Contacts of the strand formed by residues 488 - 498 (chain C) in PDB entry 2VZE
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 VAL 488 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482C LEU* 3.2 34.5 - - + +
483C MET* 3.6 14.9 - - - +
485C HIS 3.1 5.4 + - - +
486C PRO 3.3 1.3 - - - -
487C ALA* 1.3 79.9 - - - +
489C VAL* 1.3 60.6 + - - +
490C GLU 3.5 27.8 - - - +
491C THR* 3.9 13.7 - - + -
509C VAL* 4.2 16.4 - - + -
510C VAL 4.0 2.5 - - - -
527C LEU* 3.9 25.4 - - + -
1570C MG 2.4 24.5 - - - -
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Residues in contact with VAL 489 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483C MET* 3.3 18.0 - - - +
486C PRO 5.5 0.7 - - - +
487C ALA 3.6 0.6 + - - -
488C VAL* 1.3 73.1 - - - +
490C GLU* 1.3 63.7 + - + +
510C VAL* 3.0 50.2 + - + +
511C LEU 4.1 2.7 - - - +
512C ALA* 3.8 28.5 - - + -
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Residues in contact with GLU 490 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483C MET* 4.0 5.8 - - - -
488C VAL* 3.3 8.2 - - - +
489C VAL* 1.3 85.0 - - + +
491C THR* 1.3 68.7 + - - +
510C VAL* 3.0 46.6 + - + +
549C ASN* 5.4 1.0 - - - -
550C LEU* 3.8 19.9 + - + +
552C LYS* 2.9 37.6 + - - -
558C ILE* 4.1 11.6 - - + +
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Residues in contact with THR 491 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479C GLU* 3.6 47.9 - - + +
482C LEU* 3.9 10.2 - - + +
483C MET* 4.3 8.1 - - + -
488C VAL* 3.9 13.0 - - + -
490C GLU* 1.3 79.9 - - - +
492C ALA* 1.3 66.0 + - - +
493C VAL* 4.5 0.2 - - - +
507C ALA* 3.9 8.3 - - - +
508C PHE 2.6 20.4 + - - -
509C VAL* 3.5 10.7 - - - +
550C LEU* 3.7 6.1 - - - -
558C ILE* 3.6 16.1 - - - +
560C ARG* 4.9 0.2 + - - -
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Residues in contact with ALA 492 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479C GLU* 3.5 7.0 - - - +
491C THR* 1.3 77.9 + - - +
493C VAL* 1.3 62.9 + - - +
494C ILE* 5.5 0.2 - - + -
507C ALA* 3.4 1.0 - - - -
508C PHE* 2.8 33.5 + - - -
550C LEU* 4.1 7.2 - - + -
558C ILE* 3.9 21.5 - - + -
560C ARG* 4.5 7.2 - - + +
563C LEU* 3.6 28.9 - - + -
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Residues in contact with VAL 493 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464C ASP* 5.5 0.5 - - - +
466C ILE* 3.6 21.5 - - + -
475C PRO* 3.6 22.4 - - + +
478C VAL* 3.6 37.7 - - + -
479C GLU* 2.9 26.6 + - + +
482C LEU* 4.2 3.8 - - + -
491C THR* 4.5 0.9 - - - +
492C ALA* 1.3 76.1 - - - +
494C ILE* 1.3 72.2 + - - +
505C VAL* 3.8 12.8 - - + -
506C LYS 3.2 6.7 - - - +
507C ALA* 3.7 20.4 - - + -
560C ARG* 3.9 6.3 - - - +
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Residues in contact with ILE 494 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464C ASP* 5.7 1.8 - - + -
466C ILE* 3.4 18.0 - - - +
492C ALA 5.1 0.9 - - - -
493C VAL* 1.3 82.3 - - - +
495C SER* 1.3 74.2 + - - +
505C VAL* 3.7 0.2 - - - -
506C LYS* 2.8 39.9 + - + +
508C PHE* 3.6 31.0 - - + -
560C ARG* 4.1 33.0 - - + +
563C LEU* 3.8 22.9 - - + +
564C ARG* 4.0 16.6 - - + +
567C GLU* 3.8 15.9 - - + -
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Residues in contact with SER 495 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465C ILE 5.5 1.2 + - - -
466C ILE* 3.7 19.5 - - - +
494C ILE* 1.3 95.5 - - - +
496C SER* 1.3 58.6 - - - +
503C GLU* 3.3 34.8 + - - -
504C VAL 3.4 5.6 - - - -
564C ARG* 4.0 13.2 - - - +
567C GLU* 4.1 0.2 - - - +
568C TRP* 3.0 24.9 + - - -
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Residues in contact with SER 496 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495C SER* 1.3 74.5 - - - +
497C PRO* 1.3 73.2 - - - +
503C GLU* 3.5 2.8 - - - -
504C VAL* 2.9 33.8 + - - +
506C LYS* 4.0 12.3 - - - -
543C LYS* 3.0 39.3 + - - -
567C GLU* 3.3 21.7 + - - -
568C TRP* 3.9 4.5 - - - +
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Residues in contact with PRO 497 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496C SER* 1.3 90.0 + - - +
498C ASP* 1.3 60.3 + - - +
499C PRO* 4.6 1.8 - - - +
502C GLY 3.8 8.5 - - - +
543C LYS* 3.1 24.5 + - - +
567C GLU* 4.3 11.9 - - + +
568C TRP* 3.4 52.7 - - + +
569C LYS* 5.7 9.4 - - - -
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Residues in contact with ASP 498 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496C SER 3.7 1.2 + - - -
497C PRO* 1.3 76.3 - - - +
499C PRO* 1.3 74.2 - - - +
500C VAL* 3.3 8.2 + - - +
501C ARG* 3.3 30.7 + - - +
502C GLY* 2.9 38.6 + - - +
504C VAL* 3.7 29.2 - - + -
543C LYS* 4.6 9.9 + - - -
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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