO* 3.9 4.3 - - - +
474A ILE* 4.3 8.4 + - - +
477A LYS* 3.9 23.4 + - - +
478A ALA* 4.0 29.4 - - - +
481A ASN* 3.2 23.2 + - - +
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Residues in contact with LEU 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 ASP* 3.1 37.7 + - - +
185A PHE 3.9 2.0 - - - +
187A SER* 1.3 78.0 + - - +
189A ARG* 1.3 68.0 + - - +
190A PRO* 3.5 7.5 - - - +
477A LYS* 4.1 25.4 - - + +
406B PRO* 3.5 25.0 - - + +
407B ASN* 3.5 28.9 - - - +
408B SER* 3.5 15.3 - - - +
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Residues in contact with ARG 189 (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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155A ILE* 5.3 0.4 - - + -
157A ASP* 6.1 1.6 - - - +
160A LEU* 3.6 25.2 - - + +
185A PHE* 3.0 30.3 + - + +
186A TRP 3.0 5.2 - - - +
187A SER 3.1 0.2 - - - -
188A LEU* 1.3 89.5 - - - +
190A PRO* 1.3 52.3 - - - +
191A GLU* 2.9 43.2 + - - +
192A SER* 2.8 29.6 + - - -
434A THR* 5.2 2.0 + - - -
435A ALA* 3.3 39.4 - - - +
406B PRO* 3.8 27.8 - - + +
39D LEU* 3.7 35.0 + - - +
40D ASN* 5.6 1.4 + - - -
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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