Contacts of the strand formed by residues 352 - 362 (chain B) in PDB entry 5DQE
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 LYS 352 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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279B PRO* 5.2 0.2 - - - -
280B GLU 5.9 0.4 - - - +
348B CYS* 4.0 1.6 - - - -
349B SER 2.8 34.3 + - - +
350B PHE* 4.0 13.5 + - + +
351B GLY* 1.3 82.7 - - - +
353B GLN* 1.3 70.2 + - - +
354B VAL* 3.4 6.5 - - + +
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Residues in contact with GLN 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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354A VAL 5.4 0.4 + - - -
381A GLU 5.2 0.2 - - - -
382A TYR* 3.7 42.7 + - + +
385A ASN* 5.4 2.4 + - - -
279B PRO* 4.0 22.1 - - + +
280B GLU 6.0 0.4 - - - +
282B LYS 5.1 4.5 - - - +
346B LYS* 3.7 25.4 - - + +
347B VAL 3.5 8.1 - - - +
348B CYS* 3.9 5.5 - - - -
351B GLY 4.0 2.2 + - - -
352B LYS* 1.3 77.7 - - - +
354B VAL* 1.3 63.3 + - - +
355B VAL 4.0 11.1 + - - +
356B GLU* 2.9 43.9 + - - +
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Residues in contact with VAL 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A VAL* 3.6 24.4 - - - +
382A TYR* 5.7 2.9 - - - -
347B VAL* 2.9 32.6 + - + +
349B SER* 3.7 22.9 - - - +
352B LYS* 3.4 19.7 - - + +
353B GLN* 1.3 76.8 - - - +
355B VAL* 1.3 77.4 + - + +
382B TYR* 4.8 14.8 - - + +
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Residues in contact with VAL 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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353A GLN* 4.1 20.0 - - - +
354A VAL 3.3 9.0 - - - +
355A VAL 6.2 0.2 - - - -
346B LYS* 3.4 3.8 - - - -
347B VAL* 3.0 36.5 + - + +
353B GLN* 3.8 6.4 - - - +
354B VAL* 1.3 96.5 - - + +
356B GLU* 1.3 74.4 + - - +
357B LYS* 5.4 0.9 - - + -
380B CYS* 4.6 13.0 - - - -
382B TYR* 4.9 22.2 - - + -
501B 5E4 4.2 20.4 - - + -
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Residues in contact with GLU 356 (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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354A VAL 2.8 12.5 + - - +
355A VAL* 3.3 11.4 - - + +
356A GLU 2.9 25.1 + - - +
380A CYS* 3.9 7.9 - - - +
381A GLU* 3.1 19.8 + - - +
382A TYR* 3.7 18.9 + - - +
344B SER* 3.0 23.7 + - - +
345B SER 3.3 10.3 - - - +
346B LYS* 3.7 11.2 - - + -
353B GLN* 2.9 27.5 + - - +
355B VAL* 1.3 78.0 - - - +
357B LYS* 1.3 62.1 + - - +
358B VAL* 3.6 18.9 - - + +
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Residues in contact with LYS 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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356A GLU* 3.3 30.9 + - + +
358A VAL* 6.0 2.9 - - + -
343B CYS 3.5 1.9 - - - +
344B SER* 3.3 2.3 - - - -
345B SER* 2.8 42.1 + - - +
355B VAL* 5.4 1.1 - - + -
356B GLU* 1.3 74.0 - - - +
358B VAL* 1.3 63.5 + - - +
359B GLU* 3.5 45.8 - - + +
377B SER* 4.4 9.8 - - - -
378B PRO* 3.5 18.9 + - - +
380B CYS* 4.9 0.6 - - - +
501B 5E4 2.8 47.2 + - + +
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Residues in contact with VAL 358 (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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355A VAL* 5.2 2.0 - - + -
356A GLU 2.7 15.0 + - - +
357A LYS* 3.3 25.5 - - + -
358A VAL* 2.7 33.6 + - - +
359A GLU* 6.4 0.2 - - + -
380A CYS* 4.7 11.4 - - + -
342B THR* 3.7 27.1 - - + -
343B CYS 3.4 4.7 - - - +
344B SER* 4.2 6.3 - - - -
356B GLU* 3.6 31.2 - - + +
357B LYS* 1.3 80.5 - - - +
359B GLU* 1.3 62.3 + - - +
360B THR* 5.7 1.1 - - + -
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Residues in contact with GLU 359 (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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358A VAL* 3.8 14.4 - - + +
342B THR* 3.4 3.9 - - - +
343B CYS* 2.8 43.4 + - - +
345B SER* 5.2 5.2 + - - -
357B LYS* 3.5 34.9 - - + +
358B VAL* 1.3 76.6 - - - +
360B THR* 1.3 66.8 + - - +
374B LEU* 4.2 28.8 - - + +
377B SER* 3.0 25.9 + - - -
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Residues in contact with THR 360 (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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358A VAL 3.5 17.1 + - - +
359A GLU* 3.8 33.2 - - + +
360A THR* 4.2 10.9 + - - -
340B THR* 4.5 9.6 - - - -
341B LEU 3.0 6.7 - - - -
342B THR* 3.8 22.0 - - + +
358B VAL* 5.7 2.0 - - + -
359B GLU* 1.3 82.8 - - - +
361B GLU* 1.3 68.9 + - - +
374B LEU* 5.2 0.7 - - - +
415B ARG* 4.2 10.2 + - - +
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Residues in contact with GLU 361 (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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340B THR* 3.7 3.3 - - - -
341B LEU* 2.9 35.5 + - + +
343B CYS* 5.5 0.6 - - - -
360B THR* 1.3 80.3 - - - +
362B ARG* 1.3 77.4 + - - +
364B GLN* 3.9 12.1 - - - +
372B TYR* 3.6 15.5 - - + -
373B ARG 3.1 42.6 + - - +
374B LEU* 4.0 25.8 - - + +
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Residues in contact with ARG 362 (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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338B HIS* 3.6 33.1 + - + -
339B MET 4.1 2.7 - - - -
340B THR* 3.9 23.8 + - + +
361B GLU* 1.3 95.4 - - - +
363B ALA* 1.3 73.1 + - - +
364B GLN* 3.8 4.7 + - - +
371B VAL 4.5 1.2 - - - +
372B TYR* 4.0 1.9 - - - -
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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