Contacts of the helix formed by residues 174 - 186 (chain A) in PDB entry 3HA6
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 VAL 174 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A PHE* 3.6 32.3 - - + -
169A LEU* 2.8 34.1 + - + +
172A ALA* 3.6 15.5 - - + +
173A GLY* 1.3 79.0 - - - +
175A GLU* 1.3 61.1 + - - +
176A HIS 3.2 2.7 - - - -
177A GLN* 3.0 25.4 + - + +
178A LEU* 2.9 24.7 + - - +
277A TRP* 6.0 5.2 - - + -
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Residues in contact with GLU 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A LEU* 3.8 13.6 + - + +
170A GLU* 5.0 8.5 - - + +
173A GLY 3.8 1.0 - - - -
174A VAL* 1.3 77.1 - - - +
176A HIS* 1.3 65.3 + - + +
178A LEU* 3.1 9.8 + - + +
179A ARG* 2.8 40.7 + - - +
4B VAL 5.7 2.9 - - - +
6B SER* 3.0 37.3 + - - -
8B TYR* 3.7 20.6 - - + +
10B TYR* 2.7 27.5 + - - -
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Residues in contact with HIS 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A GLY 5.4 2.0 + - - +
174A VAL 3.2 0.4 - - - -
175A GLU* 1.3 90.7 - - + +
177A GLN* 1.3 78.9 + - - +
179A ARG* 3.1 34.1 + - - +
180A ARG* 3.1 58.8 + - - +
288A TPO 5.5 0.6 + - - -
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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
----------------------------------------------------------
173A GLY 3.5 7.5 + - - +
174A VAL* 3.0 40.9 + - + +
176A HIS* 1.3 91.0 + - - +
178A LEU* 1.3 63.7 + - - +
180A ARG* 3.4 9.6 + - - +
181A GLU 3.1 17.3 + - - -
276A GLY* 3.2 37.0 - - - +
277A TRP* 3.7 38.0 - - + -
288A TPO 5.4 6.1 + - - +
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Residues in contact with LEU 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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164A LEU* 3.6 26.9 - - + -
169A LEU* 3.6 33.9 - - + -
174A VAL 2.9 13.2 + - - +
175A GLU* 3.1 10.9 + - - +
177A GLN* 1.3 77.6 - - - +
179A ARG* 1.3 60.0 + - - +
181A GLU* 3.5 19.7 + - - +
182A VAL* 3.0 35.6 + - + +
206A VAL* 4.1 22.2 - - + -
208A LEU* 4.2 10.1 - - + -
276A GLY* 5.7 0.2 - - - -
8B TYR* 4.5 2.9 - - + -
10B TYR* 3.9 15.0 - - - +
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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 GLU* 2.8 21.3 + - - +
176A HIS* 3.1 49.0 + - - +
177A GLN 3.3 0.2 - - - -
178A LEU* 1.3 75.0 - - - +
180A ARG* 1.3 67.0 + - - +
183A GLU* 2.8 65.1 + - - +
9B SER 5.7 1.1 - - - -
10B TYR* 3.2 41.0 + - + -
38B LYS* 6.1 0.2 - - - +
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Residues in contact with ARG 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 HIS* 3.1 47.7 + - + +
177A GLN* 3.8 16.3 - - - +
178A LEU 3.3 0.4 - - - -
179A ARG* 1.3 81.4 - - - +
181A GLU* 1.3 64.8 + - - +
183A GLU* 4.8 2.9 - - - -
184A ILE* 2.9 39.1 + - + +
255A ARG* 3.6 9.5 - - - +
275A PHE 4.3 1.6 - - - +
276A GLY 4.8 3.4 - - - +
277A TRP* 5.9 0.4 - - - -
278A SER 3.5 21.8 - - - +
279A VAL* 3.9 13.7 - - - +
280A HIS 5.8 0.2 - - - +
