Contacts of the helix formed by residues 199 - 208 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197F THR* 2.9 30.3 + - + +
198F ASP* 1.3 84.3 - - - +
200F VAL* 1.3 64.3 + - - +
201F THR* 3.1 7.9 - - - +
202F ARG* 3.1 57.1 + - + +
203F PHE* 3.2 11.4 + - - +
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Residues in contact with VAL 200 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136F THR 5.7 0.2 - - - +
139F ALA* 3.6 33.2 - - + -
140F THR* 6.2 0.2 - - - +
143F ARG* 4.6 24.5 - - + +
149F LEU* 5.3 4.5 - - + -
151F ILE* 4.9 9.2 - - + -
198F ASP 2.7 19.8 + - - +
199F GLN* 1.3 71.0 - - - +
201F THR* 1.3 62.6 + - + +
203F PHE* 3.3 7.9 - - + +
204F ASN* 3.2 35.5 + - - +
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Residues in contact with THR 201 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199F GLN* 4.5 7.4 - - - +
200F VAL* 1.3 79.1 + - + +
202F ARG* 1.3 65.2 + - - +
203F PHE 3.1 0.2 - - - -
204F ASN* 3.5 7.9 + - - +
205F GLU* 3.2 36.3 + - - +
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Residues in contact with ARG 202 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194F LEU* 3.7 30.3 - - + +
195F THR 5.5 0.6 + - - -
197F THR* 4.4 8.3 - - - +
199F GLN* 3.1 47.7 + - + +
201F THR* 1.3 80.9 + - - +
203F PHE* 1.3 61.2 + - - +
205F GLU* 4.1 14.8 - - - +
206F GLU* 3.4 31.8 + - - +
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Residues in contact with PHE 203 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116F TYR* 4.6 11.4 - - + -
135F GLY* 3.0 36.3 - - - -
138F LEU* 5.9 0.7 - - + -
139F ALA* 4.9 4.0 - - + -
151F ILE* 3.6 46.0 - - + -
152F GLY* 3.9 17.0 - - - -
153F PHE* 4.1 4.5 - + + -
194F LEU* 3.7 25.5 - - + +
199F GLN 3.2 10.6 + - - +
200F VAL* 3.3 12.6 - - - +
202F ARG* 1.3 75.7 - - - +
204F ASN* 1.3 81.6 + - - +
206F GLU* 3.1 4.7 + - - +
207F VAL* 2.9 53.1 + - + +
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Residues in contact with ASN 204 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136F THR* 3.3 44.5 + - + +
139F ALA* 5.0 0.2 - - - +
200F VAL* 3.2 28.8 + - - +
201F THR* 3.5 7.0 + - - +
203F PHE* 1.3 95.2 - - - +
205F GLU* 1.3 64.5 + - + +
207F VAL* 4.0 2.4 - - - +
208F LYS* 3.2 37.2 + - + +
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Residues in contact with GLU 205 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201F THR* 3.2 26.0 + - - +
202F ARG* 4.1 14.4 - - + +
204F ASN* 1.3 78.7 - - + +
206F GLU* 1.3 62.4 + - - +
208F LYS* 3.8 3.9 + - - +
209F LYS* 3.2 32.6 + - + +
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Residues in contact with GLU 206 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153F PHE* 3.6 24.7 - - + -
193F VAL* 4.2 18.9 - - + +
194F LEU* 3.7 20.7 - - + +
202F ARG* 3.4 22.7 + - - +
203F PHE* 3.1 10.0 + - - +
205F GLU* 1.3 79.7 - - - +
207F VAL* 1.3 65.7 + - - +
209F LYS* 2.9 41.5 + - - +
210F GLN* 3.4 17.1 + - - +
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Residues in contact with VAL 207 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116F TYR* 5.1 1.3 - - + -
118F MET* 4.1 14.0 - - + +
131F ILE 4.7 2.2 - - - +
132F GLN* 3.6 40.5 - - + +
135F GLY* 4.7 6.7 - - - -
136F THR* 4.8 3.4 - - - +
153F PHE* 3.8 27.8 - - + -
203F PHE* 2.9 50.7 + - + +
204F ASN* 3.5 6.9 + - - +
206F GLU* 1.3 72.2 - - - +
208F LYS* 1.3 60.1 + - + +
210F GLN* 3.5 17.7 - - - +
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Residues in contact with LYS 208 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129F TRP* 5.6 6.3 - - - +
132F GLN* 3.5 39.2 + - + +
133F ASN* 5.5 2.4 - - - +
136F THR* 4.1 27.1 + - - +
204F ASN* 3.2 21.3 + - - +
205F GLU* 4.3 5.4 - - - +
206F GLU 3.1 1.2 + - - -
207F VAL* 1.3 73.8 - - + +
209F LYS* 1.3 59.4 + - + +
210F GLN 3.2 6.5 + - - +
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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