Contacts of the helix formed by residues 166 - 180 (chain A) in PDB entry 1T0R
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 GLU 166 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A TRP* 4.0 12.3 - - + -
164A THR* 3.3 15.2 + - - +
165A ASN* 1.3 77.2 - - - +
167A TRP* 1.3 76.7 + - - +
168A ALA* 3.1 9.4 + - - +
169A ALA* 2.8 36.8 + - + +
170A ILE 3.0 9.7 + - - -
341A THR 2.6 29.0 - - - +
342A VAL* 3.6 4.3 - - - +
343A TRP* 2.9 33.2 - - + -
471A MET* 3.1 25.2 - - + +
473A LEU* 3.9 11.0 - - + -
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Residues in contact with TRP 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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165A ASN 3.3 4.2 + - - -
166A GLU* 1.3 92.9 + - - +
168A ALA* 1.3 67.2 + - + +
170A ILE* 3.3 11.1 + - - +
171A ALA* 2.9 27.5 + - - +
271A VAL* 4.5 8.3 - - + -
331A MET* 6.0 0.4 - - - -
334A GLY 5.6 0.7 - - - -
335A VAL* 3.8 32.3 - - + -
338A TRP* 5.5 2.7 - - + +
341A THR* 3.0 26.0 + - + -
342A VAL* 3.7 16.0 - - + +
344A TRP* 5.6 0.9 - + - -
396A ILE* 5.0 11.2 - - + -
401A ASN 4.2 7.9 - - - +
402A LEU* 3.6 28.7 - - + -
403A PRO* 3.7 28.5 - - + -
450A LEU* 4.0 22.0 - - + +
471A MET* 3.1 28.5 - - + +
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Residues in contact with ALA 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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99A ALA* 6.0 1.4 - - - +
166A GLU* 3.1 21.1 + - - +
167A TRP* 1.3 100.7 - - + +
169A ALA* 1.3 57.0 + - - +
171A ALA* 3.2 7.5 + - - +
172A ALA* 2.9 26.9 + - - +
268A LEU* 5.8 0.5 - - - +
271A VAL* 6.3 1.3 - - + -
272A LEU* 5.9 5.8 - - + -
343A TRP* 4.0 14.6 - - + -
344A TRP* 4.4 15.0 - - + -
402A LEU* 5.6 0.2 - - - -
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Residues in contact with ALA 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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99A ALA* 6.5 0.2 - - - +
161A ALA* 3.4 31.2 - - + +
162A ILE* 4.4 5.1 - - + +
164A THR* 3.9 9.2 - - - +
166A GLU* 2.8 21.5 + - - +
168A ALA* 1.3 75.1 - - - +
170A ILE* 1.3 63.1 + - - +
172A ALA* 3.2 6.8 + - - +
173A ARG* 3.0 40.6 + - - +
343A TRP* 4.5 6.5 - - + -
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Residues in contact with ILE 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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165A ASN* 3.1 24.2 - - - +
166A GLU 3.0 8.6 + - - +
167A TRP* 3.6 13.7 - - - +
169A ALA* 1.3 75.6 - - - +
171A ALA* 1.3 53.0 - - - +
173A ARG* 3.3 23.7 + - - +
174A SER* 2.7 37.2 + - - -
401A ASN* 3.8 25.8 - - + +
447A HIS* 4.9 0.2 - - - +
449A ASN* 5.6 1.1 - - - -
450A LEU* 4.5 20.0 - - + +
453A ARG* 3.7 27.4 - - - +
47B GLU* 3.8 21.9 - - + +
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Residues in contact with ALA 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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167A TRP 2.9 14.8 + - - +
168A ALA* 3.3 11.7 - - - +
170A ILE* 1.3 77.7 - - - +
172A ALA* 1.3 63.3 + - - +
174A SER* 3.4 3.2 - - - -
175A PHE* 3.3 19.6 + - - +
264A ARG* 4.8 0.7 + - - -
268A LEU* 4.4 9.9 - - + +
400A CYS 3.9 6.1 - - - +
401A ASN* 3.6 26.7 - - - +
402A LEU* 3.6 22.2 - - + -
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Residues in contact with ALA 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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99A ALA* 4.4 15.7 - - + +
103A GLU* 3.5 10.5 - - - +
162A ILE* 4.1 13.7 - - + -
168A ALA 2.9 12.7 + - - +
169A ALA* 3.4 10.1 - - - +
170A ILE 3.2 0.2 - - - -
171A ALA* 1.3 75.7 - - - +
173A ARG* 1.3 64.6 + - - +
175A PHE* 3.0 5.4 + - - +
176A PHE* 3.0 35.0 + - + -
268A LEU* 4.3 13.4 - - + +
272A LEU* 6.0 0.9 - - + -
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Residues in contact with ARG 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A GLU* 3.4 11.4 + - - +
