Contacts of the strand formed by residues 353 - 360 (chain B) in PDB entry 2VDP
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 353 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106B GLN* 3.4 17.3 + - - -
110B TYR* 2.6 39.0 + - - -
352B ARG* 1.3 74.5 - - - +
354B LYS* 1.3 62.9 + - - +
387B MET 3.8 0.3 - - - -
388B GLY 3.1 9.1 + - - -
389B LEU* 2.8 43.7 + - - +
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Residues in contact with LYS 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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353B SER* 1.3 80.7 - - - +
355B VAL* 1.3 69.1 + - - +
356B GLU* 2.7 39.0 + - + +
385B SER* 5.9 2.0 - - - -
386B CYS 3.3 12.6 - - - +
387B MET* 4.2 13.7 - - + -
419B VAL* 5.0 16.6 - - - +
421B PHE* 4.1 12.5 - - - -
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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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104B VAL* 3.7 33.2 - - + +
106B GLN* 5.3 1.3 - - - +
354B LYS* 1.3 75.8 - - - +
356B GLU* 1.3 59.8 + - - +
357B LEU* 4.5 2.7 - - + -
385B SER* 3.0 5.0 - - - -
386B CYS 2.7 34.0 + - - +
389B LEU* 3.4 32.3 - - + -
395B VAL* 3.9 11.7 - - + -
397B PHE* 3.8 23.8 - - + -
418B PRO* 4.4 9.6 - - + -
421B PHE* 4.3 14.4 - - + -
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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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354B LYS* 2.7 46.1 + - + +
355B VAL* 1.3 74.1 - - - +
357B LEU* 1.3 65.3 + - - +
384B LYS* 4.5 3.4 - - + +
385B SER* 3.7 21.1 - - - -
418B PRO* 4.2 2.0 - - - +
419B VAL* 2.8 58.5 + - + +
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Residues in contact with LEU 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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102B ILE* 4.6 7.0 - - + -
104B VAL* 4.4 7.2 - - + -
355B VAL* 4.5 1.6 - - + -
356B GLU* 1.3 80.2 - - - +
358B GLU* 1.3 60.9 + - - +
359B VAL* 5.8 0.7 - - - -
370B PHE* 4.3 17.9 - - + -
384B LYS* 2.9 43.3 + - + +
397B PHE* 3.4 54.1 - - + -
399B ILE* 5.1 0.4 - - + -
416B ILE* 4.2 27.4 - - + -
417B LYS 4.0 1.6 - - - -
418B PRO* 4.0 26.9 - - + -
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Residues in contact with GLU 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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357B LEU* 1.3 74.6 - - - +
359B VAL* 1.3 65.9 + - - +
360B ARG* 3.4 35.9 + - + +
384B LYS* 5.9 1.6 - - - +
415B THR 4.0 0.2 - - - +
416B ILE* 3.7 1.4 - - - -
417B LYS* 3.0 53.2 + - + +
419B VAL* 3.5 29.3 - - + +
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Residues in contact with VAL 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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357B LEU 5.8 0.7 - - - -
358B GLU* 1.3 78.5 - - - +
360B ARG* 1.3 65.0 + - - +
361B ASP 4.4 0.3 + - - -
362B LEU* 3.8 30.2 + - + +
368B LEU* 3.7 31.2 - - + -
370B PHE* 3.7 21.3 - - + -
384B LYS* 6.2 1.1 - - + +
414B PHE* 4.0 8.7 - - + -
415B THR 3.4 11.2 - - - +
416B ILE* 4.2 11.0 - - + -
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Residues in contact with ARG 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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358B GLU* 3.4 30.3 + - - +
359B VAL* 1.3 76.3 - - - +
361B ASP* 1.3 77.0 + - - +
362B LEU 3.3 2.9 - - - -
414B PHE* 3.3 2.8 - - - +
415B THR* 3.0 48.1 + - + +
417B LYS* 4.0 31.7 - - + +
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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