Contacts of the helix formed by residues 201 - 210 (chain A) in PDB entry 3CTZ
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 ALA 201 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A HIS 4.7 9.0 - - - +
199A VAL* 4.4 1.0 - - - +
200A THR* 1.3 81.4 + - - +
202A LEU* 1.3 65.9 + - - +
203A ASP* 3.3 15.9 - - - +
204A GLU* 3.1 35.7 + - - +
205A ILE* 3.2 14.7 + - - +
293A LYS* 6.0 5.6 - - - -
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Residues in contact with LEU 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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38A HIS* 3.4 28.3 + - + +
40A SER* 4.3 8.3 - - - +
200A THR 4.2 0.4 - - - +
201A ALA* 1.3 72.3 - - - +
203A ASP* 1.3 57.3 + - - +
205A ILE* 3.3 6.7 + - - +
206A ALA* 3.0 27.9 + - - +
216A VAL* 4.0 11.2 - - + -
221A VAL* 3.8 29.8 - - + +
222A PHE* 3.5 27.4 + - - +
223A PHE* 3.9 23.8 - - + -
224A SER* 3.3 33.0 - - - +
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Residues in contact with ASP 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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201A ALA* 3.5 17.3 - - - +
202A LEU* 1.3 74.2 + - - +
204A GLU* 1.3 63.1 + - - +
206A ALA* 3.5 0.5 + - - +
207A TRP* 3.0 29.6 + - - +
221A VAL* 3.8 9.7 - - + +
319A LYS* 3.0 26.3 + - - -
495A LEU* 3.6 20.8 - - + +
496A ASN* 3.8 35.7 + - - +
499A GLU* 4.5 5.5 - - - +
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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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197A PHE* 4.4 0.2 - - - -
199A VAL* 3.8 20.5 - - + +
200A THR 5.5 0.3 + - - -
201A ALA* 3.1 27.3 + - + +
203A ASP* 1.3 77.6 + - - +
205A ILE* 1.3 58.8 + - - +
207A TRP* 3.5 0.6 + - - +
208A LEU* 2.9 30.8 + - - +
313A THR* 2.7 39.3 + - - +
315A ILE* 3.6 26.5 - - + +
316A CYS* 3.7 17.1 - - - +
319A LYS* 3.8 15.0 - - - +
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Residues in contact with ILE 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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199A VAL* 3.5 32.5 - - + +
200A THR 4.7 0.7 - - - -
201A ALA 3.2 13.6 + - - +
202A LEU* 3.7 7.2 - - + +
203A ASP 3.3 0.2 - - - -
204A GLU* 1.3 74.5 - - - +
206A ALA* 1.3 64.5 + - - +
208A LEU* 3.3 4.8 + - - -
209A PHE* 3.1 41.8 + - + +
222A PHE* 4.0 14.0 - - + -
224A SER* 3.4 44.2 - - - +
225A TYR* 3.5 17.9 - - - -
226A ALA* 4.4 3.1 - - + +
235A LEU* 4.1 10.8 - - + -
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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 LEU 3.0 17.0 + - - +
203A ASP* 3.7 4.9 - - - +
204A GLU 3.4 0.2 - - - -
205A ILE* 1.3 76.2 - - - +
207A TRP* 1.3 62.1 + - - +
210A ASN 3.0 18.9 + - - -
211A LEU 3.0 29.4 + - - +
212A ARG* 3.3 5.1 + - - +
220A PRO 4.7 0.9 - - - +
221A VAL* 4.4 6.7 - - + -
222A PHE* 4.2 17.6 - - + -
495A LEU* 4.0 19.3 - - + -
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Residues in contact with TRP 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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176A ILE* 5.5 2.9 - - + -
181A LYS* 2.8 73.6 + - + +
203A ASP 3.0 17.8 + - - +
204A GLU 3.8 1.6 - - - +
206A ALA* 1.3 75.1 - - - +
208A LEU* 1.3 84.3 + - + +
210A ASN* 3.3 6.9 + - - +
212A ARG* 4.0 14.1 - - - +
315A ILE* 3.5 26.9 - - + -
318A ALA* 3.6 33.4 - - + -
319A LYS* 3.3 40.7 - - + +
326A GLU* 3.6 22.2 + - - -
493A SER* 6.3 1.1 - - - -
495A LEU* 4.1 9.2 - - + +
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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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178A TRP* 3.1 23.4 - - - +
181A LYS* 3.7 27.9 - - + +
182A VAL* 4.1 14.8 - - + -
185A LEU* 4.1 17.7 - - + -
199A VAL* 4.8 4.0 - - + -
204A GLU 2.9 19.1 + - - +
205A ILE* 3.3 5.8 + - - +
207A TRP* 1.3 93.0 - - + +
209A PHE* 1.3 74.0 + - + +
226A ALA* 5.3 0.2 - - + -
228A ILE* 3.8 33.2 - - + -
315A ILE* 4.0 19.5 - - + -
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Residues in contact with PHE 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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178A TRP* 3.7 25.4 - + - +
182A VAL* 4.7 6.3 - - + -
205A ILE* 3.1 29.0 + - + +
208A LEU* 1.3 97.9 - - + +
210A ASN* 1.3 63.1 + - - +
211A LEU* 3.2 21.5 + - + +
226A ALA* 4.0 19.1 - - + -
228A ILE* 4.2 4.0 - - + -
233A ILE* 3.7 26.0 - - + -
235A LEU* 4.1 19.5 - - + -
250A HIS* 2.8 26.3 + - - -
251A LEU* 4.2 5.6 - - + -
263A ILE* 3.8 31.4 - - + -
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Residues in contact with ASN 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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168A THR* 3.9 0.3 - - - -
169A LEU* 3.1 36.4 + - - +
174A THR* 3.3 23.5 + - + +
176A ILE 3.0 24.0 + - - -
177A SER* 3.5 2.6 - - - +
178A TRP* 3.2 22.8 - - - +
181A LYS* 2.7 28.6 + - - +
206A ALA 3.0 8.0 + - - -
207A TRP* 3.3 2.9 + - - +
209A PHE* 1.3 77.3 - - - +
211A LEU* 1.3 57.3 + - - +
212A ARG* 4.3 7.5 + - - +
250A HIS* 3.2 16.6 + - + +
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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