286A ARG* 3.0 27.9 - - - +
288A TPO 2.7 34.1 + - - -
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Residues in contact with GLU 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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162A LYS* 5.2 9.4 + - - +
164A LEU* 5.5 0.7 - - - +
177A GLN 3.1 11.8 + - - +
178A LEU* 3.6 18.7 - - - +
179A ARG 3.3 0.2 - - - -
180A ARG* 1.3 76.3 - - - +
182A VAL* 1.3 58.5 + - - +
185A GLN* 2.8 56.6 + - + +
196A LEU* 4.8 0.4 - - + -
208A LEU* 3.6 26.5 - - + +
210A LEU* 6.0 0.4 - - - +
274A ASP* 3.5 10.4 + - - +
275A PHE* 2.8 45.0 + - - +
276A GLY* 3.7 6.4 + - - +
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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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178A LEU* 3.0 31.5 + - + +
179A ARG 4.0 0.7 - - - +
181A GLU* 1.3 74.8 - - - +
183A GLU* 1.3 59.5 + - - +
186A SER* 2.8 34.3 + - - +
196A LEU* 3.8 13.7 - - + -
198A GLY* 6.3 0.2 - - - -
199A TYR* 3.8 28.5 - - + +
206A VAL* 5.7 0.2 - - + -
208A LEU* 4.3 19.3 - - + -
10B TYR* 3.9 22.9 - - + -
12B ALA* 3.7 21.3 - - + -
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Residues in contact with GLU 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* 2.8 63.3 + - + +
180A ARG* 4.3 2.9 - - - +
182A VAL* 1.3 76.5 - - - +
184A ILE* 1.3 57.9 + - + +
186A SER* 4.4 0.9 - - - -
187A HIS* 2.7 28.2 + - - -
10B TYR* 3.6 14.7 - - + -
11B ASP* 3.2 35.7 + - - +
12B ALA* 4.4 0.4 - - - -
34B TRP* 3.2 18.2 - - + -
38B LYS* 3.4 23.2 + - - -
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Residues in contact with ILE 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 ARG* 2.9 31.1 + - + +
183A GLU* 1.3 78.6 - - + +
185A GLN* 1.3 68.3 + - - +
186A SER 3.2 1.8 - - - -
187A HIS 2.9 12.5 + - - -
188A LEU* 3.4 21.4 + - + +
252A VAL* 3.8 29.4 - - + -
275A PHE* 4.5 2.0 - - + -
278A SER* 3.5 22.9 - - - +
279A VAL* 3.7 9.2 - - - +
280A HIS* 3.6 31.2 - - + +
34B TRP* 4.9 3.4 - - + -
35B PHE* 3.5 18.7 - - + -
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Residues in contact with GLN 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 GLU* 2.8 48.1 + - - +
184A ILE* 1.3 74.1 - - - +
186A SER* 1.3 55.9 + - - +
188A LEU* 3.0 36.7 + - - +
193A ILE* 4.7 3.0 - - + +
194A LEU* 2.9 35.8 + - - +
195A ARG* 4.4 1.0 + - - -
196A LEU* 4.1 15.6 + - + +
210A LEU* 3.6 27.1 - - - +
273A ALA* 4.4 7.0 - - - +
274A ASP 4.5 1.2 + - - +
275A PHE* 3.4 34.2 + - + +
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Residues in contact with SER 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A VAL* 2.8 22.5 + - - -
184A ILE 3.1 0.6 + - - -
185A GLN* 1.3 77.5 - - - +
187A HIS* 1.3 66.6 + - - +
188A LEU 3.4 0.9 - - - -
189A ARG* 2.7 28.1 + - - -
196A LEU* 3.6 32.1 - - - +
198A GLY* 5.5 0.2 - - - -
12B ALA* 3.9 1.0 - - - +
13B PRO* 3.3 35.8 - - - +
31B ILE* 3.8 4.2 - - - +
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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