162A ILE* 3.0 43.3 + - + +
163A HIS 5.6 0.2 - - - -
164A THR 3.0 28.5 + - - -
165A ASN* 3.7 11.5 + - - -
169A ALA* 3.0 28.0 + - - +
170A ILE* 3.6 20.7 - - - +
172A ALA* 1.3 79.0 - - - +
174A SER* 1.3 63.4 + - - +
176A PHE 4.6 0.2 - - - +
177A ASP* 2.9 37.7 + - - +
37B TYR* 3.8 20.2 - - + -
47B GLU* 3.0 39.2 + - + +
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Residues in contact with SER 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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170A ILE 2.7 22.3 + - - -
171A ALA* 3.4 8.7 - - - -
172A ALA 3.1 0.2 - - - -
173A ARG* 1.3 76.5 - - - +
175A PHE* 1.3 64.6 + - - +
177A ASP* 4.3 1.0 - - - +
178A ASP* 3.3 12.5 + - - +
264A ARG* 3.0 25.2 + - - -
399A MET 3.1 3.9 + - - -
400A CYS 5.1 0.4 - - - -
401A ASN* 2.9 29.2 + - - -
447A HIS* 5.3 0.2 - - - -
47B GLU* 3.8 20.1 + - - +
48B LEU* 4.5 5.9 - - - +
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Residues in contact with PHE 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ALA 3.3 7.5 + - - +
172A ALA 3.0 7.7 + - - +
174A SER* 1.3 78.1 - - - +
176A PHE* 1.3 103.2 + + - +
178A ASP* 3.0 5.7 + - - +
179A MET* 2.9 52.1 + - + +
192A LEU* 6.1 1.3 - - + -
196A PHE* 3.6 30.3 - + + -
264A ARG* 3.2 37.8 - - + +
265A SER* 3.6 38.4 - - - -
268A LEU* 3.6 25.6 - - + -
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Residues in contact with PHE 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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99A ALA 4.3 6.7 - - - -
100A ILE* 4.0 17.3 - - + -
103A GLU* 2.9 61.0 - - + +
172A ALA* 3.0 21.7 + - + +
175A PHE* 1.3 107.0 - + - +
177A ASP* 1.3 60.8 + - - +
179A MET* 4.5 1.1 - - - +
180A MET* 2.8 62.9 + - + +
181A MET* 3.5 1.8 + - - -
192A LEU* 5.5 0.7 - - + -
196A PHE* 4.0 18.4 - + - -
268A LEU* 4.2 13.5 - - + -
272A LEU* 6.4 0.2 - - + -
502A AZI 4.6 8.7 - - - -
37B TYR* 4.5 0.4 - - - +
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Residues in contact with ASP 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 ARG* 2.9 26.2 + - - +
174A SER 4.3 1.3 - - - +
176A PHE* 1.3 72.2 - - - +
178A ASP* 1.3 54.2 + - - +
181A MET* 3.4 7.3 + - - +
182A THR* 2.6 39.1 + - - -
37B TYR* 2.5 36.1 + - - -
46B TRP* 3.2 32.9 - - + -
47B GLU* 2.8 31.7 + - + +
48B LEU* 4.2 5.4 - - + -
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Residues in contact with ASP 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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174A SER 3.3 4.9 + - - +
175A PHE 3.0 4.8 + - - +
177A ASP* 1.3 81.1 - - - +
179A MET* 1.3 64.1 + - + +
183A ARG* 2.7 41.0 + - - +
264A ARG* 2.8 37.0 + - - +
443A ARG* 2.7 21.0 + - - +
444A TYR* 2.6 32.1 + - - -
48B LEU* 3.7 11.8 - - + +
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Residues in contact with MET 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 PHE* 2.9 52.5 + - + +
176A PHE* 4.0 3.6 - - - +
178A ASP* 1.3 96.6 - - + +
180A MET* 1.3 61.7 + - + +
183A ARG* 3.6 15.9 - - - +
188A VAL* 4.2 7.4 - - - -
191A MET* 3.4 53.1 - - + +
192A LEU* 4.4 6.4 + - + +
260A VAL* 4.1 12.3 - - + -
261A ALA* 3.5 31.6 - - - +
264A ARG* 4.2 8.7 - - - -
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Residues in contact with MET 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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103A GLU 3.6 11.7 - - - +
106A ALA* 3.9 4.0 - - + -
107A ALA* 3.3 35.0 - - + +
110A ALA* 3.4 29.9 - - + +
113A ARG* 4.9 3.1 + - - -
176A PHE* 2.8 53.2 + - + +
179A MET* 1.3 75.8 - - + +
181A MET* 1.3 79.8 + - + +
182A THR 3.6 1.6 - - - -
183A ARG 4.6 1.0 + - - +
188A VAL* 3.7 18.0 - - + +
192A LEU* 3.6 36.8 - - + -
502A AZI 5.6 0.4 - - - -
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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