Contacts of the helix formed by residues 161 - 176 (chain A) in PDB entry 3VAH
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 161 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159A GLY 4.3 7.6 - - - +
160A ILE* 1.3 81.5 - - - +
162A GLU* 1.3 64.3 + - - +
163A GLU* 3.3 8.9 + - - +
164A ALA* 2.8 29.2 + - + +
165A MET* 3.2 22.5 + - - +
191A ILE* 4.0 4.7 - - - +
193A GLN* 5.0 1.6 - - - +
405B SO4 5.9 2.5 - - - +
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Residues in contact with GLU 162 (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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161A THR* 1.3 72.4 - - - +
163A GLU* 1.3 57.2 + - - +
165A MET* 3.7 1.6 + - - +
166A MET* 3.1 30.0 + - - +
189A VAL* 3.3 34.3 - - + +
190A GLN* 3.5 4.1 - - - +
191A ILE* 3.1 43.8 + - + +
193A GLN* 5.7 0.9 - - - +
7P U 4.4 5.2 - - - +
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Residues in contact with GLU 163 (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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161A THR* 3.2 8.9 - - - +
162A GLU* 1.3 77.1 - - - +
164A ALA* 1.3 59.7 + - - +
166A MET* 3.1 19.2 + - + +
167A ASP* 2.9 49.5 + - - +
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Residues in contact with ALA 164 (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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160A ILE* 4.0 22.2 - - + -
161A THR* 2.8 25.6 + - + +
163A GLU* 1.3 72.0 - - - +
165A MET* 1.3 58.5 + - - +
167A ASP* 3.6 9.7 + - - +
168A PHE* 3.1 27.5 + - - +
219A PHE* 4.3 5.6 - - + -
220A GLN* 5.8 0.7 - - - +
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Residues in contact with MET 165 (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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153A VAL* 4.9 3.6 - - - -
156A ILE* 4.0 34.3 - - + -
160A ILE* 4.4 8.2 - - + +
161A THR 3.2 16.0 + - - +
162A GLU 4.0 3.4 - - - +
164A ALA* 1.3 76.6 - - - +
166A MET* 1.3 64.6 + - - +
168A PHE* 3.4 4.0 + - - +
169A PHE* 3.2 49.0 + - + -
189A VAL* 4.1 19.3 - - + -
191A ILE* 4.9 6.5 - - + -
198A ALA* 4.6 14.6 - - - -
200A LEU* 4.6 2.7 - - + -
219A PHE* 3.3 38.4 - - + -
224A LEU* 4.9 3.6 - - + -
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Residues in contact with MET 166 (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 GLU 3.1 20.3 + - - +
163A GLU* 3.1 22.0 + - + +
165A MET* 1.3 74.1 - - - +
167A ASP* 1.3 69.8 + - - +
168A PHE 3.3 0.3 + - - -
169A PHE* 3.4 2.5 + - - +
170A ASN* 3.0 42.6 + - - +
186A VAL* 4.1 18.1 - - + +
187A LEU 3.9 26.5 - - - +
188A ALA* 4.2 8.1 - - - -
189A VAL* 4.3 8.3 - - + +
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Residues in contact with ASP 167 (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 GLU* 2.9 41.9 + - - +
164A ALA* 3.9 7.9 - - - +
165A MET 3.4 0.2 - - - -
166A MET* 1.3 80.0 - - - +
168A PHE* 1.3 58.1 + - - +
170A ASN* 3.9 5.0 + - - +
171A ALA* 2.9 31.9 + - - +
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Residues in contact with PHE 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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164A ALA 3.1 18.3 + - - +
165A MET 3.7 4.7 - - - +
166A MET 3.2 0.4 - - - -
167A ASP* 1.3 77.6 - - - +
169A PHE* 1.3 76.4 + + - +
171A ALA* 3.6 5.8 - - + +
172A GLN* 3.0 68.6 + - + +
217A ILE* 4.2 17.0 - - + -
218A ILE 4.0 14.6 - - - -
