Contacts of the helix formed by residues 153 - 159 (chain A) in PDB entry 2JGK
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 VAL 153 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A CYS* 4.6 7.6 - - + +
70A TYR 4.1 6.3 - - - +
71A GLN* 3.9 21.8 - - + +
119A TYR* 4.4 4.5 - - + +
123A PHE* 3.4 15.3 - - - +
124A TYR 3.6 21.5 - - - +
125A SER* 3.7 26.9 - - - +
126A GLY 4.7 0.2 - - - +
151A TYR* 3.8 26.2 - - + +
152A ARG* 1.3 78.3 - - - +
154A GLY* 1.3 70.2 + - - +
155A THR 3.6 0.5 + - - -
156A PHE* 3.6 13.2 + - - -
157A GLY 3.0 8.9 + - - -
158A PHE* 4.1 1.8 - - - -
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Residues in contact with GLY 154 (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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70A TYR 5.8 0.4 - - - -
123A PHE 2.6 20.0 + - - -
124A TYR* 3.6 11.2 - - - +
153A VAL* 1.3 72.5 - - - +
155A THR* 1.3 51.9 + - - -
156A PHE* 5.2 0.7 - - - -
157A GLY 3.0 1.4 + - - -
158A PHE* 2.7 36.4 + - - +
285A GLU* 3.8 15.9 - - - -
299A PHE* 4.0 13.9 - - - -
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Residues in contact with THR 155 (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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47A PHE* 3.7 10.5 - - - -
153A VAL 3.6 0.2 + - - -
154A GLY* 1.3 70.5 - - - -
156A PHE* 1.3 74.3 + - - +
159A LEU* 2.9 46.4 + - + +
251A LEU* 3.8 18.4 - - + -
281A LEU* 3.7 27.8 - - + +
285A GLU* 3.6 13.5 + - + +
299A PHE* 3.4 34.8 - - + -
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Residues in contact with PHE 156 (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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46A ARG* 4.0 13.5 - - + -
47A PHE* 4.1 14.4 - - - -
70A TYR* 3.7 33.7 - - + -
94A GLU* 3.3 39.3 - - + +
152A ARG* 3.8 26.8 + - + -
153A VAL 3.8 8.3 - - - +
154A GLY* 5.2 0.2 - - - -
155A THR* 1.3 89.0 + - - +
157A GLY* 1.3 61.1 + - - +
171A VAL* 3.5 14.7 - - - +
278A ALA* 3.7 35.0 - - + -
281A LEU* 3.8 17.7 - - + -
282A VAL* 3.8 14.1 - - + -
285A GLU* 5.3 1.3 - - - -
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Residues in contact with GLY 157 (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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152A ARG* 3.4 32.7 - - - +
153A VAL 3.0 6.3 + - - -
154A GLY 3.0 6.0 + - - -
156A PHE* 1.3 79.8 - - - +
158A PHE* 1.3 65.7 + - - +
159A LEU 4.0 0.2 - - - -
169A GLY 5.2 0.2 - - - -
171A VAL* 3.3 12.6 + - - +
172A GLY 3.0 22.6 + - - -
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Residues in contact with PHE 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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123A PHE* 3.5 44.6 - + - -
151A TYR* 4.5 6.1 - + - -
152A ARG 3.2 19.3 - - - -
153A VAL* 4.1 0.9 - - - -
154A GLY 2.7 18.2 + - - +
155A THR 3.2 0.2 + - - -
157A GLY* 1.3 81.2 - - - +
159A LEU* 1.3 66.0 + - - +
160A ALA* 3.3 10.9 + - - +
169A GLY* 5.3 0.2 - - - -
170A ASN* 4.2 15.1 + - - +
172A GLY* 3.6 16.2 - - - -
173A LEU* 3.9 29.2 - - + -
176A GLN* 5.3 0.2 - - - -
244A ALA* 5.9 1.0 - - - +
299A PHE* 3.4 32.0 - - - +
300A VAL 3.7 12.3 - - - +
301A PRO* 3.8 24.0 - - + -
302A VAL* 5.3 1.2 - - - +
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Residues in contact with LEU 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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47A PHE* 4.2 23.9 - - + +
155A THR* 2.9 33.0 + - + +
157A GLY 5.6 0.2 - - - -
158A PHE* 1.3 74.9 - - - +
160A ALA* 1.3 65.4 + - - +
161A LEU* 4.9 4.5 - - + +
167A ALA* 4.2 19.2 - - + +
169A GLY* 4.6 4.7 + - - -
171A VAL* 6.2 0.2 - - - +
248A ALA* 3.8 23.8 - - + +
251A LEU* 3.9 28.0 - - + -
270A ILE* 5.4 0.4 - - + -
273A LEU* 4.0 25.6 - - + -
299A PHE* 3.6 25.3 - - + -
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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