Contacts of the strand formed by residues 3296 - 3300 (chain D) 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 GLU3296 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3292D SER* 3.4 0.8 - - - -
3293D TYR* 2.7 43.8 + - - +
3294D LYS 3.0 6.9 + - - +
3295D GLY* 1.3 75.1 - - - +
3297D LYS* 1.3 68.0 + - - +
3298D ILE* 3.6 2.7 + - - +
3308D TRP* 3.8 33.7 + - - -
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Residues in contact with LYS3297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3287D ALA* 5.6 4.4 - - - +
3290D TRP* 3.7 59.2 - - + +
3291D TYR 3.7 5.2 - - - +
3292D SER* 3.9 17.3 - - - +
3295D GLY 3.6 6.5 + - - +
3296D GLU* 1.3 83.2 - - - +
3298D ILE* 1.3 61.5 + - - +
3299D GLY 3.7 0.2 - - - -
3308D TRP* 5.1 1.0 + - - -
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Residues in contact with ILE3298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3284D ILE* 4.5 21.8 - - + -
3291D TYR* 2.8 28.5 + - + +
3292D SER 4.5 0.7 - - - +
3293D TYR* 3.8 15.0 - - + +
3296D GLU* 3.8 13.9 - - - +
3297D LYS* 1.3 77.9 - - - +
3299D GLY* 1.3 58.9 + - - +
3304D ASN* 4.1 2.6 - - - +
3305D ALA* 4.1 24.5 - - + +
3308D TRP* 3.2 80.1 - - + +
3309D LEU* 5.0 4.5 - - + -
3319D ILE* 6.2 0.4 - - + -
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Residues in contact with GLY3299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3290D TRP* 3.5 13.8 - - - -
3291D TYR* 2.9 33.4 + - - +
3297D LYS 3.7 1.4 - - - -
3298D ILE* 1.3 82.8 - - - +
3300D GLN* 1.3 61.5 + - - -
3301D GLY 4.6 1.6 - - - -
3304D ASN* 4.0 13.7 - - - -
3305D ALA* 4.3 4.7 - - - -
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Residues in contact with GLN3300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1304A ASN* 5.9 3.3 - - - +
1307A ALA* 5.0 14.5 - - - +
3289D ALA* 3.5 23.0 - - + +
3290D TRP* 3.7 45.1 + - + +
3299D GLY* 1.3 71.8 - - - -
3301D GLY* 1.3 67.3 + - - +
3303D ALA* 5.5 0.3 - - - +
3304D ASN* 2.9 29.2 + - - +
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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