Contacts of the helix formed by residues 161 - 173 (chain A) in PDB entry 4TQ1
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 ARG 161 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A TRP* 4.0 2.0 - - - -
156A GLY 2.8 13.1 + - - +
159A ASN* 3.6 24.5 - - + +
160A ASP* 1.3 72.5 - - - +
162A PHE* 1.3 65.8 + - - +
163A ASP* 3.3 30.9 + - - -
164A GLN* 3.3 38.6 + - + +
165A PHE* 3.0 22.2 + - - +
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Residues in contact with PHE 162 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A LYS* 4.6 2.5 - - + -
8A LEU* 3.5 38.6 - - + -
9A ARG* 3.5 40.2 - - + +
12A TRP* 3.5 44.6 - + + +
13A PHE* 4.0 16.4 - + + -
160A ASP 3.9 1.4 + - - -
161A ARG* 1.3 71.3 - - - +
163A ASP* 1.3 70.2 + - + +
165A PHE* 3.3 1.0 + - - +
166A TRP* 3.0 58.4 + + + +
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Residues in contact with ASP 163 (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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161A ARG* 3.3 41.0 + - - -
162A PHE* 1.3 84.1 + - + +
164A GLN* 1.3 71.9 + - - +
166A TRP* 4.0 1.2 - - - -
167A ALA* 3.0 26.7 + - - +
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Residues in contact with GLN 164 (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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152A GLN* 2.9 57.0 + - + +
155A MET* 3.8 21.8 - - - +
156A GLY* 3.6 14.6 + - - -
159A ASN* 4.7 3.8 + - - +
161A ARG* 3.3 46.3 + - + +
163A ASP* 1.3 84.9 + - - +
165A PHE* 1.3 64.4 + - - +
167A ALA* 3.7 2.5 + - - -
168A ILE 4.1 0.9 + - - -
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Residues in contact with PHE 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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12A TRP* 3.4 42.0 - + + -
125A PHE* 3.9 16.6 - + - -
129A MET* 4.1 0.9 - - + -
152A GLN 4.7 2.7 - - - -
153A LEU* 3.2 45.5 - - + +
156A GLY* 4.2 6.0 - - - -
157A LEU* 4.2 1.3 - - + -
161A ARG 3.0 11.0 + - - +
162A PHE 3.8 2.7 - - - +
164A GLN* 1.3 77.6 - - - +
166A TRP* 1.3 70.8 + + - +
168A ILE* 3.2 5.0 + - - +
169A ASN* 2.9 56.6 + - + +
261A PRO* 3.3 36.1 - - + -
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Residues in contact with TRP 166 (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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8A LEU* 3.6 47.5 + - + +
12A TRP* 4.3 8.0 - + - -
162A PHE* 3.0 57.8 + + + +
163A ASP* 4.5 1.8 - - - +
165A PHE* 1.3 87.1 - + - +
167A ALA* 1.3 65.8 + - - +
168A ILE 3.0 2.0 - - - -
169A ASN* 3.4 28.5 - - - +
170A ARG* 3.0 53.1 + - + +
173A MET* 3.9 21.8 - - + -
256A GLU 3.8 13.9 - - - -
257A HIS 6.1 0.2 - - - -
259A SER 5.9 2.5 - - - -
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Residues in contact with ALA 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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152A GLN* 3.9 18.8 - - - +
163A ASP 3.0 18.4 + - - +
164A GLN* 4.9 0.2 - - - -
165A PHE 3.3 0.4 - - - -
166A TRP* 1.3 76.2 - - - +
168A ILE* 1.3 63.7 + - + +
170A ARG* 3.0 32.2 + - - +
171A LYS* 5.0 2.1 - - - +
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Residues in contact with ILE 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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145A MET* 3.7 26.8 - - + +
149A ASP* 3.8 32.1 - - + +
152A GLN* 3.6 45.8 - - + +
153A LEU* 3.6 28.5 - - + -
164A GLN 4.2 1.3 - - - +
165A PHE 3.2 3.0 + - - +
167A ALA* 1.3 85.0 - - + +
169A ASN* 1.3 64.0 + - - +
170A ARG 3.1 2.5 - - - -
171A LYS* 3.0 27.7 + - + +
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Residues in contact with ASN 169 (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 MET* 3.4 13.7 - - - +
153A LEU* 3.7 5.6 - - + +
165A PHE* 2.9 45.2 + - + +
166A TRP* 3.4 36.8 + - + -
168A ILE* 1.3 76.4 - - - +
170A ARG* 1.3 62.6 + - - +
172A LEU* 3.0 22.1 + - - +
173A MET* 3.5 14.7 + - - +
260A TYR 5.5 1.6 + - - -
261A PRO* 4.9 0.4 + - - +
263A ASN* 2.9 29.7 + - - +
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Residues in contact with ARG 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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166A TRP* 3.0 34.5 + - + +
167A ALA* 3.0 25.4 + - - +
168A ILE 4.3 0.2 - - - +
169A ASN* 1.3 76.7 - - - +
171A LYS* 1.3 92.8 + - + +
173A MET* 3.1 14.2 + - - +
174A GLU* 3.5 31.9 + - - +
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Residues in contact with LYS 171 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141A VAL* 3.4 22.3 - - + +
145A MET* 4.1 23.6 - - + +
149A ASP* 4.7 12.3 + - - +
167A ALA 5.0 0.9 - - - +
168A ILE* 3.0 19.2 + - + +
170A ARG* 1.3 113.9 - - + +
172A LEU* 1.3 60.0 + - - +
173A MET 3.1 1.5 + - - -
174A GLU* 3.5 29.5 + - - +
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Residues in contact with LEU 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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129A MET* 3.5 21.5 - - + +
133A ASP* 3.5 29.6 - - + +
136A LYS* 2.8 23.2 + - - +
137A HIS* 3.2 17.1 - - - -
141A VAL* 3.6 17.9 - - + -
142A ILE* 4.1 19.1 - - + +
145A MET* 3.8 21.3 - - + -
153A LEU* 4.4 5.2 - - + -
169A ASN* 3.0 29.2 + - - +
171A LYS* 1.3 77.4 - - - +
173A MET* 1.3 57.3 + - + +
174A GLU 3.5 0.2 - - - -
182A PHE* 3.9 1.0 - - - -
263A ASN* 3.4 17.9 - - - +
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Residues in contact with MET 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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136A LYS* 3.5 24.0 - - - +
166A TRP* 3.9 20.4 - - + -
169A ASN* 3.7 29.8 - - - +
170A ARG* 3.1 9.1 + - - +
171A LYS 3.1 1.2 - - - -
172A LEU* 1.3 76.4 - - - +
174A GLU* 1.3 64.9 + - - +
175A TYR* 4.1 6.6 - - - -
182A PHE* 3.4 26.2 - - + -
255A SER 3.6 18.6 - - - +
256A GLU* 3.8 33.2 - - + +
259A SER* 4.3 11.7 - - - +
260A TYR 5.5 0.7 - - - +
263A ASN* 4.0 10.1 - - - +
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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
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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