Contacts of the helix formed by residues 156 - 170 (chain A) in PDB entry 3NOR
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 THR 156 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A LEU* 3.9 26.2 - - + -
24A PRO* 6.0 0.4 - - - -
154A GLY 3.3 0.2 - - - -
155A ILE* 1.3 86.0 - - + +
157A ALA* 1.3 65.7 + - - +
158A GLY 3.0 3.6 - - - +
159A ILE* 2.9 44.2 + - + +
160A ASP* 3.5 9.8 + - - +
184A TYR* 5.0 6.3 + - - -
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Residues in contact with ALA 157 (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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103A VAL* 4.9 0.9 - - + -
142A ARG* 4.0 8.5 - - + +
143A VAL* 4.2 6.9 - - + +
152A GLY* 3.6 32.5 - - - +
154A GLY 3.1 22.1 + - - +
155A ILE 3.4 0.2 - - - -
156A THR* 1.3 78.0 - - - +
158A GLY* 1.3 59.4 + - - +
160A ASP* 3.2 12.8 + - - +
161A PHE* 2.9 31.2 + - + +
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Residues in contact with GLY 158 (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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24A PRO* 3.5 17.9 - - - +
103A VAL* 4.0 15.3 - - - +
155A ILE 4.8 0.4 + - - -
156A THR* 3.0 1.6 - - - +
157A ALA* 1.3 76.6 - - - +
159A ILE* 1.3 59.6 + - - +
161A PHE* 3.6 25.4 - - - -
162A ALA* 2.9 32.4 + - - +
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Residues in contact with ILE 159 (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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19A LEU* 5.1 3.6 - - + -
23A GLY* 3.6 32.5 - - - +
24A PRO* 3.9 5.1 - - + +
27A VAL* 3.9 17.6 - - + +
156A THR* 2.9 36.3 + - + +
158A GLY* 1.3 78.4 - - - +
160A ASP* 1.3 62.9 + - - +
162A ALA* 3.5 6.8 + - - +
163A LEU* 3.4 19.3 + - + +
184A TYR* 3.5 45.5 - - + +
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Residues in contact with ASP 160 (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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142A ARG* 5.9 2.9 - - - -
143A VAL* 4.9 8.3 - - + -
156A THR* 3.5 9.0 + - - +
157A ALA* 3.2 12.3 + - - +
159A ILE* 1.3 77.6 - - - +
161A PHE* 1.3 63.0 + - - +
163A LEU* 3.1 24.4 + - - +
164A THR* 3.4 7.7 + - - -
184A TYR* 2.6 36.7 + - - -
186A PRO* 5.5 0.2 - - - +
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Residues in contact with PHE 161 (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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24A PRO* 5.3 3.1 - - + -
28A LEU* 6.2 1.6 - - + -
70A CYS* 4.3 6.5 - - + -
101A THR* 3.7 37.2 - - + -
102A SER 3.5 22.7 - - - -
103A VAL* 3.9 10.1 - - + -
143A VAL* 4.1 26.4 - - + +
150A LEU* 3.9 25.4 - - + -
152A GLY* 4.2 7.2 - - - -
157A ALA 2.9 25.5 + - - +
158A GLY* 3.6 24.7 - - - -
160A ASP* 1.3 71.1 - - - +
162A ALA* 1.3 64.7 + - - +
164A THR* 3.1 9.8 + - - +
165A LEU* 2.8 42.9 + - + +
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Residues in contact with ALA 162 (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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24A PRO* 4.2 6.7 - - + -
27A VAL* 3.6 26.4 - - + +
28A LEU* 3.8 25.5 - - + +
158A GLY 2.9 21.2 + - - +
159A ILE 3.5 6.7 - - - +
161A PHE* 1.3 81.3 - - + +
163A LEU* 1.3 55.8 + - - +
165A LEU* 3.4 5.9 + - - +
166A ALA* 2.8 29.6 + - - +
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Residues in contact with LEU 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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27A VAL* 3.9 20.6 - - + -
159A ILE* 3.4 11.0 + - + +
