Contacts of the strand formed by residues 399 - 403 (chain B) in PDB entry 4PS1
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 PHE 399 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337B THR* 3.3 37.0 - - + -
340B PHE* 3.6 21.5 - - + -
341B THR* 4.3 7.2 - - - -
353B LYS* 3.3 34.5 - - + -
355B PHE* 4.1 12.1 - + - -
395B ASP 4.6 0.2 - - - -
396B GLU* 3.5 15.9 - - - -
397B ALA 3.4 17.5 - - - -
398B ASP* 1.3 80.3 - - - +
400B LEU* 1.3 61.0 + - - +
401B LEU* 4.2 0.4 - - + -
468B PHE* 3.3 3.3 - - - +
469B THR* 2.8 37.4 + - - +
470B LEU* 3.4 6.8 + - - +
501B DTT 3.8 46.9 - - + -
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Residues in contact with LEU 400 (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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353B LYS 2.9 7.0 + - - +
354B VAL* 3.4 25.6 - - + -
355B PHE* 2.8 29.6 + - - +
356B PHE* 5.0 1.6 - - + -
399B PHE* 1.3 76.3 - - - +
401B LEU* 1.3 65.9 + - - +
402B GLY 4.7 1.1 - - - +
439B ILE* 3.6 41.3 - - + -
440B LEU* 4.1 10.1 - - + -
443B LEU* 3.9 21.1 - - + -
466B PRO* 4.5 3.6 - - + -
467B THR 3.7 13.9 - - - +
468B PHE* 3.8 12.1 - - + -
470B LEU* 4.1 12.7 - - + +
474B LEU* 4.2 5.6 - - + -
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Residues in contact with LEU 401 (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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333B ILE* 4.3 18.4 - - + -
337B THR* 4.4 8.3 - - + -
355B PHE* 3.4 18.2 - - + +
357B ILE* 3.7 30.7 - - + -
399B PHE* 4.2 0.8 - - + -
400B LEU* 1.3 74.6 - - - +
402B GLY* 1.3 59.1 + - - +
403B MET* 3.7 23.4 + - + -
465B GLN 4.0 0.5 - - - +
466B PRO* 3.3 3.3 - - - +
467B THR* 2.9 52.0 + - - +
501B DTT 4.5 21.7 - - - +
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Residues in contact with GLY 402 (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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355B PHE 2.8 13.5 + - - +
356B PHE* 3.5 10.9 - - - -
357B ILE* 2.9 27.9 + - - +
400B LEU* 4.0 3.0 - - - +
401B LEU* 1.3 72.5 - - - +
403B MET* 1.3 58.9 + - - -
421B TYR* 3.2 24.3 + - - -
443B LEU* 5.1 4.0 - - - -
466B PRO* 4.4 10.3 - - - -
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Residues in contact with MET 403 (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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333B ILE* 3.6 17.5 - - + -
357B ILE* 3.7 33.9 - - + +
359B ALA 5.5 1.6 - - - +
361B GLN* 3.6 38.8 - - + +
401B LEU* 3.7 28.0 + - + -
402B GLY* 1.3 72.9 - - - -
404B ALA* 1.3 61.0 + - - +
405B THR 3.6 14.1 - - - +
421B TYR* 3.8 5.1 + - - -
464B PRO* 3.5 5.7 - - - +
465B GLN* 3.0 56.8 + - - +
467B THR* 5.5 0.4 - - - +
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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