Contacts of the helix formed by residues 173 - 189 (chain A) in PDB entry 5I4E
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 HIS 173 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A TYR* 3.8 19.1 - + - +
137A TYR* 3.6 4.7 + - - -
142A CYS* 5.2 0.7 - - - -
153A ILE* 2.9 44.5 + - + +
154A TYR* 3.6 17.2 - + - -
158A ILE* 4.1 8.2 - - + +
162A TYR* 3.4 32.4 + + + +
171A PRO 3.4 1.2 + - - -
172A PRO* 1.3 76.5 + - - +
174A VAL* 1.3 82.6 + - + +
175A TYR* 3.2 36.3 - + - +
176A ALA* 3.2 11.3 + - - +
177A VAL* 3.4 15.8 + - - +
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Residues in contact with VAL 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A TYR* 3.5 33.8 - - + +
154A TYR* 4.1 1.3 - - + -
173A HIS* 1.3 84.6 - - + +
175A TYR* 1.3 60.9 + - + +
177A VAL* 3.3 11.7 + - + +
178A THR* 2.8 39.7 + - - +
207A ASN* 3.8 19.5 - - + +
210A LYS* 3.6 22.7 - - + -
211A VAL* 3.8 26.9 - - + +
693A VAL* 5.3 10.5 - - + -
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Residues in contact with TYR 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ILE 4.2 1.6 - - - -
154A TYR* 3.3 26.4 + + - +
158A ILE* 4.1 8.7 - - + -
159A VAL* 3.5 39.5 - - + +
162A TYR* 3.7 23.8 - + + -
173A HIS* 3.2 28.7 - + + -
174A VAL* 1.3 83.5 - - + +
176A ALA* 1.3 55.0 + - - +
178A THR* 3.3 4.4 + - - -
179A GLU* 2.7 34.9 + - - +
210A LYS* 3.6 24.9 - - + -
213A GLN* 2.6 24.4 + - - -
214A TYR* 3.6 27.9 - + + -
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Residues in contact with ALA 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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137A TYR* 3.1 25.8 - - - +
162A TYR* 3.7 28.0 - - + -
165A LYS 6.2 0.2 - - - -
167A ARG* 4.7 12.9 - - + +
170A VAL* 4.2 9.9 - - + -
173A HIS 3.2 5.4 + - - +
175A TYR* 1.3 74.5 - - - +
177A VAL* 1.3 55.0 + - - +
179A GLU* 3.6 6.8 - - - +
180A GLY* 2.8 31.5 + - - -
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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
----------------------------------------------------------
137A TYR* 4.3 11.4 - - + -
142A CYS* 4.0 27.1 - - + -
167A ARG* 5.9 3.1 - - - +
173A HIS 3.6 13.0 - - - +
174A VAL* 3.3 12.5 + - + +
176A ALA* 1.3 72.4 - - - +
178A THR* 1.3 66.4 + - - +
180A GLY* 3.6 1.4 + - - -
181A ALA* 3.3 22.2 + - - +
194A ILE* 4.6 9.1 - - + +
211A VAL* 6.4 0.2 - - + -
691A SER* 3.1 30.4 + - - +
692A PHE 5.4 0.4 - - - +
693A VAL* 4.0 20.6 - - + -
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Residues in contact with THR 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 VAL 2.8 21.5 + - - -
175A TYR* 3.6 6.6 - - - -
177A VAL* 1.3 77.4 - - - +
179A GLU* 1.3 56.4 + - - +
181A ALA* 3.4 2.8 + - - +
182A TYR* 3.0 28.7 + - - +
194A ILE* 4.4 10.2 - - + +
211A VAL* 3.5 39.1 - - + +
214A TYR* 3.7 22.6 - - + +
215A LEU* 3.7 26.9 - - + +
474A LEU* 4.8 0.2 - - - +
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Residues in contact with GLU 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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162A TYR 3.9 9.4 - - - +
163A ARG* 3.9 2.3 - - - +
164A GLY* 3.0 23.6 + - - -
165A LYS 3.9 15.0 - - - +
175A TYR 2.7 20.7 + - - +
176A ALA* 3.6 8.7 - - - +
178A THR* 1.3 74.0 - - - +
180A GLY* 1.3 56.7 + - - +
182A TYR* 3.5 10.8 + - - +
183A ARG* 2.8 65.6 + - + +
214A TYR* 2.6 39.4 + - - +
218A VAL* 4.9 1.6 - - - +
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Residues in contact with GLY 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 ALA 2.8 16.8 + - - -
177A VAL* 4.0 2.5 - - - -
178A THR 3.3 0.2 - - - -
179A GLU* 1.3 77.5 - - - +
181A ALA* 1.4 48.5 + - - +
183A ARG* 3.5 4.4 + - - +
184A SER* 2.7 41.9 + - - -
