Contacts of the helix formed by residues 164 - 182 (chain A) in PDB entry 1TJY
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 VAL 164 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A LYS* 3.5 34.3 - - + +
92A ALA 3.8 5.4 - - - +
93A VAL* 3.4 22.7 - - + +
160A SER* 3.4 24.2 - - - +
161A SER* 3.0 24.2 + - - +
163A THR* 1.3 76.4 + - - +
165A THR* 1.3 68.8 + - - +
166A ASP* 3.6 3.8 - - - +
167A GLN* 3.8 21.5 - - + +
168A ASN* 2.8 22.3 + - - +
195A ASN* 6.1 0.4 - - - +
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Residues in contact with THR 165 (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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92A ALA 4.3 0.5 + - - -
93A VAL 4.5 0.6 + - - -
94A SER* 3.4 2.6 - - - -
95A PRO* 3.2 36.6 - - + +
117A SER* 3.3 6.1 + - - -
118A ASP* 2.7 40.5 + - + +
119A THR 4.8 1.3 - - - +
163A THR 3.4 3.5 + - - -
164A VAL* 1.3 80.4 - - - +
166A ASP* 1.3 64.5 + - - +
168A ASN* 4.1 1.4 - - - +
169A GLN* 3.2 47.8 + - + +
312A TYR* 4.4 1.8 - - - +
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Residues in contact with ASP 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LYS* 2.9 23.1 + - - -
116A ASP* 3.3 29.5 - - - +
117A SER* 3.2 15.0 + - - -
118A ASP 5.3 0.2 - - - +
127A TYR* 4.5 2.7 - - - +
164A VAL* 3.6 3.3 - - - +
165A THR* 1.3 76.2 - - - +
167A GLN* 1.3 81.7 + - - +
169A GLN* 3.1 12.6 + - - +
170A TRP* 3.1 48.6 + - + +
400A PAV 2.7 24.2 + - - -
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Residues in contact with GLN 167 (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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35A LYS* 3.7 8.1 - - - +
159A TYR* 3.4 17.4 - - + +
160A SER* 2.7 40.7 + - - -
164A VAL* 3.8 8.2 + - + -
166A ASP* 1.3 88.8 + - - +
168A ASN* 1.3 58.6 + - - +
170A TRP* 3.4 11.9 + - + +
171A VAL* 2.9 35.9 + - - +
220A PRO* 3.2 25.2 + - + +
221A ASP* 2.9 23.8 + - - +
400A PAV 3.0 25.2 + - - +
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Residues in contact with ASN 168 (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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159A TYR* 2.7 27.7 + - - -
161A SER 2.9 24.0 + - - -
162A PRO* 3.3 27.3 - - - +
163A THR 3.7 0.4 - - - -
164A VAL* 2.8 26.5 + - - +
165A THR 4.2 1.1 - - - +
166A ASP 3.2 0.8 - - - -
167A GLN* 1.3 76.0 - - - +
169A GLN* 1.3 64.0 + - - +
171A VAL* 4.2 3.1 - - - +
172A LYS* 3.1 26.2 + - - +
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Residues in contact with GLN 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ASP* 5.1 1.4 - - - +
127A TYR* 4.8 1.6 + - - -
133A PRO* 3.7 24.7 - - + +
165A THR* 3.2 30.5 + - + +
166A ASP* 3.1 14.7 + - - +
168A ASN* 1.3 77.6 - - + +
170A TRP* 1.3 65.1 + - + +
172A LYS* 3.6 7.2 + - - +
173A GLU* 3.5 14.6 + - - +
310A GLN* 2.9 29.9 + - - +
312A TYR* 3.0 39.1 + - - -
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Residues in contact with TRP 170 (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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116A ASP 4.6 0.7 - - - -
127A TYR* 5.2 1.8 + - - -
130A GLN* 3.2 28.5 - - - -
131A GLY 4.6 3.6 + - - -
133A PRO* 4.0 21.1 - - + -
136A LEU* 3.3 37.7 - - + +
137A GLY* 3.8 5.9 - - - +
140A LEU* 4.6 8.7 - - + -
166A ASP* 3.1 42.8 + - + +
167A GLN* 3.8 21.1 - - + +
169A GLN* 1.3 81.0 - - + +
171A VAL* 1.3 59.7 + - + +
173A GLU* 3.2 4.7 + - - +
174A ALA* 2.9 28.0 + - - +
220A PRO* 4.0 6.5 - - + -
245A PHE* 3.6 23.8 - + - -
266A TRP* 4.0 5.6 - + - -
310A GLN* 4.8 6.7 - - - +
400A PAV 3.4 28.7 - - - -
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Residues in contact with VAL 171 (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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140A LEU* 5.3 1.1 - - + -
157A PHE* 3.9 17.0 - - + -
159A TYR* 3.7 36.8 - - + +
167A GLN 2.9 20.9 + - - +
168A ASN 4.2 2.5 - - - +
170A TRP* 1.3 74.7 - - + +
172A LYS* 1.3 67.4 + - - +
174A ALA* 3.8 5.8 - - - +
175A LYS* 2.9 51.7 + - + +
220A PRO* 3.8 24.9 - - + -
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Residues in contact with LYS 172 (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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168A ASN 3.1 18.1 + - - +
