Contacts of the helix formed by residues 167 - 189 (chain A) in PDB entry 3HF8
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 THR 167 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A ARG* 3.9 22.0 - - + +
165A GLU 5.0 0.7 - - - +
166A PHE* 1.3 75.6 - - - +
168A GLU* 1.3 59.3 + - - +
169A GLU* 3.7 8.1 + - - +
170A GLU* 2.9 42.5 + - - +
171A ILE* 2.9 29.5 + - - +
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Residues in contact with GLU 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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167A THR* 1.3 73.9 - - - +
169A GLU* 1.3 56.7 - - - +
171A ILE* 3.5 9.7 + - + +
172A LYS* 3.0 34.9 + - - +
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Residues in contact with GLU 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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167A THR* 3.2 7.3 + - - +
168A GLU* 1.3 76.7 - - - +
170A GLU* 1.3 66.5 + - + +
172A LYS* 3.3 9.1 + - + +
173A THR* 3.0 26.7 + - - -
258A HIS* 5.6 2.4 + - - -
259A SER* 2.9 34.8 + - - -
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Residues in contact with GLU 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ARG* 2.8 55.4 + - - +
148A PHE* 3.8 6.3 - - - -
166A PHE* 3.3 17.3 - - + -
167A THR* 2.9 33.0 + - - +
169A GLU* 1.3 77.5 - - + +
171A ILE* 1.3 61.0 + - - +
173A THR* 3.2 5.9 + - - -
174A TRP* 3.0 22.5 + - - +
211A ILE* 3.8 4.0 - - - +
256A VAL* 4.0 34.2 + - + +
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Residues in contact with ILE 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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166A PHE* 3.5 35.7 - - + +
167A THR 2.9 16.9 + - - +
168A GLU* 3.9 7.6 - - + +
170A GLU* 1.3 74.4 - - - +
172A LYS* 1.3 57.3 + - - +
174A TRP* 3.3 2.8 + - + +
175A GLY* 2.8 26.9 + - - -
208A GLU 4.0 1.8 - - - +
209A ASP* 3.4 39.7 - - + +
210A ASN* 4.2 1.8 - - - +
211A ILE* 3.9 17.9 - - + +
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Residues in contact with LYS 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 GLU* 3.0 22.1 + - - +
169A GLU* 3.5 8.7 - - + +
170A GLU 3.3 0.2 - - - -
171A ILE* 1.3 77.2 - - - +
173A THR* 1.3 61.6 + - - +
175A GLY* 3.3 2.3 + - - +
176A THR* 3.1 29.4 + - - +
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Residues in contact with THR 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A GLU 3.0 14.5 + - - -
170A GLU* 3.2 8.6 + - - -
172A LYS* 1.3 71.8 - - - +
174A TRP* 1.3 67.8 + - - +
176A THR* 3.3 7.9 + - - -
177A VAL* 3.1 33.8 + - + +
256A VAL* 4.0 8.5 - - + -
257A ARG* 3.9 34.6 + - + +
258A HIS 4.7 0.2 - - - +
259A SER* 3.4 30.4 + - - -
262A PRO* 4.6 11.4 - - + +
271A CYS* 5.3 0.2 - - - -
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Residues in contact with TRP 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 GLU 3.0 8.1 + - - +
171A ILE 3.4 7.9 - - - +
173A THR* 1.3 77.0 - - - +
175A GLY* 1.3 55.0 + - - +
177A VAL* 3.1 3.9 + - - +
178A PHE* 2.7 59.7 + + + +
206A TYR* 4.3 3.8 - + - -
207A ARG 2.7 22.8 + - - -
208A GLU 3.4 15.0 - - - -
209A ASP 5.1 0.2 - - - -
210A ASN 3.0 15.9 + - - -
211A ILE* 3.5 30.1 - - + -
212A PRO* 3.4 28.5 - - + -
256A VAL* 4.7 1.0 - - + +
271A CYS* 3.7 36.3 - - + -
274A LEU* 3.9 21.8 - - + -
275A LEU* 3.7 36.8 - - + -
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Residues in contact with GLY 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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171A ILE 2.8 15.7 + - - -
172A LYS* 3.6 4.0 - - - -
173A THR 3.3 0.4 - - - -
174A TRP* 1.3 74.4 - - - +
176A THR* 1.3 52.8 + - - +
178A PHE* 3.8 0.6 - - - +
179A ARG* 2.8 39.2 + - - +
208A GLU* 3.3 30.9 - - - +
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Residues in contact with THR 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 LYS* 3.1 17.1 + - - +
173A THR* 3.3 8.4 + - - -
175A GLY* 1.3 74.3 - - - +
177A VAL* 1.3 63.6 + - - +
179A ARG* 3.8 32.9 + - - +
180A GLU* 3.0 32.1 + - + +
262A PRO* 4.1 26.2 - - + +
263A PHE* 5.1 8.3 - - + -
338A ILE* 4.8 3.6 - - + -
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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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173A THR* 3.1 16.8 + - + +
174A TRP* 3.5 8.5 - - - +
176A THR* 1.3 74.3 - - - +
178A PHE* 1.3 62.8 + - - +
180A GLU* 4.1 0.3 - - - +
181A LEU* 3.0 54.2 + - + +
257A ARG* 4.1 15.5 - - - +
262A PRO* 3.5 32.3 - - + +
271A CYS* 4.4 14.1 - - + -
275A LEU* 3.9 12.1 - - + -
336A SER* 4.2 11.0 - - - +
338A ILE* 3.9 8.7 - - + -
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Residues in contact with PHE 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 TRP* 2.7 50.6 + + + +
