Contacts of the strand formed by residues 522 - 527 (chain B) in PDB entry 3DDN
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 LYS 522 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340B VAL 3.8 3.4 + - - -
341B LEU* 3.1 45.4 + - + +
342B SER 4.0 1.4 + - - -
343B ASP* 3.7 31.1 - - - +
458B ILE* 4.4 4.5 - - + +
459B ILE* 3.4 5.6 - - - +
460B HIS* 3.0 39.5 + - + +
520B ALA* 3.3 4.0 - - - +
521B TYR* 1.3 85.9 - - + +
523B LEU* 1.3 64.5 + - - +
524B GLU* 3.4 29.8 + - + +
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Residues in contact with LEU 523 (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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457B LEU* 3.8 21.1 - - + -
458B ILE 3.3 4.9 - - - +
459B ILE* 4.2 13.9 - - + -
511B ARG* 3.7 46.7 - - + +
514B ILE* 3.7 31.6 - - + -
515B ALA* 4.0 13.9 - - + +
520B ALA* 4.6 6.3 - - + -
522B LYS* 1.3 77.0 - - - +
524B GLU* 1.3 83.5 + - - +
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Residues in contact with GLU 524 (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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340B VAL* 3.6 37.7 - - + +
341B LEU* 3.9 26.0 - - + -
456B ASN 3.8 0.3 - - - +
457B LEU* 3.4 5.0 - - - +
458B ILE* 2.8 36.6 + - + +
511B ARG* 5.5 3.6 + - - +
522B LYS* 3.4 26.9 + - + +
523B LEU* 1.3 90.4 - - - +
525B VAL* 1.3 64.4 + - - +
526B VAL* 4.4 1.6 - - + -
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Residues in contact with VAL 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B VAL* 4.4 6.6 - - - +
455B ILE* 3.4 30.7 - - + -
456B ASN 3.3 7.6 - - - +
457B LEU* 4.0 18.6 - - + -
502B LEU* 5.1 2.2 - - + -
505B ASP* 3.7 14.8 - - - +
506B VAL* 4.5 7.9 - - + +
511B ARG* 3.5 46.1 + - + +
523B LEU* 4.7 0.2 - - + -
524B GLU* 1.3 80.3 + - - +
526B VAL* 1.3 69.6 + - - +
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Residues in contact with VAL 526 (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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336B VAL* 3.7 17.3 - - + -
337B LEU* 3.6 23.6 - - + -
340B VAL* 3.8 28.7 - - + -
341B LEU* 5.3 1.1 - - + -
454B GLY 3.5 1.4 - - - +
455B ILE* 3.4 3.2 - - - -
456B ASN* 2.8 34.7 + - + +
458B ILE* 4.2 14.6 - - + -
524B GLU* 5.0 0.2 - - + -
525B VAL* 1.3 84.4 - - - +
527B ASP* 1.3 65.5 + - - +
528B LEU* 3.4 27.7 + - + +
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Residues in contact with ASP 527 (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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332B ARG* 5.2 5.4 + - - -
336B VAL* 4.7 4.7 - - - +
454B GLY* 3.7 8.2 - - - +
455B ILE* 4.3 21.0 - - + +
526B VAL* 1.3 75.8 - - - +
528B LEU* 1.3 75.8 + - - +
529B SER* 3.1 26.6 + - - -
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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