Contacts of the strand formed by residues 377 - 381 (chain B) in PDB entry 4DN5
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 ASN 377 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343B GLY* 3.2 27.2 + - - +
344B SER* 3.5 3.8 + - - -
345B VAL* 3.5 8.8 + - - +
375B GLU 3.3 2.2 + - - -
376B ASP* 1.3 72.1 - - - +
378B GLU* 1.3 62.5 + - - +
391B TYR 4.8 0.9 - - - +
392B GLU* 3.5 10.3 - - + +
393B TYR 3.0 44.5 + - - +
394B ARG* 3.4 35.0 - - - +
459B VAL* 4.9 2.2 - - - +
460B ARG 2.7 24.8 + - - -
461B GLU* 3.5 11.3 - - - +
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Residues in contact with GLU 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B LEU 4.6 1.6 - - - +
342B GLN* 3.3 16.0 - - - +
343B GLY* 2.9 25.2 + - - +
344B SER 3.3 16.4 - - - +
345B VAL* 4.2 2.7 - - - +
356B LEU* 4.2 10.5 - - + +
359B THR* 4.8 1.4 + - - -
360B TRP* 2.9 27.0 + - + +
376B ASP* 5.2 3.0 - - + +
377B ASN* 1.3 78.2 - - - +
379B GLY* 1.3 55.2 + - - +
459B VAL* 3.3 4.3 - - - -
460B ARG* 2.6 76.9 + - + +
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Residues in contact with GLY 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B LEU* 5.1 0.7 - - - +
344B SER 3.2 5.7 + - - +
345B VAL* 3.1 23.4 - - - +
346B SER* 3.2 4.9 + - - -
356B LEU* 3.5 15.5 - - - +
360B TRP* 3.9 2.5 - - - -
378B GLU* 1.3 77.2 - - - +
380B VAL* 1.3 69.7 + - - +
458B ALA 3.2 15.0 - - - -
459B VAL* 3.8 4.3 - - - -
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Residues in contact with VAL 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B LEU* 4.6 11.7 - - + -
346B SER* 3.2 14.1 - - - +
348B GLY* 4.6 7.0 - - - +
349B GLN 4.0 5.6 - - - +
352B SER* 4.0 13.5 - - - +
353B LEU* 3.5 47.3 - - + +
356B LEU* 4.0 10.1 - - + -
379B GLY* 1.3 79.3 - - - +
381B LEU* 1.3 65.8 + - - +
382B LEU* 3.6 16.8 - - + -
457B GLY* 3.5 3.8 - - - -
458B ALA 3.2 27.3 + - - +
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Residues in contact with LEU 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B VAL* 4.3 2.2 - - + -
346B SER 2.9 10.6 + - - +
347B SER* 3.5 12.4 - - - +
348B GLY 3.3 21.5 + - - +
380B VAL* 1.3 81.1 - - - +
382B LEU* 1.3 63.0 + - - +
383B THR 3.5 4.7 - - - +
386B LEU* 3.3 48.5 - - + +
387B LYS 4.1 0.4 - - - +
388B PRO* 3.8 24.2 - - + -
393B TYR* 4.2 15.7 - - + -
456B TYR 4.0 1.1 - - - +
457B GLY* 4.6 0.9 - - - -
458B ALA 4.6 0.4 - - - +
459B VAL* 3.6 24.5 - - + -
468B PHE* 4.1 20.6 - - + -
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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
------------------------------------------------------------
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