169A GLN* 3.7 8.1 - - - +
171A VAL* 1.3 78.6 - - - +
173A GLU* 1.3 65.5 + - + +
175A LYS* 3.5 5.7 + - - +
176A ALA* 3.1 22.9 + - - +
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Residues in contact with GLU 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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133A PRO* 3.5 45.7 - - + +
134A LYS* 3.6 36.7 - - - +
137A GLY* 4.5 3.1 - - - -
169A GLN 3.5 3.3 + - - +
170A TRP 3.2 5.8 + - - +
172A LYS* 1.3 80.1 - - + +
174A ALA* 1.3 60.2 + - - +
176A ALA* 3.3 10.7 + - - +
177A LYS* 2.9 29.3 + - - +
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Residues in contact with ALA 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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137A GLY* 3.9 15.8 - - - +
140A LEU* 4.5 7.4 - - + -
141A VAL* 3.5 22.3 - - + +
157A PHE* 4.0 20.6 - - + -
170A TRP 2.9 16.3 + - - +
171A VAL* 3.8 4.9 - - - +
173A GLU* 1.3 75.8 - - - +
175A LYS* 1.3 58.9 + - - +
177A LYS* 3.3 1.5 + - - -
178A ILE* 2.9 34.4 + - - +
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Residues in contact with LYS 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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157A PHE* 3.8 21.8 - - + -
159A TYR* 5.6 0.6 + - - -
171A VAL* 2.9 37.4 + - + +
172A LYS* 3.9 5.2 - - - +
174A ALA* 1.3 74.5 - - - +
176A ALA* 1.3 64.6 + - - +
178A ILE* 3.4 7.6 + - - +
179A SER* 3.0 23.7 + - - -
187A ILE* 3.7 27.6 - - + +
190A THR* 2.8 35.4 + - - +
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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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172A LYS* 3.1 19.1 + - + +
173A GLU* 3.3 13.0 + - - +
175A LYS* 1.3 74.8 - - - +
177A LYS* 1.3 63.1 + - - +
179A SER* 2.7 23.5 + - - -
180A GLN* 3.1 28.2 + - - +
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Residues in contact with LYS 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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137A GLY 5.7 0.2 - - - -
138A SER* 3.8 46.0 + - - +
141A VAL* 3.8 26.7 - - + -
142A GLU* 4.5 13.6 + - - +
173A GLU 2.9 17.0 + - - +
174A ALA* 3.6 5.2 - - - +
176A ALA* 1.3 76.7 - - - +
178A ILE* 1.3 57.5 - - - +
180A GLN* 3.3 10.0 + - - +
181A GLU* 2.8 75.3 + - - +
182A HIS* 5.7 0.4 - - - -
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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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141A VAL* 3.8 20.4 - - + -
155A VAL* 4.6 3.1 - - + -
157A PHE* 3.8 32.1 - - + -
174A ALA 2.9 20.1 + - - +
175A LYS* 3.7 5.2 - - - +
177A LYS* 1.3 75.8 - - - +
179A SER* 1.3 60.8 + - - +
182A HIS* 2.9 43.5 + - - +
185A TRP* 4.0 46.7 - - + +
187A ILE* 4.6 18.2 - - + -
218A ILE* 4.1 11.7 - - + -
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Residues in contact with SER 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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175A LYS 3.0 13.8 + - - -
176A ALA* 2.7 24.0 + - - -
178A ILE* 1.3 79.2 - - - +
180A GLN* 1.3 63.7 + - - +
182A HIS 5.1 0.4 - - - -
183A PRO* 4.1 17.5 - - - +
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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 ALA* 3.1 28.5 + - - +
177A LYS* 3.9 10.9 - - - +
179A SER* 1.3 86.2 + - - +
181A GLU* 1.3 71.8 + - + +
182A HIS 3.6 0.2 - - - -
183A PRO* 4.1 8.1 - - - +
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Residues in contact with GLU 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 LYS* 2.8 62.8 + - - +
180A GLN* 1.3 85.1 + - + +
182A HIS* 1.3 81.2 + - + +
183A PRO* 3.4 8.8 - - - +
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Residues in contact with HIS 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 VAL* 3.6 32.0 - - + +
145A ALA* 3.7 26.4 - - + +
150A LYS 5.5 0.6 + - - -
151A GLU 5.2 0.7 - - - -
177A LYS* 5.7 0.2 - - - -
178A ILE* 2.9 20.1 + - - +
179A SER* 5.1 0.3 - - - -
181A GLU* 1.3 99.9 + - + +
183A PRO* 1.3 60.8 - - - +
184A GLY 3.2 2.9 - - - -
185A TRP* 2.9 64.1 + + + +
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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
------------------------------------------------------------
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