Contacts of the helix formed by residues 160 - 176 (chain A) in PDB entry 2R0B
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 ASN 160 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A ASP* 3.2 23.7 + - - +
90A ASN* 3.3 23.6 + - - +
91A PRO* 3.3 20.7 - - + +
125A SER* 3.1 11.4 + - - +
158A ASN* 3.3 2.1 + - - -
159A PRO* 1.3 78.8 - - - +
161A ALA* 1.3 63.1 + - - +
162A GLY 2.8 26.5 + - - -
163A PHE* 2.9 28.9 + - - +
164A VAL* 3.0 16.8 + - - +
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Residues in contact with ALA 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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91A PRO* 5.0 4.2 - - + +
160A ASN* 1.3 74.8 - - - +
162A GLY* 1.3 62.0 + - - +
164A VAL* 3.2 9.5 + - - +
165A HIS* 3.0 38.9 + - + +
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Residues in contact with GLY 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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91A PRO* 3.4 29.2 - - - +
160A ASN* 2.8 8.6 + - - -
161A ALA* 1.3 79.2 - - - +
163A PHE* 1.3 57.4 + - - +
165A HIS* 3.4 8.0 + - - +
166A GLN* 3.0 38.8 + - - +
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Residues in contact with PHE 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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88A ALA 3.6 21.3 - - - -
89A ASP* 3.5 5.4 - - - -
90A ASN 3.6 15.7 - - - -
93A GLU* 3.9 10.1 - - + -
95A ILE* 3.5 46.5 - - + +
125A SER* 3.4 33.4 - - - -
126A ARG* 3.6 20.9 - - + -
129A ALA* 4.2 2.7 - - + -
159A PRO* 4.1 9.6 - - + -
160A ASN* 2.9 32.4 + - - +
162A GLY* 1.3 75.7 - - - +
164A VAL* 1.3 59.5 + - - +
166A GLN* 3.2 8.5 + - - +
167A LEU* 2.9 36.5 + - - +
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Residues in contact with VAL 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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143A TYR* 3.4 47.3 - - + +
159A PRO* 3.8 14.6 - - + +
160A ASN 3.0 15.3 + - - +
161A ALA* 3.2 10.5 + - - +
163A PHE* 1.3 74.1 - - - +
165A HIS* 1.3 69.0 + - + +
167A LEU* 3.1 10.0 + - - +
168A GLN* 3.1 36.8 + - - +
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Residues in contact with HIS 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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161A ALA* 3.0 34.6 + - + +
162A GLY* 3.6 9.6 - - - +
164A VAL* 1.3 81.0 - - + +
166A GLN* 1.3 57.6 + - + +
168A GLN* 3.3 19.6 + - - +
169A GLU* 2.9 29.0 + - - +
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Residues in contact with GLN 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A PRO 4.3 6.7 + - - -
92A VAL 5.0 1.2 + - - -
93A GLU 2.8 25.0 + - - -
94A ASN* 3.6 4.9 - - - +
95A ILE* 2.8 36.0 + - + +
96A ILE* 2.9 28.4 + - + +
99A PHE* 3.9 3.4 - - + -
162A GLY* 3.0 27.2 + - - +
163A PHE* 3.7 8.2 - - - +
164A VAL 3.2 0.4 - - - -
165A HIS* 1.3 74.8 - - + +
167A LEU* 1.3 60.6 + - - +
169A GLU* 3.5 19.8 - - - +
170A TYR* 3.0 30.3 + - - +
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Residues in contact with LEU 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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99A PHE* 3.7 14.8 - - + -
129A ALA* 3.5 37.7 - - + +
132A ILE* 4.0 8.7 - - + -
133A ALA* 3.6 28.7 - - + +
136A MET* 3.6 17.8 - - - +
143A TYR* 3.6 36.1 - - + -
159A PRO* 4.9 3.8 - - + -
163A PHE 2.9 21.9 + - - +
164A VAL* 3.1 6.9 + - - +
166A GLN* 1.3 77.2 - - - +
168A GLN* 1.3 61.6 + - - +
170A TYR* 3.3 5.9 + - + +
171A GLU 3.1 17.3 + - - -
