Contacts of the helix formed by residues 199 - 209 (chain D) in PDB entry 1TYE
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 GLN 199 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151D ILE* 5.8 0.2 - - - -
197D THR* 3.1 19.8 + - + +
198D ASP* 1.3 83.7 - - - +
200D VAL* 1.3 51.4 + - - +
201D THR* 2.8 11.5 + - - +
202D ARG* 2.7 69.7 + - + +
203D PHE* 3.2 8.1 + - - +
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Residues in contact with VAL 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D ALA* 3.6 31.9 - - + +
143D ARG* 4.2 24.7 - - - +
149D LEU* 4.8 5.4 - - + -
151D ILE* 4.5 10.1 - - + -
198D ASP* 2.6 21.9 + - - +
199D GLN* 1.3 70.0 - - - +
201D THR* 1.3 62.5 + - + +
203D PHE* 3.5 8.8 + - + +
204D ASN* 3.0 37.9 + - - +
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Residues in contact with THR 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D GLN* 2.8 9.7 + - - +
200D VAL* 1.3 75.6 - - + +
202D ARG* 1.3 63.4 + - - +
204D ASN* 3.4 7.0 + - - +
205D GLU* 3.2 33.3 + - - +
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Residues in contact with ARG 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194D LEU* 3.5 30.0 - - + +
197D THR* 3.8 12.1 + - - +
199D GLN* 2.7 56.5 + - + +
201D THR* 1.3 73.6 + - - +
203D PHE* 1.3 64.8 + - - +
205D GLU* 3.1 18.2 + - - +
206D GLU* 3.0 48.4 + - - +
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Residues in contact with PHE 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D TYR* 4.5 11.7 - + + -
135D GLY* 3.0 34.5 - - - -
138D LEU* 5.6 0.7 - - + -
139D ALA* 4.7 3.6 - - + -
151D ILE* 3.6 49.1 - - + +
152D GLY* 3.4 35.9 - - - -
153D PHE* 3.8 12.6 - + + -
194D LEU* 3.5 21.4 - - + +
197D THR* 5.2 0.9 - - + -
199D GLN 3.2 7.3 + - - +
200D VAL 3.7 6.7 - - - +
202D ARG* 1.3 80.0 - - - +
204D ASN* 1.3 72.6 + - - +
206D GLU* 3.9 1.0 - - - +
207D VAL* 3.1 43.6 + - + +
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Residues in contact with ASN 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D THR* 3.1 54.6 + - + +
139D ALA* 5.1 0.2 - - - +
200D VAL* 3.0 34.5 + - - +
201D THR* 3.9 6.1 - - - +
202D ARG 3.2 0.4 - - - -
203D PHE* 1.3 89.9 - - - +
205D GLU* 1.3 60.8 + - - +
207D VAL* 3.9 5.0 + - - +
208D LYS* 3.3 33.4 + - - +
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Residues in contact with GLU 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D THR* 3.2 21.6 + - - +
202D ARG* 3.1 18.8 + - - +
204D ASN* 1.3 76.9 - - - +
206D GLU* 1.3 72.8 + - - +
208D LYS* 2.9 16.9 + - - +
209D LYS* 3.1 24.7 + - + +
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Residues in contact with GLU 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D PHE* 3.6 18.4 - - + -
193D VAL* 4.3 18.8 - - + -
194D LEU* 4.7 9.3 - - + +
202D ARG* 3.0 43.8 + - - +
203D PHE 3.9 1.3 - - - +
205D GLU* 1.3 82.9 - - - +
207D VAL* 1.3 62.3 + - - +
209D LYS* 3.1 40.8 + - - +
210D GLN* 3.0 24.4 + - - +
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Residues in contact with VAL 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D TYR* 4.9 2.2 - - + -
118D MET* 4.0 14.3 - - + +
131D ILE 4.5 2.0 - - - +
132D GLN* 3.1 49.7 + - + +
135D GLY* 4.7 6.3 - - - -
136D THR* 5.3 0.9 - - - +
153D PHE* 3.6 32.3 - - + -
203D PHE* 3.1 38.8 + - + +
204D ASN* 4.1 7.2 - - - +
205D GLU 3.2 0.4 - - - -
206D GLU* 1.3 75.2 - - - +
208D LYS* 1.3 59.2 + - + +
210D GLN* 3.7 12.2 - - - +
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Residues in contact with LYS 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D GLN* 3.2 35.6 + - + +
133D ASN* 5.1 2.8 - - - +
136D THR* 3.8 24.5 + - - +
204D ASN* 3.3 17.7 + - - +
205D GLU* 2.9 11.8 + - - +
207D VAL* 1.3 78.5 - - + +
209D LYS* 1.3 58.3 + - + +
210D GLN 3.1 10.3 + - - +
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Residues in contact with LYS 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205D GLU* 3.4 16.0 + - + +
206D GLU* 3.1 43.7 + - - +
208D LYS* 1.3 78.2 - - + +
210D GLN* 1.3 65.9 + - - +
211D SER* 5.2 1.0 + - - -
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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