Contacts of the helix formed by residues 199 - 211 (chain A) in PDB entry 4C48
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 199 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A LEU* 4.0 6.3 - - - +
198A LEU* 1.3 78.5 - - - +
200A PRO* 1.3 75.9 - - - +
201A VAL* 3.1 26.5 + - + +
202A ASP* 3.0 20.7 + - - +
203A VAL* 3.5 12.8 + - - +
745A ASP* 5.9 1.3 - - + -
749A THR* 4.2 6.7 - - - -
790A TYR 3.9 2.7 - - - +
791A VAL* 3.8 14.4 - - + -
792A ARG* 3.4 40.7 + - + +
798A MET* 5.0 0.7 - - - -
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Residues in contact with PRO 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A MET* 3.8 32.3 - - + -
193A LEU* 4.3 7.2 - - + -
199A THR* 1.3 88.9 - - - +
201A VAL* 1.3 55.0 - - - +
203A VAL* 3.3 4.9 + - + +
204A ILE* 2.9 36.3 + - + +
748A THR* 5.3 0.2 - - + -
749A THR* 3.7 39.7 - - + +
752A ALA* 4.2 19.5 - - + -
753A ALA* 4.9 0.4 - - + -
789A TRP* 4.1 14.8 - - + -
790A TYR 4.8 2.5 - - - +
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Residues in contact with VAL 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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199A THR* 3.0 13.4 - - - +
200A PRO* 1.3 78.0 - - - +
202A ASP* 1.3 59.6 + - - +
204A ILE* 3.8 7.6 - - - +
205A THR* 2.6 46.1 + - - +
745A ASP* 3.7 36.3 - - - +
748A THR* 3.7 29.4 - - + -
749A THR* 4.3 4.0 - - - +
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Residues in contact with ASP 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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198A LEU* 3.5 24.8 - - + +
199A THR* 3.0 23.2 + - - +
201A VAL* 1.3 81.2 - - - +
203A VAL* 1.3 57.9 + - - +
205A THR* 3.7 6.0 - - - -
206A ALA* 2.9 31.1 + - - +
251A LEU* 4.1 5.9 - - + +
792A ARG* 2.8 45.4 + - - -
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Residues in contact with VAL 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A ILE* 4.4 6.3 - - + -
188A MET* 4.6 11.2 - - + -
193A LEU* 4.0 19.5 - - + -
199A THR 3.5 10.5 + - - +
200A PRO* 3.3 9.2 + - + +
202A ASP* 1.3 78.5 - - + +
204A ILE* 1.3 57.1 + - - +
206A ALA* 3.3 1.9 + - - +
207A ILE* 3.0 53.8 + - + +
251A LEU* 4.1 22.8 - - + +
262A LEU* 4.3 11.4 - - + +
265A VAL* 4.9 4.0 - - + -
266A ALA* 5.5 2.5 - - + -
773A VAL* 3.9 20.0 - - + -
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Residues in contact with ILE 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 PRO 2.9 27.1 + - - +
201A VAL* 3.8 5.2 - - - +
203A VAL* 1.3 73.9 - - - +
205A THR* 1.3 63.8 + - - +
207A ILE* 3.4 1.7 + - - -
208A LYS* 3.0 45.5 + - - +
748A THR* 4.3 15.0 - - + -
752A ALA* 4.1 18.6 - - + -
757A SER* 4.1 11.2 - - - +
759A VAL* 3.7 21.9 - - + +
773A VAL* 3.6 32.3 - - + -
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Residues in contact with THR 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 VAL* 2.6 31.5 + - - +
202A ASP* 3.7 6.6 + - - -
204A ILE* 1.3 77.2 - - - +
206A ALA* 1.3 63.7 + - - +
208A LYS* 3.3 16.4 + - - +
209A ALA* 3.1 24.1 + - + +
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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 ASP 2.9 18.0 + - - +
203A VAL 3.7 2.5 - - - +
205A THR* 1.3 75.6 - - - +
207A ILE* 1.3 59.7 + - + +
209A ALA* 3.2 4.8 + - - -
210A GLN* 2.9 37.6 + - - +
249A ILE* 4.1 12.3 - - + -
250A LEU 4.6 6.3 - - - +
251A LEU* 3.6 26.0 - - + +
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Residues in contact with ILE 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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186A ILE* 4.0 24.5 - - + -
203A VAL* 3.0 40.7 + - + +
204A ILE* 3.8 7.2 - - - +
206A ALA* 1.3 75.5 - - - +
208A LYS* 1.3 58.2 + - - +
211A ASN* 2.8 30.2 + - + +
246A PHE* 4.2 15.0 - - + -
249A ILE* 4.3 11.4 - - + -
262A LEU* 3.9 17.7 - - + -
759A VAL* 3.8 17.9 - - + -
760A ASN* 3.5 19.7 + - - +
771A VAL* 4.1 12.1 - - + -
773A VAL* 4.8 1.6 - - + -
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Residues in contact with LYS 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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204A ILE* 3.0 41.8 + - - +
205A THR* 3.3 12.1 + - - +
207A ILE* 1.3 77.1 - - - +
209A ALA* 1.3 61.1 + - - +
211A ASN 4.1 2.9 - - - +
212A ALA* 3.7 17.2 - - - +
759A VAL* 3.6 26.5 - - + +
760A ASN* 3.7 13.2 + - + +
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Residues in contact with ALA 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 THR* 3.1 19.4 + - + +
206A ALA* 3.7 6.5 - - - +
207A ILE 3.1 0.2 - - - -
208A LYS* 1.3 78.1 - - - +
210A GLN* 1.3 66.3 + - + +
212A ALA* 3.7 6.9 - - - +
237A GLN* 3.6 17.7 + - - +
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Residues in contact with GLN 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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206A ALA* 2.9 19.7 + - - +
209A ALA* 1.3 83.1 - - + +
211A ASN* 1.3 57.7 + - - +
212A ALA 3.4 3.9 + - - +
237A GLN* 4.8 8.1 - - - +
238A THR 5.0 0.2 - - - +
240A LEU* 3.1 20.5 - - - +
248A LYS 4.6 0.9 - - - +
249A ILE* 3.3 27.6 - - + +
250A LEU* 3.0 50.2 + - - +
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Residues in contact with ASN 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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207A ILE* 2.8 22.6 + - + +
208A LYS 4.1 0.7 - - - -
210A GLN* 1.3 70.5 - - - +
212A ALA* 1.3 58.4 + - - +
239A ARG* 3.2 14.4 + - - +
240A LEU* 2.7 37.5 + - + +
246A PHE* 3.3 38.1 - - + -
249A ILE* 5.0 0.6 - - + +
760A ASN* 2.7 43.6 + - - +
761A ASP 3.1 21.7 + - - -
762A PHE* 3.8 3.2 - - - +
771A VAL* 3.9 0.6 - - - +
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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