Contacts of the helix formed by residues 184 - 189 (chain A) in PDB entry 3V4V
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 GLY 184 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A GLY 4.1 1.4 - - - +
164A SER* 3.3 30.5 + - - +
165A CYS* 3.0 15.0 + - - -
166A GLN* 5.1 2.3 + - - +
183A PRO* 1.3 77.9 - - - +
185A SER* 1.3 65.7 + - - +
186A SER 3.1 3.3 + - - -
187A TYR* 3.6 3.5 + - - -
188A TRP* 3.3 30.4 + - - -
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Residues in contact with SER 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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162A PHE* 3.4 33.3 - - - +
165A CYS* 3.5 6.1 - - - +
182A ALA* 2.7 36.2 + - - +
183A PRO 3.2 1.4 - - - -
184A GLY* 1.3 74.1 - - - +
186A SER* 1.3 60.8 + - - +
189A THR* 2.7 27.5 + - - -
190A GLY 3.1 20.9 + - - -
191A SER* 3.3 7.1 - - - -
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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
----------------------------------------------------------
159A GLY 3.6 8.6 + - - -
160A GLU* 4.2 1.8 - - - +
161A ASN* 3.6 20.4 + - - +
162A PHE* 3.7 14.6 - - - +
184A GLY 3.1 4.2 + - - -
185A SER* 1.3 77.3 - - - +
187A TYR* 1.3 70.6 + - - +
189A THR* 3.2 17.7 + - - +
214A PHE* 3.3 17.7 - - - -
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Residues in contact with TYR 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A LYS* 4.0 21.1 - - - +
158A PHE* 6.2 0.2 - + - -
159A GLY* 3.2 28.0 + - - -
160A GLU* 3.3 38.4 + - + +
184A GLY 3.6 1.4 + - - -
186A SER* 1.3 76.9 - - - +
188A TRP* 1.3 91.1 + + + +
189A THR 3.4 0.9 + - - -
214A PHE* 3.4 29.9 - + + +
215A GLY* 3.5 9.4 + - - -
236B LEU 5.5 4.5 - - - -
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Residues in contact with TRP 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A PHE* 3.6 26.0 - + - -
159A GLY* 5.2 1.3 - - - -
164A SER* 4.5 6.4 + - - -
166A GLN* 4.2 2.2 + - - -
183A PRO 3.1 12.8 - - - -
184A GLY* 3.3 31.8 + - - -
185A SER 3.8 0.7 - - - -
186A SER 3.1 1.6 - - - -
187A TYR* 1.3 115.6 - + + +
189A THR* 1.3 64.8 + - - +
190A GLY 3.0 0.9 - - - -
215A GLY* 2.9 17.6 + - - -
216A SER 3.0 8.8 + - - -
217A TYR* 3.0 39.3 + + + -
184B PRO* 3.6 48.6 - - + +
236B LEU 4.0 9.6 - - - -
237B ASP* 3.6 34.8 - - + -
238B SER 5.7 0.2 - - - -
281B LEU* 4.0 8.9 - - + +
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Residues in contact with THR 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 SER* 2.7 20.1 + - - -
186A SER* 3.2 20.8 + - - +
187A TYR 3.3 0.8 - - - -
188A TRP* 1.3 76.8 - - - +
190A GLY* 1.3 64.3 + - - +
207A ASP* 4.4 14.5 - - + +
210A ASN* 5.7 0.7 - - - +
212A VAL* 3.8 18.7 - - - +
213A LYS 3.4 15.9 - - - +
214A PHE* 3.4 33.4 - - + +
215A GLY 3.7 0.2 - - - +
216A SER* 3.6 10.4 - - - -
218A LEU* 3.2 21.0 + - - +
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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