Contacts of the helix formed by residues 177 - 188 (chain A) in PDB entry 1TF5
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 ASN 177 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A VAL* 3.0 23.7 - - - +
128A THR 3.4 19.0 + - - -
129A VAL* 4.1 4.4 + - - +
176A THR* 1.3 73.9 - - - +
178A ASN* 1.3 66.7 + - - +
180A LEU* 3.7 2.5 + - - +
181A GLY* 3.2 18.2 + - - -
206A ILE* 4.0 2.8 - - - +
207A ASP 5.4 0.4 + - - -
212A ILE* 3.1 41.4 - - - +
221A LEU* 4.3 2.9 - - - +
357A PHE* 3.9 23.5 - - + -
360A TYR* 4.8 1.9 - - - -
361A PHE* 3.2 29.3 - - + -
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Residues in contact with ASN 178 (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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129A VAL 4.6 9.1 + - - -
176A THR* 3.3 9.0 + - - +
177A ASN* 1.3 79.2 - - - +
179A GLU* 1.3 61.9 + - + +
181A GLY* 3.3 1.9 + - - -
182A PHE* 2.9 49.1 + - + -
219A THR* 4.9 2.9 - - - +
221A LEU* 3.8 17.6 - - + +
357A PHE* 3.7 25.3 - - - -
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Residues in contact with GLU 179 (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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131A GLU* 4.0 7.0 - - - +
155A ASN* 3.8 10.3 - - - +
156A LEU 4.2 2.9 - - - -
157A ASN* 2.9 54.7 + - - +
164A LYS* 3.0 24.4 + - - -
175A SER* 3.7 13.0 - - - +
176A THR* 3.3 17.9 + - - +
178A ASN* 1.3 75.8 - - + +
180A LEU* 1.3 60.6 + - - +
182A PHE* 3.3 14.5 + - - +
183A ASP* 2.8 37.3 + - - +
186A ARG* 3.7 12.3 + - - -
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Residues in contact with LEU 180 (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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125A HIS* 4.1 17.3 - - + +
127A VAL* 3.5 36.1 - - + -
168A TYR* 3.1 34.3 - - + +
173A THR* 5.7 0.4 - - + -
175A SER* 3.5 24.9 - - - +
176A THR 3.2 17.6 + - - +
177A ASN 3.9 1.8 - - - +
179A GLU* 1.3 77.8 - - - +
181A GLY* 1.3 62.8 + - - +
184A TYR* 3.1 19.8 + - - +
198A GLN* 3.1 11.3 + - - -
360A TYR* 3.5 17.8 + - + +
361A PHE* 4.4 6.7 - - + -
364A TYR* 4.1 11.0 - - - +
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Residues in contact with GLY 181 (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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177A ASN 3.2 9.6 + - - -
180A LEU* 1.3 80.4 - - - +
182A PHE* 1.3 61.1 + - - +
184A TYR* 3.1 5.7 + - - +
185A LEU* 3.0 26.9 + - - +
221A LEU* 3.6 22.9 - - - -
355A ILE* 4.7 1.5 - - - +
360A TYR* 4.0 21.2 - - - -
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Residues in contact with PHE 182 (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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157A ASN* 5.4 2.7 - - - -
178A ASN* 2.9 34.2 + - + +
179A GLU* 3.8 15.0 - - - +
181A GLY* 1.3 75.0 - - - +
183A ASP* 1.3 62.8 + - - +
185A LEU* 3.4 6.3 + - + +
186A ARG* 3.0 47.4 + - - +
220A PRO 5.5 0.2 - - - -
221A LEU* 3.9 25.7 - - + +
222A ILE 3.3 37.9 - - - -
223A ILE* 3.9 19.6 - - + +
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Residues in contact with ASP 183 (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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155A ASN* 2.9 19.8 + - - -
164A LYS* 3.0 26.5 + - - +
168A TYR* 2.8 34.4 + - - +
179A GLU 2.8 16.2 + - - +
180A LEU 3.7 1.8 - - - +
182A PHE* 1.3 75.9 - - - +
184A TYR* 1.3 53.6 + - - +
186A ARG* 3.1 20.0 + - - +
187A ASP* 2.7 39.8 + - - +
197A VAL* 3.9 17.0 - - + +
198A GLN* 4.0 4.7 - - - +
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Residues in contact with TYR 184 (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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180A LEU 3.1 5.2 + - - +
181A GLY 3.1 8.7 + - - +
183A ASP* 1.3 77.3 - - - +
185A LEU* 1.3 69.2 + - + +
187A ASP* 3.3 4.0 + - + +
188A ASN* 2.6 53.6 + - - -
198A GLN* 3.4 19.3 + - - +
201A LEU* 3.9 22.9 - - + -
355A ILE* 4.0 20.6 - - + -
360A TYR* 3.4 29.4 - + + -
363A MET* 3.6 30.7 - - + +
607A ARG* 5.2 2.8 + - - +
608A GLU* 5.6 1.9 - - - +
611A TYR* 3.6 29.2 - + - +
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Residues in contact with LEU 185 (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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181A GLY 3.0 17.8 + - - +
182A PHE* 3.7 9.2 - - + +
184A TYR* 1.3 84.0 - - + +
186A ARG* 1.3 63.4 + - - +
188A ASN* 3.2 14.3 + - - +
189A MET* 3.2 19.2 - - - +
221A LEU* 3.2 32.8 - - + +
223A ILE* 4.0 24.5 - - + -
353A ALA* 4.1 4.6 - - + +
354A THR* 3.8 23.8 - - - +
355A ILE* 3.7 25.4 - - + -
611A TYR* 3.9 20.3 + - + +
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Residues in contact with ARG 186 (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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157A ASN* 5.3 3.2 - - - +
161A LYS* 3.8 37.1 + - - +
164A LYS* 4.2 10.5 - - - +
179A GLU* 3.7 14.6 + - - -
182A PHE* 3.0 36.4 + - - +
183A ASP* 3.1 30.8 + - - +
185A LEU* 1.3 73.8 - - - +
187A ASP* 1.3 67.3 + - - +
188A ASN 3.0 1.6 - - - -
189A MET* 3.0 24.8 + - - +
190A VAL* 3.6 12.4 + - - +
223A ILE* 4.0 25.3 - - + +
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Residues in contact with ASP 187 (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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183A ASP 2.7 21.5 + - - +
184A TYR* 3.6 8.5 - - + +
185A LEU 3.3 0.2 - - - -
186A ARG* 1.3 73.8 - - - +
188A ASN* 1.3 60.8 + - - +
189A MET 3.3 0.2 - - - -
190A VAL* 3.5 22.1 - - - +
195A GLN 4.6 0.3 - - - +
196A MET* 3.3 36.6 - - + +
197A VAL* 2.8 33.9 + - - +
198A GLN* 2.8 38.9 + - - +
614A ARG* 4.8 1.2 + - - -
618A ILE* 5.4 1.2 - - - +
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Residues in contact with ASN 188 (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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184A TYR* 2.6 54.3 + - - -
185A LEU 3.2 6.6 + - - +
186A ARG 3.0 1.2 - - - -
187A ASP* 1.3 80.7 - - - +
189A MET* 1.3 61.4 + - - +
190A VAL 3.5 1.3 - - - -
196A MET* 6.1 1.4 - - - +
611A TYR* 3.4 53.0 - - + +
614A ARG* 3.3 29.6 + - - +
615A PHE* 5.6 2.9 - - - +
721A ASP* 4.5 0.9 - - - +
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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