Contacts of the helix formed by residues 297 - 306 (chain A) in PDB entry 1MJN
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 ASP 297 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A ASP* 4.2 2.1 - - - +
157A VAL* 6.1 0.9 - - - +
160A LYS* 3.0 37.6 + - - +
295A LEU* 3.3 5.8 + - - -
296A LYS* 1.3 72.4 - - - +
298A LEU* 1.3 67.1 + - - +
299A CYS* 3.6 9.2 + - - +
300A THR* 2.9 39.5 + - - +
301A GLU* 3.0 23.6 + - - +
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Residues in contact with LEU 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A PHE* 5.1 1.1 - - + -
153A PHE* 3.7 25.2 - - + -
157A VAL* 4.2 19.0 - - + +
235A ILE* 4.0 35.4 - - + -
257A TYR* 5.3 11.9 - - + -
259A ILE* 4.6 4.3 - - + -
287A LYS* 5.8 5.4 - - + -
295A LEU* 4.1 19.1 - - + +
296A LYS 3.1 5.1 + - - +
297A ASP* 1.3 73.5 + - - +
299A CYS* 1.3 68.2 + - - +
301A GLU* 3.2 8.1 + - + +
302A LEU* 2.8 54.6 + - + +
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Residues in contact with CYS 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A VAL* 3.9 19.4 - - + +
160A LYS* 3.5 20.0 - - + -
161A CYS* 2.1 57.9 - - - -
297A ASP* 3.4 10.3 + - - +
298A LEU* 1.3 78.8 - - - +
300A THR* 1.3 64.1 + - - +
302A LEU* 3.3 4.1 + - - +
303A GLN* 3.0 38.6 + - - +
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Residues in contact with THR 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A ASP* 2.9 29.3 + - - +
299A CYS* 1.3 76.6 - - - +
301A GLU* 1.3 70.3 + - - +
303A GLN* 3.3 7.4 + - - +
304A LYS* 2.9 35.6 + - + +
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Residues in contact with GLU 301 (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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257A TYR* 6.0 2.0 - - + +
284A GLU* 6.1 0.2 - - - +
296A LYS* 3.5 40.0 + - + +
297A ASP 3.0 19.8 + - - +
298A LEU* 3.2 11.0 + - + +
300A THR* 1.3 84.8 - - - +
302A LEU* 1.3 64.9 + - + +
304A LYS* 2.8 41.5 + - - +
305A LYS* 3.0 50.2 + - + +
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Residues in contact with LEU 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A LEU* 3.4 31.2 - - + -
157A VAL* 5.0 4.7 - - + -
161A CYS* 5.7 0.7 - - - -
166A TYR* 3.2 25.5 + - + +
233A VAL* 4.5 7.2 - - + -
235A ILE* 4.5 1.1 - - + -
257A TYR* 3.8 33.4 - - + +
298A LEU* 2.8 48.1 + - + +
299A CYS* 3.8 7.4 - - - +
301A GLU* 1.3 79.2 - - - +
303A GLN* 1.3 57.4 + - - +
305A LYS* 5.0 0.4 - - - -
306A ILE* 2.9 44.5 + - + +
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Residues in contact with GLN 303 (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 LYS 4.5 4.9 + - - -
161A CYS* 3.6 13.4 - - - +
164A THR* 4.1 20.7 - - - +
166A TYR* 3.9 17.8 - - + -
299A CYS* 3.0 40.7 + - - +
300A THR* 3.8 6.7 - - - +
302A LEU* 1.3 76.2 - - - +
304A LYS* 1.3 62.0 + - - +
306A ILE* 4.4 7.4 - - - +
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Residues in contact with LYS 304 (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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296A LYS* 4.4 9.9 - - - +
300A THR* 2.9 21.0 + - + +
301A GLU* 2.8 45.0 + - - +
303A GLN* 1.3 80.2 - - - +
305A LYS* 1.3 71.3 + - + +
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Residues in contact with LYS 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A TYR* 4.3 9.0 - - - +
284A GLU* 2.7 44.1 + - - +
287A LYS* 5.7 0.4 - - - +
301A GLU* 3.0 39.2 + - + +
302A LEU* 5.0 0.2 - - - -
304A LYS* 1.3 92.6 - - + +
306A ILE* 1.3 69.6 + - + +
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Residues in contact with ILE 306 (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 VAL* 3.9 21.6 - - + +
166A TYR* 3.9 9.1 + - + +
231A THR* 3.8 31.6 + - + +
233A VAL* 4.1 11.9 - - + -
255A ILE* 3.9 35.7 - - + -
257A TYR* 4.4 9.4 - - + +
285A PHE* 5.6 0.9 - - + -
302A LEU* 2.9 48.9 + - + +
303A GLN* 4.4 7.4 - - - +
304A LYS 5.2 0.2 - - - +
305A LYS* 1.3 79.4 - - + +
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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