Contacts of the helix formed by residues 161 - 170 (chain A) in PDB entry 4JXJ
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 GLY 161 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A ARG* 5.9 3.4 - - - -
159A ALA 3.3 2.0 + - - -
160A TYR* 1.3 77.7 - - - +
162A ARG* 1.3 66.8 + - - -
163A LEU* 3.3 3.1 - - - -
164A SER* 2.9 10.6 + - - -
165A VAL* 3.1 24.6 + - - +
220A PHE* 3.8 15.9 - - - -
305A IOD 3.8 15.9 - - - -
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Residues in contact with ARG 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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123A THR* 5.3 0.6 - - - +
127A ILE* 3.9 14.5 - - - +
161A GLY* 1.3 71.8 - - - -
163A LEU* 1.3 62.7 + - - +
165A VAL* 3.2 5.1 + - - +
166A ILE* 3.0 33.2 + - + +
213A GLU* 2.9 50.9 + - - +
216A THR* 3.1 19.2 + - - +
217A LYS* 3.5 25.4 - - - +
220A PHE* 3.7 21.2 - - + -
305A IOD 3.6 13.9 - - + +
306A IOD 3.6 30.6 - - + +
310A IOD 4.1 10.1 - - - +
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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
----------------------------------------------------------
123A THR* 4.0 23.1 - - + +
126A VAL* 4.6 7.0 - - + -
127A ILE* 4.1 18.6 - - + -
147A VAL* 3.8 25.8 - - + +
150A ARG* 3.8 30.7 - - + +
151A ILE* 3.4 32.3 - - + +
161A GLY 3.3 0.8 - - - -
162A ARG* 1.3 79.9 - - - +
164A SER* 1.3 62.3 + - - +
166A ILE* 3.4 3.7 + - + +
167A CYS* 3.0 44.7 + - - -
306A IOD 4.2 6.9 - - + +
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Residues in contact with SER 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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150A ARG* 2.7 24.7 + - - +
151A ILE 4.0 6.7 - - - +
153A ALA* 3.4 22.3 - - - +
159A ALA 3.5 7.3 + - - -
160A TYR* 3.6 13.8 - - - -
161A GLY* 2.9 24.8 + - - -
163A LEU* 1.3 79.1 - - - +
165A VAL* 1.3 52.8 + - - +
167A CYS* 3.8 0.7 - - - +
168A SER* 2.8 40.7 + - - -
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Residues in contact with VAL 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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160A TYR* 3.4 27.1 - - + +
161A GLY 3.1 14.6 + - - +
162A ARG 3.2 7.6 + - - +
164A SER* 1.3 76.2 - - - +
166A ILE* 1.3 63.2 + - - +
168A SER* 3.3 1.4 + - - -
169A LEU* 3.1 26.9 + - + +
212A VAL* 4.0 14.1 - - + -
216A THR* 3.9 19.5 - - + -
220A PHE* 4.1 8.7 - - + -
258A PRO* 4.0 19.5 - - + +
261A TYR* 3.9 26.5 - - + -
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Residues in contact with ILE 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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127A ILE* 4.0 42.6 - - + -
130A LEU* 4.4 8.1 - - + -
131A LYS* 6.0 0.4 - - + -
162A ARG* 3.0 46.0 + - + +
163A LEU* 4.0 3.1 - - - +
165A VAL* 1.3 77.9 - - + +
167A CYS* 1.3 65.1 + - - +
169A LEU* 3.3 12.0 + - - +
170A ILE* 3.5 31.6 + - + +
209A ILE* 5.1 9.9 - - + +
212A VAL* 4.5 17.0 - - + -
213A GLU* 4.3 14.8 - - + +
216A THR* 4.2 3.8 - - - +
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Residues in contact with CYS 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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126A VAL* 4.1 6.1 - - - -
130A LEU* 3.7 26.2 - - + -
151A ILE* 3.9 35.9 - - - +
163A LEU* 3.0 40.1 + - - +
166A ILE* 1.3 77.4 - - - +
168A SER* 1.3 57.0 + - - +
170A ILE 3.2 0.9 + - - -
171A ALA* 2.8 35.6 + - - +
173A VAL* 4.1 12.7 - - + +
197A LEU* 4.1 1.8 - - - -
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Residues in contact with SER 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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151A ILE 5.2 2.6 + - - -
153A ALA 4.5 8.8 + - - -
154A LYS* 6.0 0.7 + - - -
155A PRO* 6.0 1.2 - - - +
160A TYR* 5.7 0.7 - - - -
164A SER 2.8 28.2 + - - -
165A VAL 3.8 0.2 - - - -
166A ILE 3.3 0.2 - - - -
167A CYS* 1.3 73.1 - - - +
169A LEU* 1.3 62.2 + - - +
170A ILE 3.4 0.3 + - - -
171A ALA 4.0 7.8 - - - +
173A VAL* 5.7 5.5 - - - +
200A LEU* 3.8 12.3 - - - +
258A PRO* 3.7 24.9 - - - +
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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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165A VAL* 3.1 22.4 + - + +
166A ILE* 3.8 6.5 - - - +
167A CYS 3.3 0.4 - - - -
168A SER* 1.3 76.7 - - - +
170A ILE* 1.3 58.9 + - - +
200A LEU* 3.5 11.7 - - - +
202A ASN 4.9 0.3 - - - +
203A ILE* 4.7 0.9 - - - -
204A PRO* 3.4 21.1 - - + +
209A ILE* 4.2 23.3 - - + -
212A VAL* 4.0 31.2 - - + -
258A PRO* 3.6 38.8 - - + +
259A ASN* 3.8 15.7 - - - +
262A LEU* 4.2 18.6 - - + -
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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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130A LEU* 3.7 53.6 - - + +
131A LYS* 4.5 1.3 - - - +
133A SER* 3.7 20.6 - - - +
166A ILE* 3.6 22.0 - - + +
167A CYS 3.2 2.1 + - - +
168A SER 3.2 0.2 - - - -
169A LEU* 1.3 85.0 - - - +
171A ALA* 1.3 58.3 + - - +
199A PRO* 3.4 2.2 - - + +
200A LEU* 2.8 27.1 + - - +
203A ILE* 3.6 10.6 - - + +
204A PRO* 4.7 3.6 - - + -
209A ILE* 3.9 39.9 - - + -
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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