Contacts of the strand formed by residues 499 - 506 (chain C) in PDB entry 3VI4
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 ILE 499 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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452C VAL* 4.3 13.2 - - + -
490C ALA* 3.6 31.4 - - + +
492C GLY 3.8 13.2 - - - +
493C LYS* 4.4 9.2 - - + -
496C ALA* 3.8 20.0 - - + -
497C ASP 4.5 3.8 - - - +
498C SER* 1.3 74.3 - - - +
500C GLY* 1.3 75.1 + - - +
501C PHE* 3.6 20.3 - - + -
534C LEU* 3.6 2.5 - - - -
535C ILE 2.7 33.4 + - - +
536C GLN 3.7 12.6 - - - +
571C LEU* 3.9 17.7 - - + -
576C PRO* 5.1 2.5 - - + -
584C PRO* 4.8 5.4 - - + -
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Residues in contact with GLY 500 (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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498C SER 3.8 4.4 + - - -
499C ILE* 1.3 80.1 - - - +
501C PHE* 1.3 69.0 + - - -
533C LEU 3.4 8.7 - - - -
534C LEU* 3.9 11.7 - - - +
571C LEU* 4.0 4.9 - - - +
572C ASP* 3.4 29.9 + - - -
575C ALA* 5.9 0.4 - - - -
576C PRO* 4.3 14.0 - - - +
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Residues in contact with PHE 501 (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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452C VAL* 4.2 15.9 - - + -
454C ALA* 3.9 21.3 - - + -
490C ALA* 4.0 14.1 - - + -
499C ILE* 3.6 23.8 - - + -
500C GLY* 1.3 84.4 - - - -
502C THR* 1.3 64.2 + - - +
503C VAL* 4.0 6.0 + - + -
532C THR* 3.4 4.0 - - - -
533C LEU* 2.8 39.8 + - + +
535C ILE* 3.5 31.4 - - + -
569C PHE* 3.6 35.0 - + - -
570C SER 3.5 15.3 - - - -
571C LEU* 4.2 13.0 - - + -
572C ASP* 3.6 4.8 - - - +
586C LEU* 5.0 8.1 - - + -
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Residues in contact with THR 502 (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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501C PHE* 1.3 73.0 - - - +
503C VAL* 1.3 63.2 - - - +
531C GLN 3.3 6.5 - - - +
532C THR* 3.9 14.1 - - + -
570C SER* 2.6 55.3 + - - +
572C ASP* 3.8 27.6 - - - +
573C PRO* 4.2 8.5 - - + +
2016C NAG 3.3 11.6 - - - +
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Residues in contact with VAL 503 (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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486C PHE* 4.1 26.9 - - + -
488C LEU* 3.8 29.6 - - + -
501C PHE* 4.0 4.0 + - + -
502C THR* 1.3 79.0 - - - +
504C GLU* 1.3 72.1 + - - +
505C LEU* 4.7 2.9 - - + -
529C LEU 3.4 2.3 - - - +
530C THR* 3.4 3.7 - - - -
531C GLN* 2.7 46.0 + - + +
533C LEU* 4.4 15.3 - - + -
567C LEU* 4.4 14.4 - - + -
568C ASN 3.9 7.6 - - - +
569C PHE* 5.2 4.7 - - + -
2016C NAG 3.9 2.7 - - - -
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Residues in contact with GLU 504 (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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503C VAL* 1.3 78.3 - - - +
505C LEU* 1.3 69.9 + - - +
506C GLN* 2.9 28.8 - - - +
528C THR* 5.7 5.2 - - - -
529C LEU 3.5 4.3 - - - +
530C THR* 3.2 33.0 - - + +
566C ALA 4.1 0.2 - - - +
567C LEU* 3.7 3.5 - - - -
568C ASN* 3.2 33.9 + - - +
2016C NAG 3.3 41.3 + - + +
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Residues in contact with LEU 505 (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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458C LEU* 5.3 0.7 - - + -
484C LEU* 3.6 39.9 - - + -
486C PHE* 3.9 30.5 - - + -
503C VAL* 4.7 4.5 - - + +
504C GLU* 1.3 77.1 - - - +
506C GLN* 1.3 62.7 + - - +
507C LEU* 5.3 2.5 - - + -
521C PHE* 3.8 16.4 - - + -
527C ALA 3.9 0.9 - - - +
528C THR* 3.2 10.9 - - - -
529C LEU* 3.1 57.8 + - + +
531C GLN* 5.9 0.9 - - + -
546C MET* 4.6 2.9 - - - -
565C ILE* 6.4 1.3 - - + -
566C ALA 3.5 6.3 - - - +
567C LEU* 4.2 15.9 - - + -
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Residues in contact with GLN 506 (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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504C GLU* 2.9 26.8 - - + +
505C LEU* 1.3 74.6 - - - +
507C LEU* 1.3 65.8 + - - +
508C ASP 4.8 6.7 + - - +
509C TRP* 4.6 25.6 - - + +
528C THR* 3.6 24.2 - - + -
564C HIS* 6.1 0.2 - - - -
565C ILE* 3.6 2.3 - - - +
566C ALA* 2.9 50.9 + - + +
568C ASN* 4.4 3.0 + - - +
593C ARG* 4.7 6.9 + - - +
2016C NAG 3.9 16.1 - - - +
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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