Contacts of the strand formed by residues 352 - 357 (chain B) in PDB entry 1PJS
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 SER 352 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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307A PHE* 4.4 0.2 - - - -
354A ARG* 3.2 29.6 + - - +
355A LEU 3.4 7.6 - - - -
356A VAL* 3.9 15.9 - - - +
366A LEU* 6.5 0.7 - - - -
371A LEU* 5.4 2.7 - - - +
350B ALA* 4.5 0.2 - - - +
351B GLN* 1.3 77.8 + - - +
353B VAL* 1.3 62.5 + - - +
375B LYS* 4.6 2.9 - - - -
376B GLN* 3.3 19.2 + - - +
377B THR* 3.0 23.9 + - - -
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Residues in contact with VAL 353 (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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306A ILE* 5.4 7.6 - - + -
307A PHE* 5.0 4.5 - - + -
353A VAL 3.6 0.7 - - - +
354A ARG* 3.2 5.5 - - - +
355A LEU* 2.8 58.3 + - + +
344B LEU* 3.5 55.2 - - + +
345B THR* 4.8 8.3 - - - -
350B ALA* 6.3 0.4 - - + -
351B GLN* 5.8 0.4 - - - -
352B SER* 1.3 79.7 + - - +
354B ARG* 1.3 69.6 + - - +
355B LEU* 4.5 7.9 - - + -
377B THR* 3.7 10.1 - - - +
379B VAL* 4.8 0.4 - - + -
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Residues in contact with ARG 354 (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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352A SER* 3.1 22.8 + - - +
353A VAL 3.2 12.1 - - - +
354A ARG* 2.2 49.0 - - + +
376A GLN* 4.2 3.0 + - - -
352B SER* 4.2 0.6 + - - +
353B VAL* 1.3 75.1 - - - +
355B LEU* 1.3 64.0 + - - +
356B VAL* 3.2 18.5 + - + +
367B ASP* 4.3 5.1 + - - -
370B ASN* 2.3 49.1 + - - +
371B LEU* 3.6 17.1 - - - +
376B GLN* 2.8 23.1 + - - +
377B THR 2.9 15.4 + - - +
378B LEU* 4.4 5.3 - - + +
379B VAL* 2.9 32.9 + - - +
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Residues in contact with LEU 355 (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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344A LEU* 5.9 0.7 - - + -
352A SER* 3.2 2.8 - - - -
353A VAL* 2.6 54.4 + - + +
355A LEU* 4.1 22.4 - - + -
306B ILE* 4.2 29.4 - - + -
307B PHE* 3.7 18.8 - - + -
331B THR* 5.4 2.7 - - + -
333B ALA* 3.6 29.8 - - + -
344B LEU* 5.6 0.7 - - + -
353B VAL* 4.5 7.9 - - + -
354B ARG* 1.3 72.1 - - - +
356B VAL* 1.3 60.6 + - - +
379B VAL* 3.7 20.0 - - + -
381B TYR* 4.0 7.9 - - + +
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Residues in contact with VAL 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A GLN 3.7 4.5 - - - +
352A SER* 3.2 26.0 - - - +
307B PHE* 3.7 5.3 - - - -
354B ARG* 3.2 28.0 - - + +
355B LEU* 1.3 71.7 - - - +
357B THR* 1.3 75.2 + - - +
366B LEU* 4.3 18.6 - - + -
367B ASP* 5.5 2.7 - - - +
371B LEU* 3.8 15.3 - - + -
378B LEU* 5.7 1.1 - - + -
379B VAL 3.0 12.6 + - - +
380B PHE* 3.5 15.3 - - + -
381B TYR* 2.8 29.5 + - - +
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Residues in contact with THR 357 (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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351A GLN* 2.7 41.1 + - + +
307B PHE* 2.6 29.0 - - - -
356B VAL* 1.3 88.2 - - - +
358B GLY* 1.3 71.7 + - - +
359B HIS 4.7 5.2 - - - +
366B LEU* 4.0 12.9 - - - +
380B PHE* 4.8 1.5 - - - -
381B TYR 3.7 2.5 - - - -
382B MET* 3.4 26.2 - - + -
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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