Contacts of the helix formed by residues 321 - 325 (chain B) in PDB entry 6CM9
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 MET 321 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318B LYS 4.9 0.4 + - - +
319B HIS 3.8 3.4 + - - -
320B GLU* 1.3 74.6 - - - +
322B LYS* 1.3 65.5 + - + +
323B VAL 3.3 0.9 - - - -
324B PHE* 3.0 20.7 + - - +
325B PHE* 3.7 25.6 + - + -
342B MET* 4.0 27.1 - - - +
345B LEU* 3.4 39.9 - - + +
346B ALA* 3.8 1.8 - - - +
350B ASN* 3.4 34.0 - - - +
353B GLN* 4.5 8.5 - - + +
354B VAL* 3.7 27.6 - - + -
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Residues in contact with LYS 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320B GLU* 3.6 8.6 - - - +
321B MET* 1.3 77.0 - - + +
323B VAL* 1.3 62.9 - - + +
324B PHE 3.2 1.1 + - - -
325B PHE* 3.4 30.4 + - + +
353B GLN* 3.8 32.8 - - - +
189M VAL 4.8 3.2 + - - -
190M LEU* 3.4 35.9 + - - +
191M ARG* 3.8 20.1 - - + +
272M HIS* 5.5 10.1 - - - +
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Residues in contact with VAL 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B VAL* 3.7 37.7 - - + +
292B LEU* 4.2 18.9 - - + +
320B GLU* 3.7 20.6 + - + +
322B LYS* 1.3 78.8 - - + +
324B PHE* 1.3 84.3 + - + +
325B PHE 3.4 1.2 + - - -
338B LYS* 4.3 6.6 + - - -
191M ARG* 3.9 23.8 + - + +
193M GLU* 4.0 20.9 - - - +
268M ARG* 5.3 2.0 - - - +
270M ASN* 5.5 3.6 - - - +
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Residues in contact with PHE 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B VAL* 5.3 2.5 - - + -
292B LEU* 3.5 25.6 - - + -
303B LEU* 3.7 18.4 - - + -
306B ILE* 3.9 26.9 - - + -
317B LEU* 4.3 13.0 - - + -
320B GLU* 3.2 30.5 - - + -
321B MET* 3.0 12.1 + - - +
323B VAL* 1.3 92.1 - - + +
325B PHE* 1.3 61.7 + - - +
338B LYS* 3.6 23.2 - - + +
341B ILE* 3.6 26.0 - - + -
342B MET* 3.3 29.7 - - + +
345B LEU* 3.9 13.2 - - + -
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Residues in contact with PHE 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321B MET* 3.7 30.3 - - + -
322B LYS* 3.4 28.3 + - + +
324B PHE* 1.3 81.0 - - - +
326B VAL* 1.3 68.2 + - - +
327B LYS* 3.8 0.3 + - - +
338B LYS* 3.7 10.8 + - - -
342B MET* 3.7 26.5 - - + -
353B GLN* 3.9 36.6 - - + -
354B VAL* 4.9 0.2 - - - -
357B GLU* 3.6 33.9 - - + +
361B TYR* 3.6 5.2 - - - +
182M LEU* 5.1 7.7 - - + +
190M LEU* 4.5 24.7 - - + -
191M ARG* 3.9 17.0 + - + +
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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