Contacts of the strand formed by residues 404 - 408 (chain B) in PDB entry 4P3N
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 GLU 404 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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379B ASN* 3.0 28.8 + - - +
381B ARG* 3.3 23.5 + - - -
400B GLU* 3.2 8.0 - - - +
401B VAL 2.9 34.3 + - - +
402B GLU* 3.9 7.9 - - + +
403B LYS* 1.3 85.1 - - - +
405B LEU* 1.3 64.0 + - - +
406B PHE* 3.5 8.3 + - + -
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Residues in contact with LEU 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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379B ASN* 3.4 6.7 + - - +
380B SER* 2.6 50.9 + - - +
389B TRP* 3.5 34.1 - - + -
398B SER* 3.7 15.5 - - - -
399B PHE* 3.6 9.9 - - - +
400B GLU* 3.3 33.4 + - + +
404B GLU* 1.3 71.3 - - - +
406B PHE* 1.3 65.5 + - - +
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Residues in contact with PHE 406 (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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337A GLU 5.6 0.2 - - - -
338A LEU 3.8 7.2 - - - -
339A SER* 4.6 1.6 - - - -
340A PRO* 3.9 27.1 - - + -
456A ARG* 4.7 8.5 - - - -
377B ILE* 3.9 24.5 - - + -
378B PHE* 3.2 21.3 - - - -
379B ASN* 3.6 38.1 - - + -
380B SER 5.1 0.4 - - - -
389B TRP* 5.2 0.4 - - - -
398B SER* 3.3 6.6 - - - -
399B PHE* 2.9 43.1 + - + +
401B VAL* 3.7 33.7 - - + -
404B GLU* 3.5 17.9 + - + -
405B LEU* 1.3 80.5 - - - +
407B ALA* 1.3 60.7 + - - +
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Residues in contact with ALA 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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377B ILE* 3.3 3.2 - - - -
378B PHE 2.9 31.5 + - - +
383B TRP* 3.7 19.9 + - + +
389B TRP* 3.9 13.2 - - + -
396B MET* 4.0 10.8 - - + -
397B PHE 3.3 14.1 - - - +
398B SER* 3.8 12.1 - - - +
399B PHE* 4.2 5.2 - - - -
406B PHE* 1.3 77.8 - - - +
408B LEU* 1.3 63.8 + - - +
409B LYS 3.7 0.2 + - - -
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Residues in contact with LEU 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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377A ILE* 4.2 8.3 - - + -
399A PHE* 4.5 5.6 - - + -
408A LEU* 3.8 38.8 - - + -
441A HIS* 4.9 0.7 - - + -
376B ASN* 3.3 27.6 - - + +
377B ILE* 3.6 16.2 - - + -
396B MET* 4.4 2.1 - - - +
397B PHE* 3.1 32.2 + - + +
399B PHE* 4.1 5.1 - - + -
407B ALA* 1.3 77.8 - - - +
409B LYS* 1.3 65.1 + - + +
410B PRO* 3.1 9.9 - - - +
439B VAL 5.7 0.4 - - - +
441B HIS* 3.9 43.5 - - + +
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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