Contacts of the strand formed by residues 404 - 408 (chain B) in PDB entry 5N4D
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 ALA 404 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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382B ASP* 3.4 9.4 - - - +
401B PHE* 3.3 4.2 - - - -
403B GLY* 1.3 74.7 - - - -
405B ALA* 1.3 60.3 + - - +
419B THR 3.8 1.0 - - - +
420B LEU* 3.6 1.4 - - - -
421B SER* 2.7 39.9 + - - +
504B ASP* 4.3 19.3 - - + +
505B PRO* 3.6 23.7 - - + +
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Residues in contact with ALA 405 (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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363B GLN* 4.5 1.6 - - - +
375B ILE* 4.0 14.5 - - + +
382B ASP* 2.8 26.3 + - + +
384B ILE* 3.8 24.9 - - + -
401B PHE* 4.1 1.6 - - + -
404B ALA* 1.3 75.3 - - - +
406B SER* 1.3 66.4 + - - +
419B THR 3.3 6.3 - - - -
420B LEU* 3.6 22.4 - - + -
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Residues in contact with SER 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B GLN* 3.6 12.5 + - - -
375B ILE* 5.0 1.1 - - - -
405B ALA* 1.3 78.3 + - - +
407B ILE* 1.3 65.5 + - - +
418B LEU* 3.3 9.1 - - - +
419B THR* 2.9 44.1 + - - -
19D ALA* 5.2 4.7 - - - +
22D ASN* 3.4 14.1 + - - -
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Residues in contact with ILE 407 (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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363B GLN* 3.3 30.1 + - + +
365B ASN* 3.6 31.6 + - + +
373B VAL* 3.5 43.1 - - + +
375B ILE* 3.8 27.4 - - + -
406B SER* 1.3 80.6 - - - +
408B ALA* 1.3 65.8 + - - +
409B ASN* 4.0 11.9 - - + +
416B PHE* 4.6 11.2 - - + -
417B PHE 3.5 10.5 - - - +
418B LEU* 4.1 4.5 - - + -
22D ASN* 3.7 18.0 + - - +
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Residues in contact with ALA 408 (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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86B ALA* 3.9 19.5 - - + -
87B PRO 5.3 2.0 - - - +
88B THR* 5.8 1.3 - - - +
406B SER 4.3 0.2 + - - -
407B ILE* 1.3 72.5 - - - +
409B ASN* 1.3 61.9 + - - +
416B PHE* 3.8 0.5 - - - -
417B PHE* 2.8 47.9 + - + +
419B THR* 5.0 0.9 - - + -
21D GLY 4.4 2.5 - - - +
22D ASN* 3.4 39.7 - - - +
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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