Contacts of the strand formed by residues 2296 - 2300 (chain A) in PDB entry 3CMT
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 GLU2296 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2292A SER* 3.4 1.4 - - - -
2293A TYR* 2.7 43.7 + - - +
2294A LYS 3.0 6.8 + - - +
2295A GLY* 1.3 76.1 - - - +
2297A LYS* 1.3 69.9 + - - +
2298A ILE* 3.8 2.3 - - - +
2308A TRP* 3.8 35.1 + - - -
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Residues in contact with LYS2297 (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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2287A ALA* 5.6 4.6 - - - +
2290A TRP* 3.7 59.6 - - + +
2291A TYR 3.7 4.7 - - - +
2292A SER* 3.9 18.2 - - - +
2295A GLY 3.6 6.9 + - - +
2296A GLU* 1.3 85.7 - - - +
2298A ILE* 1.3 60.5 + - - +
2308A TRP* 5.1 1.4 + - - -
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Residues in contact with ILE2298 (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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2284A ILE* 4.5 21.1 - - + -
2291A TYR* 2.8 29.2 + - + +
2292A SER 4.5 0.4 - - - +
2293A TYR* 3.8 15.3 - - + +
2296A GLU* 3.8 14.6 - - - +
2297A LYS* 1.3 77.7 - - - +
2299A GLY* 1.3 57.8 + - - +
2304A ASN 4.1 2.8 - - - +
2305A ALA* 4.1 25.1 - - + +
2308A TRP* 3.2 79.8 - - + +
2309A LEU* 5.0 4.7 - - + -
2319A ILE* 6.2 0.4 - - + -
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Residues in contact with GLY2299 (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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2290A TRP* 3.5 14.2 - - - -
2291A TYR* 2.9 33.9 + - - +
2297A LYS 3.7 0.8 - - - -
2298A ILE* 1.3 81.9 - - - +
2300A GLN* 1.3 60.8 + - - -
2301A GLY 4.6 1.6 - - - -
2304A ASN* 4.0 14.4 - - - -
2305A ALA* 4.2 4.7 - - - -
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Residues in contact with GLN2300 (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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2289A ALA* 3.4 23.7 - - + +
2290A TRP* 3.7 46.3 + - + +
2299A GLY* 1.3 71.2 - - - -
2301A GLY* 1.3 67.8 + - - +
2303A ALA* 5.5 0.5 - - - +
2304A ASN* 2.9 28.7 + - - +
2303D ALA* 5.8 1.7 - - - +
2304D ASN* 6.0 0.7 - - - +
2307D ALA* 5.2 11.7 - - - +
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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