Contacts of the helix formed by residues 172 - 184 (chain A) in PDB entry 1TU8
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 PHE 172 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A PRO* 3.4 32.1 - - + -
125A LEU* 3.7 19.1 - - + -
126A ALA* 3.6 26.2 - - + -
129A GLU* 3.4 31.4 - - + +
168A CYS 3.3 26.7 - - - -
169A LEU* 3.1 9.3 + - - +
170A ASP 3.4 0.4 - - - -
171A LYS* 1.3 92.4 - - + +
173A PRO* 1.3 61.5 - - - +
174A LEU 3.3 2.0 - - - -
175A LEU* 3.3 14.4 + - + -
176A LYS* 2.9 28.2 + - - +
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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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129A GLU* 3.1 13.2 - - - +
170A ASP 5.0 2.2 - - - +
171A LYS 3.4 9.6 - - - +
172A PHE* 1.3 86.0 - - - +
174A LEU* 1.3 60.8 + - + +
176A LYS* 4.2 8.5 - - + -
177A VAL* 2.8 40.3 + - + +
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Residues in contact with LEU 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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129A GLU* 2.9 45.3 + - + +
132A LEU* 3.8 11.4 - - + +
133A ALA* 3.8 17.9 - - + +
137A ASN 3.7 22.2 - - - +
138A GLY 3.6 23.4 - - - +
139A ARG* 4.1 16.2 - - + +
173A PRO* 1.3 77.5 - - + +
175A LEU* 1.3 55.7 + - - +
177A VAL* 3.4 5.3 + - + +
178A PHE* 2.9 29.6 + - - +
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Residues in contact with LEU 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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90A PHE* 5.8 0.2 - - + -
125A LEU* 3.4 45.1 - - + +
128A PHE* 4.0 23.8 - - + -
129A GLU* 2.9 23.5 + - - +
132A LEU* 4.0 17.5 - - + -
154A LEU* 4.4 9.9 - - + -
158A LEU* 3.7 28.6 - - + +
169A LEU* 4.3 7.0 - - + -
172A PHE* 3.9 15.7 - - + +
174A LEU* 1.3 72.0 - - - +
176A LYS* 1.3 67.0 + - - +
178A PHE* 3.3 5.2 + - - +
179A HIS* 2.9 24.4 + - - +
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Residues in contact with LYS 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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162A GLN* 5.3 8.4 - - - +
169A LEU* 3.7 34.3 - - + +
170A ASP* 4.7 19.5 + - - +
172A PHE 2.9 18.2 + - - +
173A PRO* 3.6 8.5 - - + +
175A LEU* 1.3 77.9 - - - +
177A VAL* 1.3 61.4 + - + +
179A HIS* 3.3 6.6 + - - +
180A GLN* 3.0 25.2 + - + +
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Residues in contact with VAL 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ARG* 5.2 5.2 - - - +
173A PRO* 2.8 29.3 + - + +
174A LEU* 3.9 5.4 - - + +
176A LYS* 1.3 78.8 - - + +
178A PHE* 1.3 61.2 + - - +
180A GLN* 3.2 10.5 + - + +
181A ARG* 2.8 47.6 + - + +
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Residues in contact with PHE 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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132A LEU* 4.2 15.3 - - + -
138A GLY 5.6 0.2 - - - +
140A ASN 3.6 21.1 - - - +
141A LEU* 4.0 10.8 - - + -
142A ILE* 4.4 1.6 - - + -
151A ASP* 3.3 39.7 - - + -
154A LEU* 3.7 32.1 - - + -
155A PHE* 3.8 14.1 - - - -
158A LEU* 3.9 14.1 - - + -
174A LEU 2.9 18.7 + - - +
175A LEU 3.6 3.4 - - - +
177A VAL* 1.3 76.3 - - - +
179A HIS* 1.3 60.0 + - - +
181A ARG* 3.2 6.6 + - + +
182A MET* 2.9 55.1 + - + +
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Residues in contact with HIS 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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155A PHE* 3.4 30.5 - + - -
158A LEU* 4.1 7.6 - - + +
159A ASP* 2.9 47.4 + - + -
162A GLN* 3.2 25.6 + - - -
169A LEU* 4.2 11.4 - - + -
175A LEU 2.9 13.3 + - - +
176A LYS 3.4 9.6 - - - +
178A PHE* 1.3 81.4 - - - +
180A GLN* 1.3 63.3 + - - +
182A MET 3.4 0.2 + - - -
183A LYS* 3.0 49.1 + - + +
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Residues in contact with GLN 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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176A LYS* 3.0 13.6 + - + +
177A VAL* 3.2 15.7 + - + +
179A HIS* 1.3 77.7 - - - +
181A ARG* 1.3 65.1 + - - +
183A LYS* 3.2 43.3 + - - +
184A ASP* 3.0 46.1 + - - +
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Residues in contact with ARG 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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139A ARG 2.8 22.2 + - - -
140A ASN* 3.1 50.3 + - - +
141A LEU* 4.0 12.6 - - + -
177A VAL* 2.8 34.1 + - + +
178A PHE* 3.5 7.1 - - - +
180A GLN* 1.3 75.2 - - - +
182A MET* 1.3 64.9 + - + +
184A ASP* 3.4 13.9 + - - +
185A ARG* 3.5 14.8 + - + +
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Residues in contact with MET 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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141A LEU* 3.9 22.2 - - + -
147A ILE* 4.1 6.1 - - + -
151A ASP* 3.7 24.7 - - + +
152A TYR* 3.7 30.7 - - + -
155A PHE* 3.5 24.5 - - + -
178A PHE* 2.9 42.2 + - + +
181A ARG* 1.3 76.9 - - - +
183A LYS* 1.3 62.0 + - - +
185A ARG* 3.1 35.7 + - - +
188A LEU* 3.5 25.2 - - + +
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Residues in contact with LYS 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A PHE* 3.8 20.5 - - + -
179A HIS* 3.0 38.6 + - - +
180A GLN* 3.2 45.0 + - - +
182A MET* 1.3 76.0 - - - +
184A ASP* 1.3 62.8 + - - +
185A ARG 4.4 0.2 - - - -
188A LEU* 5.2 2.5 - - - -
189A LYS* 3.4 31.8 - - - +
192A CYS* 6.2 1.1 - - + -
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Residues in contact with ASP 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 GLN* 3.0 42.2 + - - +
181A ARG* 3.7 7.4 - - - +
182A MET 3.1 1.2 - - - -
183A LYS* 1.3 83.7 - - - +
185A ARG* 1.3 64.0 + - - +
186A PRO* 3.1 6.2 - - - +
189A LYS* 3.0 31.9 + - - +
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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