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Residues in contact with ALA 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 3.3 17.0 + - - +
178A THR 3.8 3.4 - - - +
180A GLY* 1.4 70.3 - - - +
182A TYR* 1.3 59.0 - - - +
184A SER* 3.3 1.2 + - - -
185A MET* 3.0 24.9 + - - +
192A GLN* 3.2 35.6 - - + +
193A SER 5.4 0.7 - - - +
194A ILE* 3.8 26.0 - - + -
474A LEU* 4.4 4.0 - - + -
689A ASN 6.0 0.2 - - - +
691A SER* 4.9 8.5 - - - -
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Residues in contact with TYR 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 THR 3.0 17.4 + - - +
179A GLU* 3.6 19.3 - - - +
181A ALA* 1.3 77.0 - - - +
183A ARG* 1.3 70.7 + - - +
185A MET* 3.5 13.5 + - + +
186A LEU* 3.1 60.2 + - + +
214A TYR* 5.6 0.4 - - + -
215A LEU* 4.1 22.9 - - + -
218A VAL* 4.2 22.1 + - + -
219A ALA* 3.6 23.5 - - + +
270A PHE* 4.0 9.2 - + - -
273A ALA 5.4 0.2 + - - -
274A GLY 2.7 29.8 + - - -
275A TYR* 5.4 1.0 - - - -
474A LEU* 4.2 7.0 - - - +
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Residues in contact with ARG 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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163A ARG* 5.8 1.0 - - - +
164A GLY* 3.9 20.6 - - - +
165A LYS 5.9 0.9 - - - +
179A GLU* 2.8 49.4 + - + +
180A GLY* 3.8 5.2 - - - +
182A TYR* 1.3 82.0 - - + +
184A SER* 1.3 64.0 + - - +
186A LEU* 3.3 24.8 + - - +
187A GLN* 2.9 46.4 + - - +
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Residues in contact with SER 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 GLY 2.7 25.5 + - - -
181A ALA* 3.3 2.2 + - - -
183A ARG* 1.3 75.8 - - - +
185A MET* 1.3 56.4 + - - +
187A GLN* 4.5 6.2 + - - -
188A ASP* 3.0 45.5 + - - +
192A GLN* 3.5 25.9 + - - -
689A ASN* 5.1 5.9 + - - -
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Residues in contact with MET 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 ALA 3.0 17.2 + - - +
182A TYR* 3.6 12.6 - - + +
184A SER* 1.3 75.5 - - - +
186A LEU* 1.4 80.5 + - + +
189A ARG* 2.9 38.3 + - - +
190A GLU 3.3 23.3 - - - +
192A GLN* 3.5 10.2 - - + +
270A PHE* 3.3 52.9 - - + -
274A GLY* 5.0 0.4 - - - -
472A SER* 3.8 24.0 - - - +
473A PHE 3.9 13.5 - - - +
474A LEU* 4.7 5.6 - - - -
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Residues in contact with LEU 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 TYR* 3.1 46.1 + - + +
183A ARG* 3.6 32.3 - - - +
184A SER 3.3 0.2 - - - -
185A MET* 1.4 94.0 - - + +
187A GLN* 1.3 61.1 - - + +
189A ARG* 3.7 23.1 + - - +
273A ALA 5.1 0.7 - - - -
274A GLY* 3.4 32.5 - - - +
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Residues in contact with GLN 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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166A LYS* 5.9 3.1 + - - +
183A ARG* 2.9 33.2 + - - +
184A SER* 4.1 4.4 - - - +
186A LEU* 1.3 79.9 - - + +
188A ASP* 1.3 70.1 + - - +
189A ARG* 3.3 6.0 - - - +
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Residues in contact with ASP 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 SER* 3.0 24.4 + - - +
187A GLN* 1.3 84.4 - - - +
189A ARG* 1.3 70.2 + - - +
190A GLU* 3.3 28.9 - - + +
192A GLN* 5.4 1.4 + - - +
689A ASN* 5.4 4.5 + - - -
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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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185A MET* 2.9 25.0 + - - +
186A LEU* 3.7 31.4 + - - +
187A GLN 4.5 4.3 - - - +
188A ASP* 1.3 82.1 - - - +
190A GLU* 1.3 60.4 + - - +
271A ASP 4.8 2.8 + - - -
272A VAL* 4.1 31.6 + - - +
274A GLY* 5.3 0.6 - - - -
470A GLY* 2.2 35.2 + - - -
471A ALA* 4.0 22.2 + - + +
472A SER* 3.6 15.5 + - - -
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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