175A GLY* 3.8 4.5 - - - +
177A VAL* 1.3 74.2 - - - +
179A ARG* 1.3 62.0 + - - +
181A LEU* 4.1 1.0 - - - +
182A ASN* 2.9 56.4 + - + +
197A LEU* 5.7 3.4 - - + -
201A SER* 4.5 6.7 - - - -
206A TYR* 3.9 39.3 - + + -
207A ARG* 4.0 1.6 - - - -
208A GLU* 3.4 36.1 - - + -
275A LEU* 3.8 23.3 - - + -
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Residues in contact with ARG 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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175A GLY 2.8 20.5 + - - +
176A THR* 3.8 31.2 + - - +
178A PHE* 1.3 81.1 - - - +
180A GLU* 1.3 106.2 + - - +
182A ASN* 3.6 4.1 + - - +
183A LYS* 3.5 36.1 + - - +
208A GLU* 3.9 24.1 + - - +
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Residues in contact with GLU 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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176A THR* 3.0 23.9 + - + +
179A ARG* 1.3 108.9 + - - +
181A LEU* 1.3 66.8 + - - +
183A LYS* 3.3 40.7 + - - +
184A LEU* 3.5 12.5 - - - +
263A PHE* 4.9 8.5 - - + -
338A ILE* 3.6 30.3 - - + +
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Residues in contact with LEU 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 VAL* 3.0 42.6 + - + +
178A PHE* 4.2 2.5 - - - +
180A GLU* 1.3 76.3 - - - +
182A ASN* 1.3 58.0 + - - +
184A LEU* 2.9 21.7 + - + +
185A TYR* 2.9 35.9 + - + +
275A LEU* 4.1 6.7 - - + -
335A LEU 3.4 26.9 - - - +
336A SER* 3.8 11.7 - - - +
337A SER 3.8 4.9 - - - +
338A ILE* 3.6 34.5 - - + +
341A LEU* 3.9 16.8 - - + -
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Residues in contact with ASN 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 PHE* 2.9 68.7 + - + +
179A ARG* 4.0 5.2 - - - +
180A GLU 3.3 0.2 - - - -
181A LEU* 1.3 75.7 - - - +
183A LYS* 1.3 61.2 + - - +
184A LEU 3.2 0.2 - - - -
185A TYR* 3.6 13.1 - - - +
186A PRO* 3.2 20.4 - - - +
197A LEU* 3.4 26.6 - - - +
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Residues in contact with LYS 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 ARG* 3.5 26.9 + - - +
180A GLU* 3.3 41.2 + - - +
181A LEU 3.1 0.6 - - - -
182A ASN* 1.3 78.4 - - - +
184A LEU* 1.3 65.5 + - + +
186A PRO* 3.7 8.4 - - - +
187A THR* 4.8 5.4 + - - +
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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 GLU 3.5 14.4 - - - +
181A LEU* 2.9 9.0 + - + +
183A LYS* 1.3 84.7 - - + +
185A TYR* 1.3 66.7 + - - +
186A PRO* 3.3 0.9 - - - -
187A THR* 3.1 6.7 + - - -
188A HIS* 3.0 42.4 + - + +
338A ILE* 3.7 36.1 - - + +
341A LEU* 3.7 24.7 - - + -
342A LYS* 3.8 27.1 - - + -
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Residues in contact with TYR 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 LEU* 2.9 42.7 + - + +
182A ASN* 3.6 18.2 - - - +
184A LEU* 1.3 75.2 - - - +
186A PRO* 1.4 67.5 - - + +
188A HIS* 4.6 0.2 - - - -
189A ALA* 2.8 31.2 + - + +
193A TYR* 3.0 34.0 + + - -
194A LEU* 3.6 20.6 - - + +
197A LEU* 3.6 24.0 - - + -
275A LEU* 3.6 14.2 - - + +
335A LEU* 2.6 49.7 + - + -
341A LEU* 4.1 9.4 - - + -
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Residues in contact with PRO 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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182A ASN 3.2 20.6 - - - +
183A LYS* 3.7 7.6 - - - +
184A LEU 3.3 4.9 - - - -
185A TYR* 1.4 91.6 - - + +
187A THR* 1.3 62.1 + - + +
194A LEU* 3.9 17.8 - - + +
328A ARG* 3.0 19.1 + - - -
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Residues in contact with THR 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 LYS 4.8 3.9 + - - +
184A LEU* 3.1 6.5 + - - -
186A PRO* 1.3 80.6 - - + +
188A HIS* 1.3 87.0 + - - +
326A GLN* 5.7 0.2 + - - -
327A LEU 5.1 0.7 - - - +
328A ARG* 3.4 26.9 + - - +
345A LEU* 4.4 4.0 - - - +
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Residues in contact with HIS 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 35.5 + - + +
187A THR* 1.3 107.6 + - - +
189A ALA* 1.3 64.3 + - - +
328A ARG* 3.5 7.6 - - - -
329A VAL* 2.9 28.8 + - - +
341A LEU* 3.4 47.9 + - + -
342A LYS* 4.1 14.3 + - + +
345A LEU* 3.5 26.5 - - + +
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Residues in contact with ALA 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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185A TYR* 2.8 27.0 + - - +
188A HIS* 1.3 75.2 - - - +
190A CYS* 1.3 68.2 + - - +
193A TYR* 3.7 30.5 - - + -
194A LEU* 3.7 8.7 - - + +
328A ARG* 3.1 22.2 + - - -
329A VAL 3.7 5.8 - - - -
335A LEU* 3.8 17.5 - - + -
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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