Contacts of the strand formed by residues 466 - 471 (chain B) in PDB entry 4MVY
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 ASN 466 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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356B LEU* 4.6 10.1 - - - +
403B GLU* 4.7 4.2 + - - -
405B TYR* 2.8 30.6 + - - +
463B VAL* 2.9 21.3 + - + +
464B PRO 3.2 0.6 - - - +
465B GLY* 1.3 82.1 - - - +
467B PRO* 1.3 63.5 - - - +
468B ASP* 3.0 22.9 + - - +
469B HIS* 3.0 43.7 + - - +
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Residues in contact with PRO 467 (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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453B ARG* 3.7 15.6 - - - +
462B PRO* 4.8 11.8 - - + +
463B VAL 4.1 2.6 - - - +
465B GLY 3.9 5.4 - - - +
466B ASN* 1.3 88.3 - - - +
468B ASP* 1.3 65.8 + - - +
469B HIS 3.2 5.3 + - - +
470B CAS 5.0 4.3 - - - -
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Residues in contact with ASP 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B ALA* 4.0 2.3 - - - +
453B ARG* 3.2 40.1 + - - +
466B ASN* 3.0 13.3 + - - +
467B PRO* 1.3 81.8 - - - +
469B HIS* 1.3 73.0 + - + +
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Residues in contact with HIS 469 (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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402B GLU* 6.0 0.9 - - + -
403B GLU* 3.1 48.8 + - + +
404B ASN* 5.8 0.2 + - - -
405B TYR* 4.1 13.0 - + + -
450B SER* 4.5 7.4 + - - -
451B ARG 3.7 6.1 + - - +
452B ALA* 4.1 19.7 + - + -
462B PRO* 3.7 5.0 - - - +
463B VAL* 2.9 35.9 + - + -
466B ASN* 3.0 37.8 + - - +
467B PRO 4.1 1.4 - - - +
468B ASP* 1.3 92.2 + - + +
470B CAS 1.3 65.9 + - - +
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Residues in contact with CAS 470 (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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450B SER* 3.0 25.1 - - - -
451B ARG 2.9 13.6 + - - +
453B ARG* 3.5 31.2 - - - -
456B LEU* 3.6 28.7 - - + -
458B ASN* 3.1 52.7 - - + +
460B ALA* 2.8 33.9 - - + +
461B ILE 2.2 55.0 - - - +
462B PRO* 2.5 20.2 - - + -
463B VAL* 3.8 5.2 - - - -
467B PRO 5.0 4.0 - - - -
469B HIS* 1.3 77.0 - - - +
471B VAL* 1.3 62.1 + - - +
803B GOL 3.7 3.8 - - - +
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Residues in contact with VAL 471 (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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341B VAL* 4.0 19.7 - - + -
342B LYS* 6.2 0.2 - - + -
345B TRP* 3.7 26.2 - - + -
449B VAL 3.8 4.3 - - - -
456B LEU* 4.5 0.2 - - - +
460B ALA* 4.1 4.3 - - - +
461B ILE* 2.8 29.5 + - + +
462B PRO 4.0 14.1 - - - +
463B VAL* 4.3 4.7 - - - -
464B PRO* 4.7 2.9 - - + -
470B CAS 1.3 76.7 - - - +
472B TYR* 1.3 74.5 + - - +
475B LEU* 3.9 24.2 - - + -
476B ASP* 3.9 11.0 - - + +
806B 387 3.6 15.1 - - - -
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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