Contacts of the helix formed by residues 177 - 189 (chain A) in PDB entry 1JR9
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 LYS 177 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A LYS 5.1 1.4 + - - -
174A TYR* 3.0 39.3 + - - +
175A GLN* 4.8 7.0 - - - +
176A ASN* 1.3 90.2 + - - +
178A ARG* 1.3 62.9 + - - +
179A PRO* 3.4 6.3 - - - -
180A ASP* 3.3 43.8 + - - +
181A TYR 3.3 8.5 + - - -
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Residues in contact with ARG 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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123A ALA 2.9 28.6 + - - -
124A ALA* 4.1 11.0 + - + +
126A ARG 2.8 29.6 + - - -
127A PHE* 5.1 0.6 - - - +
128A GLY 3.6 18.8 + - - +
165A VAL* 2.9 24.4 + - - +
167A GLU* 5.2 4.9 - - - +
170A TYR* 3.2 40.4 + - + +
176A ASN 2.8 11.8 + - - +
177A LYS* 1.3 69.2 - - - +
179A PRO* 1.3 75.6 - - + +
181A TYR* 2.9 10.5 + - + +
182A ILE* 2.8 39.6 + - + +
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Residues in contact with PRO 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ALA* 5.1 12.8 - - + -
176A ASN 4.7 1.1 - - - +
177A LYS* 3.6 6.5 - - - -
178A ARG* 1.3 92.3 - - + +
180A ASP* 1.3 61.2 + - - +
182A ILE* 3.1 13.4 + - + +
183A SER* 2.8 34.7 + - - +
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Residues in contact with ASP 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A TYR* 3.8 18.7 - - + -
177A LYS* 3.3 40.7 + - + +
178A ARG 3.1 0.4 - - - -
179A PRO* 1.3 81.2 - - - +
181A TYR* 1.3 63.9 + - - +
183A SER* 3.1 8.7 + - - -
184A ALA* 2.9 24.4 + - - +
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Residues in contact with TYR 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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18A THR* 6.1 0.4 - - + -
19A ILE* 4.7 20.8 - - + +
85A PHE* 3.7 14.0 - - - -
163A LEU* 3.3 28.7 - - + +
164A ASP 3.2 27.7 + - - -
165A VAL* 4.9 2.2 - - + -
169A ALA* 3.8 21.5 + - + +
170A TYR* 3.4 40.2 - + + -
174A TYR* 3.7 36.6 - + + -
177A LYS 3.3 4.8 + - - +
178A ARG* 2.9 11.3 + - + +
180A ASP* 1.3 78.3 - - - +
182A ILE* 1.3 65.0 + - + +
184A ALA* 3.4 2.8 + - + +
185A PHE* 3.0 28.0 + + + +
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Residues in contact with ILE 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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119A PHE* 5.4 2.2 - - + -
120A ALA* 3.8 39.5 - - + +
123A ALA* 3.6 31.6 - - + -
124A ALA* 3.8 14.4 - - + +
163A LEU* 4.0 11.2 - - + -
165A VAL* 5.3 0.7 - - + -
178A ARG* 2.8 39.6 + - + +
179A PRO* 3.3 9.2 - - + +
181A TYR* 1.3 81.2 - - + +
183A SER* 1.3 67.5 + - - +
185A PHE* 3.1 22.1 - - + +
186A TRP* 3.7 11.9 + - + +
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Residues in contact with SER 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A ALA* 6.5 0.2 - - - -
179A PRO* 2.8 21.6 + - - +
180A ASP* 3.5 10.0 - - - -
182A ILE* 1.3 74.9 - - - +
184A ALA* 1.3 64.6 + - - +
185A PHE 3.2 0.2 + - - -
186A TRP* 3.2 29.7 + - - +
187A ASN* 4.4 2.6 + - - -
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Residues in contact with ALA 184 (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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18A THR* 3.5 19.6 - - + +
174A TYR* 3.2 28.7 - - + +
180A ASP 2.9 15.1 + - - +
181A TYR* 3.5 4.3 - - + +
183A SER* 1.3 77.4 - - - +
185A PHE* 1.3 63.3 + - - +
187A ASN* 3.0 32.5 + - - +
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Residues in contact with PHE 185 (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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18A THR* 4.3 3.3 - - - +
19A ILE* 5.3 3.8 - - + -
85A PHE* 4.1 13.5 - + - -
88A LEU* 4.1 16.2 - - + -
89A MET* 4.2 9.6 - - + -
119A PHE* 5.0 4.7 - + - -
161A LEU* 4.7 16.4 - - + -
162A GLY 4.0 14.4 - - - -
163A LEU* 3.4 48.2 - - + -
181A TYR* 3.0 18.5 + + + +
182A ILE* 3.1 15.0 + - + +
184A ALA* 1.3 73.6 - - - +
186A TRP* 1.3 75.2 + + - +
187A ASN 2.9 2.1 + - - -
188A VAL* 2.9 31.8 + - + +
189A VAL* 3.3 35.9 - - + +
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Residues in contact with TRP 186 (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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94A GLY* 3.7 9.7 - - - -
95A GLY 4.3 9.8 + - - +
112A PHE* 4.4 7.9 - + + -
115A PHE* 4.0 14.4 - + - -
116A GLN* 3.9 38.2 - - + +
119A PHE* 3.9 43.5 - + + -
120A ALA* 4.7 11.1 - - - +
161A LEU* 4.7 8.7 - - + -
182A ILE* 3.7 13.6 + - + +
183A SER* 3.2 26.7 - - - +
184A ALA 3.1 0.2 + - - -
185A PHE* 1.3 83.1 - + - +
187A ASN* 1.3 65.0 + - - +
188A VAL 3.4 0.5 + - - -
189A VAL* 3.5 21.8 + - + +
191A TRP* 3.7 34.7 + + - -
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Residues in contact with ASN 187 (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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18A THR* 4.4 13.2 + - - +
90A SER 4.9 0.2 - - - +
93A GLY 3.4 5.7 - - - +
94A GLY* 2.8 23.6 + - - -
95A GLY 5.1 1.3 - - - +
183A SER 4.8 1.9 + - - +
184A ALA* 3.0 26.0 + - - +
185A PHE 2.9 4.4 + - - -
186A TRP* 1.3 75.9 - - - +
188A VAL* 1.3 58.1 + - + +
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Residues in contact with VAL 188 (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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15A LEU* 3.8 30.7 - - + +
18A THR* 3.5 31.6 - - + +
19A ILE* 4.5 5.6 - - + -
89A MET* 3.2 22.6 - - + -
90A SER 2.9 33.0 + - - +
93A GLY* 4.3 0.2 - - - -
94A GLY 3.9 2.2 + - - -
185A PHE* 2.9 32.9 + - + +
187A ASN* 1.3 76.6 - - + +
189A VAL* 1.3 69.3 + - - +
190A ASN* 3.1 0.5 + - - -
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Residues in contact with VAL 189 (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 LEU 3.6 11.4 - - - +
94A GLY* 2.7 30.1 + - - -
161A LEU* 3.6 29.2 - - + -
185A PHE* 3.3 50.7 - - + +
186A TRP* 3.5 18.2 + - + +
188A VAL* 1.3 75.1 - - - +
190A ASN* 1.3 63.3 + - - +
191A TRP* 3.5 29.8 + - + +
194A VAL* 4.6 0.2 - - + -
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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