Contacts of the strand formed by residues 451 - 456 (chain B) in PDB entry 1MV0
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 TRP 451 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A THR* 5.9 0.2 - - - -
59A PRO* 3.5 30.2 - - + +
60A PRO* 2.9 32.2 + - - +
61A LEU* 5.2 2.2 - - + -
62A SER* 3.9 15.7 - - - -
420B TYR* 3.3 40.4 - + - -
427B GLU* 4.9 0.2 - - - -
447B GLN* 3.4 5.5 + - - +
448B ASP* 2.4 65.4 + - - +
449B GLU 3.1 9.8 + - - -
450B GLY* 1.3 88.0 - - - +
452B LEU* 1.3 63.4 + - - +
472B VAL* 3.4 16.4 - - + -
473B PHE* 3.0 18.6 - - - +
474B PRO* 2.9 46.2 - - + -
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Residues in contact with LEU 452 (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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411B MET* 6.4 0.4 - - + -
412B PHE* 5.9 0.7 - - + -
438B VAL* 4.6 14.6 - - + -
441B PHE* 5.7 0.9 - - + -
447B GLN* 3.3 34.8 - - + +
450B GLY* 4.5 2.7 - - - +
451B TRP* 1.3 82.1 - - - +
453B MET* 1.3 62.2 - - - +
472B VAL* 3.4 7.5 - - - -
473B PHE* 2.9 50.8 + - + +
475B GLU* 3.3 53.8 - - + +
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Residues in contact with MET 453 (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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65A ARG* 5.6 0.2 - - + -
67A SER* 2.7 32.5 - - - +
438B VAL* 4.3 2.4 - - - +
439B ILE* 2.8 48.2 + - + +
441B PHE* 3.6 40.9 - - + -
442B GLN* 4.5 5.4 - - - +
447B GLN* 4.7 4.2 - - - +
452B LEU* 1.3 74.2 - - - +
454B GLY* 1.3 59.7 + - - +
470B ARG* 3.9 21.8 - - - -
471B GLY* 2.8 39.5 - - - +
472B VAL* 3.7 13.0 - - + +
473B PHE* 3.8 2.4 - - - -
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Residues in contact with GLY 454 (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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428B LEU* 3.2 23.7 - - - +
436B VAL* 3.8 5.4 - - - -
437B LEU 3.3 7.4 - - - -
438B VAL* 4.5 0.2 - - - -
439B ILE* 3.2 12.8 - - - -
453B MET* 1.3 74.1 - - - +
455B VAL* 1.3 60.4 + - - +
470B ARG* 4.7 0.2 - - - -
471B GLY 3.2 13.4 + - - +
473B PHE* 3.3 23.2 - - - -
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Residues in contact with VAL 455 (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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407B PRO* 5.3 4.0 - - + -
428B LEU* 4.4 0.4 - - - -
436B VAL* 2.9 6.4 - - - +
437B LEU* 2.5 74.6 + - + +
439B ILE* 3.7 17.0 - - + -
454B GLY* 1.3 74.4 - - - +
456B LYS* 1.3 57.4 + - - +
459B ASP* 2.9 46.7 - - + +
460B TRP* 5.0 2.5 - - - +
466B LEU* 5.5 10.1 - - + -
469B CYS* 3.9 13.5 - - + +
470B ARG* 4.9 4.3 - - + +
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Residues in contact with LYS 456 (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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428B LEU* 3.6 17.9 - - + +
429B GLN* 3.0 30.3 - - - +
431B LYS* 3.8 8.7 - - - +
434B ASP* 2.6 34.8 - - - +
435B VAL 3.3 3.4 - - - +
436B VAL* 3.4 15.5 - - + +
437B LEU* 4.3 0.9 - - - -
455B VAL* 1.3 81.3 - - - +
457B GLU* 1.3 65.2 + - - +
458B SER* 3.2 15.2 - - - +
459B ASP* 3.0 23.7 + - - +
460B TRP* 3.0 19.6 + - - +
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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