219A PHE* 3.3 52.3 - + + -
224A LEU* 4.9 2.9 - - + -
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Residues in contact with PHE 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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153A VAL* 4.4 3.1 - - + -
165A MET* 3.2 45.2 + - + +
166A MET* 4.1 1.3 - - - +
168A PHE* 1.3 89.8 - + - +
170A ASN* 1.3 65.7 + - - +
172A GLN* 4.1 4.4 - - + +
173A MET* 3.1 31.5 + - + +
186A VAL* 3.9 19.3 - - + -
200A LEU* 4.1 30.3 - - + -
202A PHE* 5.5 2.9 - + - -
211A ALA* 5.8 2.5 - - + -
214A PHE* 4.6 26.5 - + + -
217A ILE* 5.4 3.6 - - + -
224A LEU* 3.6 31.0 - - + -
226A ILE* 4.1 19.7 - - + -
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Residues in contact with ASN 170 (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 MET* 3.0 30.7 + - - +
167A ASP* 4.0 5.5 + - - +
169A PHE* 1.3 76.4 - - - +
171A ALA* 1.3 62.7 + - - +
173A MET* 3.6 4.4 + - - +
174A ARG* 3.3 32.7 + - - +
184A ASN* 3.2 41.7 + - - +
185A PRO* 3.3 12.0 - - + +
186A VAL* 2.8 42.9 + - - +
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Residues in contact with ALA 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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167A ASP 2.9 21.4 + - - +
168A PHE* 3.6 7.2 - - + +
170A ASN* 1.3 77.2 - - - +
172A GLN* 1.3 59.1 + - + +
174A ARG* 3.1 15.7 + - - +
175A LEU* 3.0 40.6 + - + +
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Residues in contact with GLN 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 PHE* 3.0 59.0 + - + +
169A PHE* 4.1 6.7 - - + +
170A ASN 3.3 0.2 - - - -
171A ALA* 1.3 74.8 - - + +
173A MET* 1.3 59.6 + - - +
175A LEU* 4.6 15.0 - - - +
176A GLY* 2.8 31.4 + - - -
214A PHE* 3.8 25.2 - - + -
217A ILE* 3.9 17.6 - - + +
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Residues in contact with MET 173 (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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169A PHE* 3.1 24.2 + - + +
170A ASN 3.8 5.2 - - - +
171A ALA 3.4 0.2 - - - -
172A GLN* 1.3 75.3 - - - +
174A ARG* 1.3 59.0 + - - +
177A GLY 3.2 2.1 + - - -
178A LEU* 2.9 59.1 + - + +
179A THR* 3.4 13.9 + - - +
185A PRO* 3.9 26.0 - - + -
186A VAL* 5.1 1.1 - - + -
202A PHE* 4.5 7.9 - - + -
207A GLU* 3.8 35.7 - - + +
210A GLN* 4.9 0.2 - - + -
211A ALA* 4.0 15.7 - - - -
214A PHE* 3.7 26.6 - - + -
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Residues in contact with ARG 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 ASN* 3.3 24.1 + - - +
171A ALA* 3.1 13.5 + - - +
173A MET* 1.3 74.2 - - - +
175A LEU* 1.3 68.2 + - + +
177A GLY* 3.1 12.8 + - - -
179A THR* 3.9 16.2 - - + +
183A GLY* 4.1 20.5 + - - +
184A ASN* 2.7 35.1 + - - +
185A PRO* 5.8 1.1 - - + -
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Residues in contact with LEU 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 ALA* 3.0 26.7 + - + +
172A GLN* 4.1 16.8 - - - +
174A ARG* 1.3 79.2 - - + +
176A GLY* 1.3 60.1 + - - +
177A GLY 3.5 0.7 + - - -
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Residues in contact with GLY 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 GLN* 2.8 18.8 + - - -
173A MET 4.2 0.2 - - - -
175A LEU* 1.3 76.9 - - - +
177A GLY* 1.3 61.7 + - - +
178A LEU* 3.3 18.2 + - - +
214A PHE* 5.4 5.2 - - - -
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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