Contacts of the helix formed by residues 199 - 207 (chain A) in PDB entry 4XZC
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 199 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198A HIS* 1.3 90.4 - - + +
200A ASN* 1.3 65.5 + - - +
201A TRP 3.2 1.6 - - - -
202A GLY 3.5 2.0 + - - -
203A ARG* 3.2 18.9 + - + +
235A SER* 4.0 6.5 - - - +
238A LYS* 3.6 39.0 - - + +
239A VAL* 3.6 11.9 - - + +
242A LEU* 5.2 14.6 - - + -
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Residues in contact with ASN 200 (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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198A HIS 3.6 1.9 - - - +
199A VAL* 1.3 79.9 - - + +
201A TRP* 1.3 56.1 + - - +
203A ARG* 3.6 12.4 - - - +
204A GLU* 2.8 55.6 + - - +
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Residues in contact with TRP 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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198A HIS* 3.9 6.2 + - - +
199A VAL 4.2 0.4 - - - +
200A ASN* 1.3 78.7 - - - +
202A GLY* 1.3 66.2 + - - +
204A GLU* 3.2 6.1 + - - +
205A LEU* 2.8 55.4 + - + +
212A VAL* 3.1 42.5 + - + +
213A VAL* 4.1 7.0 - - + -
215A ASN 4.9 0.2 - - - -
216A PRO* 4.0 5.6 - - + +
217A PRO* 3.5 30.6 - - + +
218A TRP* 3.3 32.3 - + + -
221A ILE* 3.5 24.5 - - + -
232A ALA* 3.5 39.3 - - + -
235A SER* 3.4 15.9 - - - -
236A MET* 4.4 8.1 - - + -
281A LEU* 5.4 1.1 - - + -
284A GLN* 5.0 1.3 - - - -
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Residues in contact with GLY 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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199A VAL 3.5 1.2 + - - -
200A ASN 3.3 0.2 - - - -
201A TRP* 1.3 89.0 - - - +
203A ARG* 1.3 61.3 + - - +
205A LEU* 3.3 6.1 + - - +
206A ALA* 3.0 23.6 + - - +
235A SER* 3.3 21.5 + - - -
236A MET* 5.2 1.3 - - - -
239A VAL* 3.6 16.3 - - - +
251A ILE* 4.0 9.0 - - - +
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Residues in contact with ARG 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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199A VAL* 3.2 17.1 + - + +
200A ASN* 3.2 16.3 + - - +
202A GLY* 1.3 76.5 - - - +
204A GLU* 1.3 62.7 + - - +
206A ALA* 3.5 7.6 + - - +
207A ALA* 3.3 21.7 + - - +
239A VAL* 3.6 10.4 - - + +
243A ASP* 4.6 13.7 - - - +
247A ARG* 5.0 2.6 + - - +
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Residues in contact with GLU 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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200A ASN* 2.8 41.1 + - - +
201A TRP* 3.6 4.5 - - - +
203A ARG* 1.3 77.8 - - - +
205A LEU* 1.3 65.2 + - - +
206A ALA 3.1 2.2 + - - -
207A ALA* 3.1 14.0 + - - +
208A GLY 3.3 0.3 + - - -
209A LYS* 3.1 44.7 + - + +
212A VAL* 3.9 20.7 - - + +
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Residues in contact with LEU 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 TRP* 2.8 47.0 + - + +
202A GLY* 3.3 7.2 + - - +
204A GLU* 1.3 79.0 - - - +
206A ALA* 1.3 56.1 + - - +
208A GLY 3.6 0.2 + - - -
209A LYS 4.2 1.6 - - - -
210A PHE* 3.8 10.8 - - + -
212A VAL* 4.0 8.4 - - + +
213A VAL* 3.6 28.5 - - + -
236A MET* 4.7 5.8 - - + -
251A ILE* 4.1 27.9 - - + +
254A THR* 3.0 50.8 + - + +
255A LEU* 4.6 10.5 - - + -
281A LEU* 5.2 2.7 - - + -
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Residues in contact with ALA 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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202A GLY 3.0 15.8 + - - +
203A ARG* 3.8 8.5 - - - +
204A GLU 3.1 0.4 - - - -
205A LEU* 1.3 75.0 - - - +
207A ALA* 1.3 58.6 + - - +
208A GLY 3.1 5.7 + - - -
239A VAL* 4.9 1.6 - - + -
247A ARG* 4.1 35.9 + - + +
250A ASP* 3.4 21.3 - - - +
251A ILE* 3.5 23.1 - - + +
254A THR* 3.8 5.1 + - - -
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Residues in contact with ALA 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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203A ARG 3.3 15.0 + - - +
204A GLU* 3.1 13.4 + - - +
206A ALA* 1.3 78.1 - - - +
208A GLY* 1.3 57.8 + - - +
209A LYS* 3.6 12.9 - - + -
247A ARG* 4.4 13.2 - - - +
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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