Contacts of the helix formed by residues 172 - 182 (chain A) in PDB entry 5TSQ
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 ASP 172 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A PRO* 3.4 5.9 - - + +
71A LEU* 2.9 33.7 + - - +
72A VAL 4.7 0.7 + - - -
73A ARG* 5.6 0.8 + - - -
129A LEU 4.7 6.5 + - - +
130A THR* 2.7 30.2 + - - +
168A ASN 3.9 1.8 + - - +
169A ILE 3.1 8.2 + - - +
171A VAL* 1.3 86.4 - - + +
173A PRO* 1.3 65.6 - - - +
174A GLU* 3.6 6.8 + - - +
175A ALA* 2.9 31.8 + - + +
176A ALA* 3.1 18.9 + - - +
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Residues in contact with PRO 173 (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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73A ARG* 3.7 36.3 - - + +
169A ILE 3.4 9.9 - - - +
170A PHE* 3.4 17.7 - - + +
171A VAL 3.9 0.9 - - - -
172A ASP* 1.3 89.7 - - - +
174A GLU* 1.3 62.1 + - - +
176A ALA* 3.2 3.3 + - + +
177A HIS* 2.8 24.9 + - - +
263A ILE* 3.6 7.5 - - + +
264A GLU 4.3 0.4 - - - +
265A LEU* 3.5 23.8 - - + +
271A ALA* 4.9 0.9 - - + -
272A GLY* 4.1 24.5 - - - +
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Residues in contact with GLU 174 (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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71A LEU* 4.2 12.8 - - + -
72A VAL* 3.9 31.9 - - + +
73A ARG* 2.7 51.6 + - - +
172A ASP* 3.3 6.6 - - - +
173A PRO* 1.3 78.6 - - - +
175A ALA* 1.3 62.4 + - - +
177A HIS* 3.2 5.3 + - - +
178A ILE* 3.0 27.5 + - + +
265A LEU* 4.0 21.6 - - + +
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Residues in contact with ALA 175 (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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71A LEU* 3.8 6.9 - - + +
129A LEU* 3.5 29.6 - - + +
130A THR* 3.6 4.9 - - - +
133A ALA* 3.6 13.4 - - + +
172A ASP* 2.9 34.6 + - + +
174A GLU* 1.3 76.0 - - - +
176A ALA* 1.3 61.6 + - - +
178A ILE* 3.3 4.0 + - - +
179A VAL* 3.0 26.5 + - - +
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Residues in contact with ALA 176 (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 LEU* 3.7 26.4 - - + +
168A ASN 5.7 0.2 - - - +
169A ILE* 3.7 33.4 - - + -
172A ASP 3.1 11.3 + - - +
173A PRO 3.5 7.2 - - - +
175A ALA* 1.3 77.4 - - - +
177A HIS* 1.3 57.0 + - - +
179A VAL 3.2 0.7 + - - -
180A PHE* 2.8 35.8 + - + -
263A ILE* 3.7 9.0 - - + -
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Residues in contact with HIS 177 (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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173A PRO 2.8 13.3 + - - +
174A GLU* 3.2 9.6 + - - +
176A ALA* 1.3 75.1 - - - +
178A ILE* 1.3 66.9 + - + +
181A ASN* 2.9 50.2 + - + +
262A ASN* 3.5 18.4 + - - -
263A ILE* 3.5 35.8 - - + +
265A LEU* 3.9 24.6 - - + +
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Residues in contact with ILE 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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71A LEU* 3.6 30.5 - - + -
133A ALA* 3.8 28.3 - - + +
136A ALA* 4.7 6.5 - - + -
137A ARG* 3.7 50.9 + - + +
174A GLU* 3.0 11.2 + - + +
175A ALA 3.5 6.5 - - - +
176A ALA 3.2 0.2 - - - -
177A HIS* 1.3 82.0 - - + +
179A VAL* 1.3 63.8 + - - +
181A ASN* 3.4 2.5 + - - +
182A GLU* 3.3 22.7 + - + +
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Residues in contact with VAL 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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129A LEU* 4.0 17.3 - - + -
132A ILE* 3.8 30.1 - - + -
133A ALA* 4.0 10.1 - - - +
149A VAL* 4.6 7.9 - - + -
151A LEU* 4.4 23.3 - - + -
175A ALA 3.0 15.7 + - - +
176A ALA 3.7 5.6 - - - +
178A ILE* 1.3 76.8 - - + +
180A PHE* 1.3 65.2 + - + +
181A ASN 3.3 0.9 + - - -
182A GLU 3.4 2.6 + - - -
184A TRP* 2.8 47.0 + - + +
186A VAL* 4.0 8.6 - - + +
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Residues in contact with PHE 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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129A LEU* 4.3 2.7 - - + -
151A LEU* 3.9 26.9 - - + -
169A ILE* 4.2 15.0 - - + -
176A ALA* 2.8 28.3 + - - +
177A HIS 4.3 1.6 - - - +
179A VAL* 1.3 81.4 - - + +
181A ASN* 1.3 63.3 + - - +
182A GLU 3.5 0.2 - - - -
186A VAL* 4.0 15.0 - - + -
188A MET* 3.9 31.9 - - + -
261A VAL* 3.6 48.6 - - + +
262A ASN* 5.1 0.4 - - - -
263A ILE* 3.8 25.6 - - + -
274A THR* 4.6 1.6 - - + -
287A HIS* 3.0 27.4 + - - -
288A THR* 4.3 13.5 - - + +
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Residues in contact with ASN 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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137A ARG* 6.2 1.6 - - - +
177A HIS* 2.9 49.5 + - + +
178A ILE* 3.9 3.6 - - - +
179A VAL 3.2 0.2 - - - -
180A PHE* 1.3 82.0 - - - +
182A GLU* 1.3 68.5 + - - +
261A VAL 5.4 1.4 - - - +
262A ASN* 2.9 34.8 + - - +
287A HIS* 4.9 2.0 - - - -
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Residues in contact with GLU 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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136A ALA* 4.7 4.7 - - + -
137A ARG* 2.8 35.1 + - - +
143A VAL* 3.7 32.6 - - + +
178A ILE 3.3 15.0 + - - +
179A VAL 3.4 1.0 + - - -
181A ASN* 1.3 83.7 - - - +
183A SER* 1.3 62.5 + - - +
184A TRP* 3.3 31.5 + - + +
287A HIS* 2.9 27.5 + - - -
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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