160A ASP* 3.1 11.5 + - - +
162A ALA* 1.3 74.9 - - - +
164A THR* 1.3 64.2 + - - +
166A ALA* 3.4 3.0 + - + -
167A ALA* 3.1 19.4 + - - +
175A ALA* 3.5 37.1 - - + +
178A VAL* 4.4 5.8 - - + -
179A GLN* 4.2 26.7 - - + +
182A LEU* 6.3 0.2 - - + -
184A TYR* 3.8 34.5 - - + -
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Residues in contact with THR 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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145A ARG* 3.9 24.7 - - - +
150A LEU* 4.6 10.1 - - + -
160A ASP 3.4 8.5 + - - -
161A PHE* 3.1 16.7 + - - +
163A LEU* 1.3 77.0 - - - +
165A LEU* 1.3 64.5 + - + +
167A ALA* 3.2 8.7 + - + +
168A GLU* 3.2 27.6 + - + +
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Residues in contact with LEU 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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28A LEU* 4.5 18.6 - - + -
68A VAL* 3.9 32.3 - - + -
99A TYR* 3.5 43.3 - - + -
101A THR* 4.5 5.2 - - + -
145A ARG* 6.0 0.4 - - - +
150A LEU* 4.5 14.8 - - + -
161A PHE* 2.8 36.0 + - + +
162A ALA* 3.6 5.2 - - - +
164A THR* 1.3 78.6 - - + +
166A ALA* 1.3 64.6 + - - +
168A GLU* 3.2 5.4 + - - +
169A LEU* 2.9 36.3 + - + +
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Residues in contact with ALA 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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27A VAL* 5.5 2.0 - - + -
31A LEU* 3.6 39.0 - - + +
162A ALA 2.8 18.6 + - - +
163A LEU* 3.5 11.4 - - + +
165A LEU* 1.3 76.4 - - - +
167A ALA* 1.3 56.0 + - - +
169A LEU* 4.8 0.2 - - - -
170A PHE* 3.0 35.6 + - - +
171A ASP 3.7 1.0 + - - +
175A ALA* 3.9 17.7 + - + +
178A VAL* 5.6 0.7 - - + -
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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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163A LEU 3.1 13.2 + - - +
164A THR* 3.2 11.4 + - + +
166A ALA* 1.3 77.5 - - - +
168A GLU* 1.3 61.1 + - + +
170A PHE 3.5 1.2 - - - +
171A ASP* 3.2 33.5 + - - -
172A ALA* 3.8 15.3 + - + -
175A ALA* 3.8 11.6 - - + +
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Residues in contact with GLU 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 TYR* 2.6 36.8 + - + +
145A ARG* 2.6 43.1 + - - -
164A THR* 3.2 19.2 + - + +
165A LEU* 3.2 4.1 + - - +
167A ALA* 1.3 78.4 - - + +
169A LEU* 1.3 66.5 + - - +
170A PHE 3.2 4.8 + - - +
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Residues in contact with LEU 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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6A VAL* 4.3 34.3 - - + -
8A ILE* 4.9 4.0 - - + -
28A LEU* 5.4 0.2 - - + -
31A LEU* 4.8 7.6 - - + -
67A ASP* 5.5 0.4 - - + -
68A VAL* 4.4 14.6 - - + -
98A ARG* 4.1 19.3 - - - +
99A TYR* 3.7 25.6 - - + -
165A LEU* 2.9 29.1 + - + +
166A ALA 4.8 0.7 - - - +
168A GLU* 1.3 76.8 - - - +
170A PHE* 1.3 87.4 + - + +
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Residues in contact with PHE 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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4A MET 5.9 2.2 - - - -
6A VAL* 4.4 12.3 - - + -
31A LEU* 3.8 33.2 - - + -
32A PRO* 3.4 51.1 - - + -
33A ASP* 5.0 2.0 - - - -
34A VAL* 4.2 8.1 - - + -
166A ALA 3.0 13.8 + - - +
167A ALA 3.5 4.8 - - - +
168A GLU 4.2 2.9 - - - +
169A LEU* 1.3 101.3 - - + +
171A ASP* 1.3 68.0 + - - +
174A THR* 3.9 19.7 - - + +
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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