Contacts of the strand formed by residues 514 - 520 (chain C) in PDB entry 2VKX
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 THR 514 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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510C PRO* 3.8 0.5 - - - +
511C TYR* 2.7 45.7 + - - +
512C SER 3.7 0.4 - - - +
513C SER* 1.3 93.2 - - - +
515C ALA* 1.3 59.3 + - - +
562C THR* 4.2 2.2 - - - -
563C ILE 3.2 10.8 - - - -
564C VAL* 3.5 28.5 - - + -
565C GLY 4.7 0.2 - - - +
566C LEU* 3.6 7.7 - - - +
595C THR* 4.9 0.2 - - - +
511D TYR* 4.2 2.1 + - - -
516D GLN* 3.5 27.9 + - - +
560D ILE* 5.8 1.1 - - + -
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Residues in contact with ALA 515 (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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508C VAL* 4.5 9.0 - - + -
509C GLU 3.3 12.8 - - - +
510C PRO* 3.9 9.2 - - + -
511C TYR* 4.6 1.1 - - - -
514C THR* 1.3 78.8 - - - +
516C GLN* 1.3 66.4 + - - +
517C VAL* 3.8 2.8 + - + +
561C VAL 3.6 0.7 - - - +
562C THR* 3.4 5.7 - - - +
563C ILE* 3.2 34.0 + - + +
566C LEU* 4.1 5.2 - - + -
593C PHE* 4.0 24.7 - - + -
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Residues in contact with GLN 516 (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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507C GLN* 3.9 1.9 - - - +
508C VAL* 3.5 2.6 + - - -
509C GLU* 3.0 39.2 + - + +
511C TYR* 3.1 34.7 + - + -
515C ALA* 1.3 74.5 - - - +
517C VAL* 1.3 62.7 + - - +
518C GLN* 4.0 0.7 + - - +
560C ILE* 4.6 19.1 - - + +
561C VAL 3.5 4.0 - - - +
562C THR* 3.7 18.8 + - + +
511D TYR* 4.6 3.2 - - - -
514D THR* 3.2 36.7 + - - +
516D GLN* 4.6 5.4 - - - +
562D THR* 3.7 17.2 - - - +
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Residues in contact with VAL 517 (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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505C ILE* 3.7 30.1 - - + -
507C GLN 3.5 11.0 - - - +
508C VAL* 4.3 15.5 - - + -
515C ALA* 4.5 6.7 - - + +
516C GLN* 1.3 76.4 - - - +
518C GLN* 1.3 65.4 + - - +
519C PHE* 4.2 1.6 - - - -
560C ILE* 3.0 7.4 - - - -
561C VAL* 2.7 59.3 + - + +
563C ILE* 4.9 11.4 - - + -
574C VAL* 4.7 17.7 - - + -
576C LEU* 4.4 13.5 - - + -
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Residues in contact with GLN 518 (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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505C ILE* 3.5 4.5 - - - +
506C ASP* 2.8 28.9 + - + +
507C GLN* 2.9 40.4 + - + +
516C GLN 4.0 0.8 + - - +
517C VAL* 1.3 71.5 - - - +
519C PHE* 1.3 63.1 + - - +
559C GLY 3.3 10.8 - - - +
560C ILE* 3.2 27.8 - - + +
630D PRO* 3.8 26.6 - - - +
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Residues in contact with PHE 519 (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 PRO* 4.4 3.6 - - + -
504C SER 3.0 20.4 - - - +
505C ILE* 3.9 3.4 - - - -
506C ASP* 3.3 8.9 + - - -
517C VAL 4.2 8.5 - - - -
518C GLN* 1.3 79.3 - - - +
520C ASP* 1.3 70.8 + - - +
521C GLU* 4.0 2.4 + - + +
533C TYR* 3.4 56.1 - + + -
555C ALA* 4.5 7.4 - - + -
559C GLY 4.6 5.7 + - - +
560C ILE* 4.9 3.1 - - - -
561C VAL* 3.5 32.1 - - + -
576C LEU* 3.3 30.5 - - + -
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Residues in contact with ASP 520 (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 PRO* 3.6 4.5 - - - +
504C SER* 2.7 39.5 + - - +
506C ASP* 2.7 32.8 - - - +
519C PHE* 1.3 78.8 - - - +
521C GLU* 1.3 69.6 + - - +
522C PRO 3.4 1.2 - - - -
523C GLU* 6.2 2.2 - - + -
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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