Contacts of the helix formed by residues 162 - 175 (chain A) in PDB entry 4JRX
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 162 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158A ALA 3.0 17.4 + - - -
159A TYR 3.3 0.8 + - - -
161A GLU* 1.3 80.4 - - - +
163A LEU* 1.3 63.6 + - - -
164A CYS 3.3 1.6 - - - -
165A VAL* 3.2 12.8 + - - +
166A GLU* 3.3 19.8 + - - +
30D THR* 4.2 14.8 - - - -
36D THR* 3.9 10.7 - - - +
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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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62A ARG* 3.4 29.6 - - - +
158A ALA 4.1 2.4 + - - -
159A TYR* 3.2 12.8 + - + -
162A GLY* 1.3 67.7 - - - -
164A CYS* 1.3 59.9 + - - +
166A GLU* 4.4 10.1 - - + -
167A TRP* 2.8 56.8 + - + +
1C LEU* 3.8 13.5 - - + -
4C PRO* 3.9 6.1 - - + -
36D THR* 4.9 0.6 + - - -
111D TYR* 3.5 35.2 + - + +
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Residues in contact with CYS 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A MET* 3.6 20.7 - - - +
100A GLY* 4.0 6.7 - - - -
101A CYS* 2.2 63.0 - - - -
159A TYR* 2.9 51.9 + - + +
160A LEU* 3.6 9.0 - - - +
163A LEU* 1.3 72.0 - - - +
165A VAL* 1.4 55.8 + - - +
167A TRP* 5.0 0.2 - - - -
168A LEU* 3.1 24.3 + - - +
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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
----------------------------------------------------------
101A CYS* 4.3 7.9 - - + -
102A ASP 5.4 1.3 - - - +
103A LEU* 4.2 10.0 - - + +
107A GLY 3.5 24.5 - - - +
108A ARG* 4.5 4.9 - - - +
109A LEU* 3.9 33.2 - - + +
160A LEU 3.4 17.9 + - - +
161A GLU 4.0 8.7 - - - +
162A GLY 3.2 8.9 + - - +
164A CYS* 1.4 72.1 - - - +
166A GLU* 1.4 68.6 + - - +
168A LEU* 3.5 4.2 + - - +
169A ARG* 3.1 41.3 + - - +
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Residues in contact with GLU 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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161A GLU 5.0 0.3 - - - +
162A GLY 3.3 16.9 + - - +
163A LEU* 3.8 15.0 - - + +
165A VAL* 1.4 76.2 - - - +
167A TRP* 1.3 68.9 + - + +
169A ARG* 3.2 32.4 + - - +
170A ARG* 3.2 21.0 + - - +
30D THR* 3.0 32.1 + - - +
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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
----------------------------------------------------------
5A MET* 4.6 1.1 - - + -
55A GLU* 3.9 12.1 - - - -
59A TYR* 3.6 31.2 - + - -
62A ARG* 4.1 18.2 - - - +
163A LEU* 2.8 51.6 + - + +
164A CYS 4.3 1.6 - - - +
166A GLU* 1.3 72.7 - - + +
168A LEU* 1.3 64.3 + - - +
170A ARG* 3.2 46.3 + - - +
171A TYR* 3.0 46.4 + + + -
303A IOD 4.1 12.6 - - + -
1C LEU* 3.5 47.6 - - + +
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Residues in contact with LEU 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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3A HIS 4.1 4.7 - - - +
4A SER* 3.7 28.7 - - - +
5A MET* 3.6 34.9 - - + +
28A VAL* 3.9 21.3 - - + -
101A CYS* 4.0 15.3 - - + +
103A LEU* 3.8 24.5 - - + +
164A CYS 3.1 18.1 + - - +
165A VAL 3.7 4.3 - - - +
167A TRP* 1.3 73.9 - - - +
169A ARG* 1.4 57.8 + - - +
171A TYR* 3.0 13.9 + - - +
172A LEU* 2.9 39.8 + - + +
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Residues in contact with ARG 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A LEU* 4.1 18.7 - - + +
106A ASP 5.0 1.2 + - - -
107A GLY* 2.6 43.0 + - - -
108A ARG* 4.0 3.6 - - - +
165A VAL* 3.1 24.3 + - - +
166A GLU* 3.2 44.4 + - - +
167A TRP 3.3 0.2 - - - -
168A LEU* 1.4 74.8 - - - +
170A ARG* 1.3 62.6 + - - +
172A LEU* 3.4 10.9 + - + +
173A GLU* 3.0 24.3 + - - +
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Residues in contact with ARG 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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54A GLN* 5.3 8.1 + - - +
55A GLU* 2.7 37.5 + - - +
166A GLU 3.2 11.8 + - - +
167A TRP* 3.2 40.9 + - + +
169A ARG* 1.3 76.9 - - - +
171A TYR* 1.4 53.8 + - + +
173A GLU* 3.2 6.1 + - - +
174A ASN* 2.8 58.4 + - - +
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Residues in contact with TYR 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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5A MET* 3.4 33.2 - - - -
28A VAL* 4.0 15.0 - - + -
33A PHE* 3.9 8.3 - + - -
51A TRP* 3.6 29.7 - + + -
52A ILE* 3.2 21.5 - - + -
55A GLU* 4.3 10.1 - - - -
59A TYR* 2.5 31.6 + - - -
167A TRP* 3.0 32.5 + + - -
168A LEU* 3.0 8.6 + - - +
170A ARG* 1.4 75.5 - - + +
172A LEU* 1.3 53.9 + - - +
174A ASN* 3.2 4.7 + - - +
175A GLY 2.8 31.9 + - - -
179A LEU* 3.6 8.7 - - - +
1C LEU 2.8 18.7 + - - -
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Residues in contact with LEU 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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3A HIS* 3.5 57.7 - - + +
28A VAL* 4.2 15.3 - - + -
103A LEU* 4.4 15.3 - - + -
168A LEU* 2.9 33.7 + - + +
169A ARG* 3.5 13.7 - - + +
171A TYR* 1.3 73.5 - - - +
173A GLU* 1.3 57.4 + - - +
175A GLY 3.9 0.2 - - - -
176A LYS* 3.2 28.9 + - - +
179A LEU* 4.3 14.3 - - + +
180A GLN* 3.4 19.6 - - - +
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Residues in contact with GLU 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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169A ARG 3.0 13.1 + - - +
170A ARG* 3.5 9.9 - - - +
172A LEU* 1.3 75.7 - - - +
174A ASN* 1.3 67.9 + - - +
176A LYS* 3.3 45.4 + - - +
180A GLN* 5.1 2.5 - - - +
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Residues in contact with ASN 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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51A TRP* 3.9 17.1 + - + +
54A GLN* 3.2 41.9 + - - +
55A GLU* 3.8 7.5 + - - -
170A ARG* 2.8 55.1 + - - +
171A TYR* 3.8 6.5 - - + +
173A GLU* 1.3 79.9 - - - +
175A GLY* 1.3 55.9 + - - +
176A LYS* 3.6 0.9 + - - +
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Residues in contact with GLY 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A TRP* 3.7 21.0 - - - +
171A TYR 2.8 16.3 + - - -
172A LEU 3.9 1.3 - - - -
174A ASN* 1.3 72.3 - - - +
176A LYS* 1.4 52.3 + - - +
177A GLU* 3.3 3.6 - - - -
178A THR* 3.0 8.2 + - - -
179A LEU* 2.7 44.8 + - - +
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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