Contacts of the helix formed by residues 200 - 213 (chain A) in PDB entry 3V50
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 SER 200 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A ASP* 2.7 36.7 + - - -
198A ARG 4.2 0.2 + - - -
199A LEU* 1.3 76.3 - - - +
201A ALA* 1.3 65.5 + - - +
202A ARG* 3.7 7.0 + - - +
203A SER* 3.1 15.8 + - - -
204A GLN* 2.9 21.0 + - - +
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Residues in contact with ALA 201 (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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197A GLN* 5.6 3.1 + - - +
200A SER* 1.3 73.4 - - - +
202A ARG* 1.3 63.9 + - - +
204A GLN* 3.3 13.5 + - - +
205A ARG* 3.0 56.9 + - - +
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Residues in contact with ARG 202 (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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91A LEU* 5.6 7.5 - - - +
92A GLU* 5.2 7.9 + - - -
200A SER* 3.3 6.5 + - - +
201A ALA* 1.3 79.0 - - - +
203A SER* 1.3 58.5 + - - +
205A ARG* 3.3 13.0 + - + +
206A GLN* 2.9 29.2 + - + +
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Residues in contact with SER 203 (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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81A LEU* 3.4 40.6 + - - +
84A VAL* 5.1 3.6 - - - +
85A ASP* 2.7 30.8 + - - -
199A LEU* 3.9 7.4 - - - -
200A SER* 3.1 15.7 + - - -
202A ARG* 1.3 74.3 - - - +
204A GLN* 1.3 65.2 + - - +
206A GLN* 3.2 6.0 + - - -
207A LEU* 3.0 20.8 + - - +
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Residues in contact with GLN 204 (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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192A LYS 4.6 0.2 - - - +
193A LEU 3.6 17.8 - - - +
194A LEU* 3.3 27.2 + - - +
195A THR* 3.2 13.7 + - - +
196A SER 3.4 1.4 + - - -
197A GLN* 2.9 48.7 + - - -
198A ARG 4.5 0.5 + - - -
199A LEU* 3.7 16.0 + - + +
200A SER 2.9 18.8 + - - +
201A ALA* 3.6 10.2 + - - +
203A SER* 1.3 74.5 - - - +
205A ARG* 1.3 63.9 + - + +
207A LEU* 3.5 4.3 + - - +
208A LEU* 3.1 24.3 + - - +
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Residues in contact with ARG 205 (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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201A ALA* 3.0 45.4 + - - +
202A ARG* 3.6 9.9 - - + +
204A GLN* 1.3 78.3 - - + +
206A GLN* 1.3 58.5 + - - +
208A LEU* 3.5 11.2 + - + +
209A GLN* 3.0 28.9 + - - +
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Residues in contact with GLN 206 (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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81A LEU* 4.1 8.5 - - + -
91A LEU* 3.9 14.2 - - + +
202A ARG* 2.9 18.3 + - + +
203A SER* 3.5 9.0 - - - +
205A ARG* 1.3 75.2 - - - +
207A LEU* 1.3 66.5 + - - +
209A GLN* 3.2 11.3 + - - +
210A TRP* 3.0 76.8 + - + +
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Residues in contact with LEU 207 (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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74A VAL* 3.7 36.3 - - + +
77A CYS* 4.3 3.6 - - + -
78A GLY* 4.2 15.5 - - - +
81A LEU* 3.9 6.0 - - + +
127A ILE* 4.3 4.9 - - + -
190A LEU* 5.9 0.2 - - + -
193A LEU* 3.7 39.0 - - + -
194A LEU* 4.1 15.9 - - + -
199A LEU* 4.5 5.6 - - + -
203A SER 3.0 16.8 + - - +
204A GLN* 3.9 5.2 - - - +
206A GLN* 1.3 76.2 - - - +
208A LEU* 1.3 63.9 + - - +
210A TRP* 3.3 22.9 + - + +
211A MET* 3.2 22.9 + - - +
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Residues in contact with LEU 208 (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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51A LEU* 6.1 0.9 - - + -
194A LEU* 3.8 14.3 - - + +
204A GLN 3.1 17.9 + - - +
205A ARG* 3.7 10.3 - - + +
207A LEU* 1.3 77.4 - - - +
209A GLN* 1.3 58.6 + - - +
211A MET* 3.1 7.8 + - + +
212A VAL* 2.9 44.3 + - + +
230A PHE* 4.5 9.9 - - + -
232A ALA* 4.8 0.4 - - + -
249A LEU* 3.4 33.2 - - + -
257A ALA* 5.3 3.1 - - + -
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Residues in contact with GLN 209 (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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205A ARG 3.0 18.2 + - - +
206A GLN* 3.2 13.9 + - - +
208A LEU* 1.3 76.7 - - - +
210A TRP* 1.3 64.6 + - + +
212A VAL* 3.2 22.4 + - - +
213A ASP* 2.9 59.8 + - - +
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Residues in contact with TRP 210 (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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77A CYS* 3.8 12.8 - - + -
80A VAL* 5.9 0.2 - - + -
81A LEU* 3.8 23.1 - - + -
91A LEU* 4.3 9.4 - - + -
120A GLY* 3.7 16.1 + - - -
123A CYS* 3.3 33.0 - - + -
124A ALA* 3.7 29.7 - - + +
127A ILE* 3.6 36.0 - - + +
128A THR* 3.3 22.1 - - + +
206A GLN* 3.0 59.8 + - + +
207A LEU* 3.6 14.8 - - + +
208A LEU 3.3 0.2 - - - -
209A GLN* 1.3 77.5 - - + +
211A MET* 1.3 62.1 + - - +
213A ASP* 3.2 13.0 + - - -
214A ASP 3.4 2.6 + - - -
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Residues in contact with MET 211 (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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74A VAL* 4.0 33.0 - - + -
127A ILE* 4.4 4.7 - - + -
190A LEU* 5.2 6.7 - - + -
194A LEU* 4.6 22.7 - - + -
207A LEU* 3.2 12.7 + - + +
208A LEU* 3.1 8.6 + - + +
210A TRP* 1.3 73.6 - - - +
212A VAL* 1.3 66.2 + - - +
214A ASP* 3.2 10.7 + - - +
232A ALA* 3.6 15.4 - - + +
233A ASP* 3.1 40.7 + - - +
234A LYS 4.1 0.9 - - - +
247A VAL* 3.7 36.6 - - + +
248A ALA* 4.6 0.4 - - - -
249A LEU* 4.6 14.4 - - + -
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Residues in contact with VAL 212 (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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208A LEU* 2.9 26.1 + - + +
209A GLN* 3.2 29.6 + - - +
211A MET* 1.3 75.9 - - - +
213A ASP* 1.3 60.1 + - - +
214A ASP* 3.3 4.4 + - - +
218A GLY* 5.8 0.2 - - - -
222A ARG* 3.2 30.0 + - - +
230A PHE* 4.1 20.0 - - + -
231A ILE 4.5 1.8 - - - +
232A ALA* 3.8 19.7 - - + +
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Residues in contact with ASP 213 (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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128A THR* 3.4 25.0 - - + -
209A GLN* 2.9 48.1 + - - +
210A TRP* 3.7 5.3 - - - -
211A MET 3.1 0.8 - - - -
212A VAL* 1.3 79.1 - - - +
214A ASP* 1.3 65.6 + - - +
215A ARG* 2.9 37.1 + - - +
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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