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Residues in contact with GLN 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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2A SO4 3.0 38.0 + - - +
136A MET* 4.8 1.8 - - - -
143A TYR* 4.1 14.9 - - + +
164A VAL* 3.1 30.9 + - - +
165A HIS* 3.6 23.7 + - - +
167A LEU* 1.3 72.4 - - - +
169A GLU* 1.3 65.2 + - - +
171A GLU* 3.3 13.1 + - - +
172A ALA* 3.1 21.8 + - - +
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Residues in contact with GLU 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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96A ILE* 3.6 26.5 - - + +
165A HIS 2.9 15.6 + - - +
166A GLN* 3.5 22.5 - - - +
167A LEU 3.3 0.2 - - - -
168A GLN* 1.3 76.7 - - - +
170A TYR* 1.3 61.1 + - - +
172A ALA* 3.3 9.2 + - - +
173A ILE* 3.2 29.9 + - + +
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Residues in contact with TYR 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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96A ILE* 3.7 21.3 - - + +
99A PHE* 3.5 41.7 + + + -
100A PRO* 4.0 30.5 - - + +
103A LYS* 4.8 2.2 - - + +
133A ALA* 4.7 12.6 - - + -
137A GLU* 2.8 33.1 + - + -
166A GLN 3.0 16.9 + - - +
167A LEU* 3.7 5.8 - - + +
168A GLN 3.3 0.4 - - - -
169A GLU* 1.3 73.8 - - - +
171A GLU* 1.3 65.9 + - - +
173A ILE* 3.0 21.1 + - + +
174A TYR* 3.0 52.5 + + + +
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Residues in contact with GLU 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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2A SO4 4.8 9.5 + - - -
136A MET* 3.8 20.5 - - + +
141A MET 4.0 5.7 - - - +
142A LYS* 3.8 34.2 + - - +
143A TYR 5.1 0.2 + - - -
167A LEU 3.1 6.5 + - - -
168A GLN* 3.3 11.9 + - - +
170A TYR* 1.3 76.5 - - - +
172A ALA* 1.3 62.5 + - - +
174A TYR* 3.3 29.3 + - + +
175A LEU* 3.0 47.7 + - + +
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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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168A GLN 3.1 12.7 + - - +
169A GLU* 3.5 12.6 - - + +
170A TYR 3.2 0.2 - - - -
171A GLU* 1.3 75.4 - - - +
173A ILE* 1.3 62.5 + - + +
175A LEU* 4.0 5.1 - - - +
176A ALA* 3.2 24.6 + - - +
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Residues in contact with ILE 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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96A ILE* 3.9 28.5 - - + -
169A GLU* 3.2 15.4 + - + +
170A TYR* 3.0 19.4 + - + +
172A ALA* 1.3 76.9 - - + +
174A TYR* 1.3 65.2 + - + +
176A ALA* 3.2 22.2 + - - +
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Residues in contact with TYR 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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133A ALA 5.1 0.4 - - - -
136A MET* 3.2 37.0 + - + +
137A GLU* 3.6 46.9 - - + +
140A GLY* 6.3 0.2 - - - -
141A MET 4.4 1.2 + - - -
170A TYR* 3.0 55.6 + + + +
171A GLU* 3.6 38.9 + - + +
173A ILE* 1.3 78.5 - - + +
175A LEU* 1.3 77.4 + - + +
176A ALA 3.4 5.4 + - - +
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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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142A LYS* 6.2 2.0 - - - +
171A GLU* 3.0 48.6 + - + +
172A ALA* 4.2 4.0 - - - +
174A TYR* 1.3 90.1 - - + +
176A ALA* 1.3 64.1 + - - +
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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 ALA 3.2 17.8 + - - +
173A ILE* 3.2 14.0 + - - +
174A TYR 4.0 5.2 - - - +
175A LEU* 1.3 82.2 - - - +
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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