Contacts of the helix formed by residues 292 - 299 (chain A) in PDB entry 7MHN
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 THR 292 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A GLY 3.7 17.3 - - - +
110A GLN* 4.1 17.0 + - - +
111A THR* 3.4 34.3 - - + +
203A ASN* 3.4 5.8 - - - +
206A ALA* 3.9 2.2 - - - -
291A PHE* 1.3 74.6 - - - +
293A PRO* 1.3 76.2 - - - +
294A PHE* 3.3 9.1 + - - +
295A ASP* 3.0 29.3 + - - -
296A VAL* 3.1 21.8 + - - +
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Residues in contact with PRO 293 (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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202A VAL* 3.9 13.7 - - + -
203A ASN* 3.8 10.5 - - - +
206A ALA* 3.6 25.1 - - + -
249A ILE* 3.7 48.9 - - + +
250A LEU* 4.1 7.9 - - + -
253A LEU* 4.6 6.9 - - + +
292A THR* 1.3 87.2 - - - +
294A PHE* 1.3 66.2 + - + +
296A VAL* 3.3 2.9 + - - +
297A VAL* 3.0 26.9 + - - +
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Residues in contact with PHE 294 (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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110A GLN* 4.2 22.2 - - - +
249A ILE* 4.6 32.3 - - + -
252A PRO* 6.6 0.2 - - + -
292A THR* 3.3 7.4 + - - +
293A PRO* 1.3 80.4 - - + +
295A ASP* 1.3 60.1 + - - +
297A VAL* 3.1 11.0 + - + +
298A ARG* 2.8 37.8 + - + +
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Residues in contact with ASP 295 (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 PHE* 5.2 0.9 - - - -
8A PHE* 5.3 6.6 - - - -
110A GLN* 5.6 0.2 - - - +
111A THR* 2.7 31.0 + - - +
127A GLN* 4.1 10.9 + - - -
290A GLU 4.1 0.9 - - - +
291A PHE* 3.9 15.8 - - + -
292A THR* 3.0 31.2 + - - +
294A PHE* 1.3 77.5 - - - +
296A VAL* 1.3 58.0 + - - +
298A ARG* 3.1 1.6 + - - -
299A GLN* 2.7 32.9 + - - +
401A DMS 3.5 24.3 - - + +
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Residues in contact with VAL 296 (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 PHE* 3.7 24.7 - - + -
206A ALA* 3.6 29.2 - - + +
207A TRP 4.3 0.4 - - - +
210A ALA* 3.5 28.7 - - + +
213A ILE* 5.1 1.3 - - + -
253A LEU* 4.4 16.8 - - + -
291A PHE* 4.1 9.2 - - + -
292A THR 3.1 13.5 + - - +
293A PRO 3.8 5.6 - - - +
295A ASP* 1.3 74.0 - - - +
297A VAL* 1.3 62.7 + - - +
299A GLN 3.3 0.9 + - - -
300A CYS* 3.1 39.8 + - - +
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Residues in contact with VAL 297 (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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252A PRO* 4.7 15.0 - - + -
253A LEU* 3.7 26.0 - - + -
293A PRO 3.0 16.1 + - - +
294A PHE* 3.1 11.6 + - + +
296A VAL* 1.3 76.0 - - - +
298A ARG* 1.3 69.3 + - + +
300A CYS* 4.5 1.3 - - - -
301A SER* 2.6 29.3 + - - +
302A GLY* 3.2 11.3 + - - +
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Residues in contact with ARG 298 (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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8A PHE* 5.4 15.6 - - - -
152A ILE* 5.9 1.2 - - - +
154A TYR* 2.9 55.7 + - - +
294A PHE* 2.8 24.0 + - + +
295A ASP* 3.7 2.5 - - - +
297A VAL* 1.3 80.3 - - + +
299A GLN* 1.3 53.5 + - - +
300A CYS 2.4 19.2 + - - -
301A SER 3.0 10.9 + - - -
302A GLY* 3.5 16.6 + - - +
303A VAL* 2.9 47.4 + - + +
305A PHE* 3.2 34.6 - - - -
401A DMS 3.2 18.2 - - + +
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Residues in contact with GLN 299 (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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2A GLY 4.1 8.0 - - - +
3A PHE* 3.2 40.0 - - + -
4A ARG* 2.5 51.8 + - - +
6A MET* 3.2 31.1 - - + +
291A PHE* 4.0 4.8 - - - -
295A ASP 2.7 17.1 + - - +
296A VAL 3.5 0.4 - - - -
298A ARG* 1.3 67.0 - - - +
300A CYS* 1.3 62.7 + - - +
301A SER 3.9 0.2 - - - -
401A DMS 2.6 21.9 + - - +
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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