Contacts of the strand formed by residues 480 - 487 (chain F) in PDB entry 3CB4
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 MET 480 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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372F TYR* 4.5 5.4 - - + -
390F LEU* 5.6 0.7 - - - +
396F ILE* 6.1 0.2 - - - +
399F LEU* 3.6 33.4 - - + +
401F GLU* 3.4 40.6 - - + +
426F ARG* 4.5 0.9 - - - -
448F ALA* 6.1 0.7 - - - -
478F SER* 2.8 48.5 + - - +
479F ASP* 1.3 75.2 + - - +
481F VAL* 1.3 64.4 + - - +
498F ILE* 3.4 27.4 - - + -
499F THR* 3.4 11.4 - - - +
500F HIS* 3.8 22.9 - - - -
501F ARG* 5.2 0.5 + - - -
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Residues in contact with VAL 481 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B THR* 5.1 2.7 - - + -
390F LEU* 5.6 2.2 - - - -
480F MET* 1.3 74.7 - - - +
482F ARG* 1.3 60.2 + - - +
483F VAL* 4.1 1.3 + - + -
498F ILE* 3.5 6.0 - - - +
499F THR* 2.9 37.5 + - + +
501F ARG* 3.6 50.7 - - + +
504F SER* 3.4 35.4 - - - +
532F ILE* 4.5 21.5 - - + -
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Residues in contact with ARG 482 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387F PRO* 2.9 33.5 + - + +
388F SER* 3.7 23.1 + - - +
390F LEU* 4.0 38.4 + - + +
391F PRO 5.1 3.0 + - - -
392F ALA* 5.7 3.4 - - - +
481F VAL* 1.3 75.4 - - - +
483F VAL* 1.3 63.5 + - - +
484F ASP* 3.1 36.6 + - - +
491F ARG* 4.7 12.1 - - - +
493F ASP* 5.8 0.6 + - - -
496F ALA* 5.5 0.2 - - + -
497F LEU 3.5 9.2 - - - +
498F ILE* 4.6 3.4 - - + +
531F ALA 3.7 3.5 - - - +
532F ILE* 3.7 24.2 - - + +
533F GLY 4.9 0.5 + - - -
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Residues in contact with VAL 483 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481F VAL 5.0 0.9 - - - +
482F ARG* 1.3 74.8 - - - +
484F ASP* 1.3 65.0 + - - +
485F VAL* 4.6 1.4 - - - +
496F ALA* 3.4 5.7 - - - +
497F LEU* 2.9 57.1 + - + +
499F THR* 4.3 9.6 - - + -
504F SER* 4.1 21.5 - - - +
508F GLY* 4.5 7.0 - - - +
511F LEU* 4.7 7.9 - - + -
530F ALA* 3.8 28.9 - - + -
531F ALA 3.4 7.2 - - - +
532F ILE* 4.2 13.0 - - + -
537F ILE* 4.2 5.6 - - + -
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Residues in contact with ASP 484 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388F SER* 5.3 0.5 - - - -
482F ARG* 3.1 42.8 + - - +
483F VAL* 1.3 74.2 - - - +
485F VAL* 1.3 64.4 + - - +
486F LEU* 4.2 4.8 + - + +
491F ARG* 3.5 34.1 + - + +
496F ALA* 4.4 9.8 - - - +
529F GLN 3.9 0.3 - - - +
530F ALA* 3.5 3.1 - - - -
531F ALA* 2.8 43.4 + - + +
533F GLY* 4.4 14.4 + - - +
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Residues in contact with VAL 485 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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483F VAL 3.9 2.2 + - - +
484F ASP* 1.3 77.8 - - - +
486F LEU* 1.3 64.9 + - - +
487F ILE* 3.8 17.7 - - + -
491F ARG* 3.9 5.9 - - - +
492F VAL* 3.0 29.3 + - + +
495F LEU* 3.6 42.4 - - + +
496F ALA* 4.8 2.0 - - - +
511F LEU* 3.6 39.0 - - + -
515F MET* 5.3 0.2 - - + -
528F ILE* 4.8 6.3 - - + -
529F GLN 3.5 13.0 - - - +
530F ALA* 4.9 5.6 - - + -
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Residues in contact with LEU 486 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484F ASP* 4.8 6.5 - - + +
485F VAL* 1.3 77.7 - - - +
487F ILE* 1.3 62.9 + - - +
489F GLY* 3.8 25.6 - - - +
490F GLU 3.3 19.1 - - - +
491F ARG* 4.0 20.4 - - + +
492F VAL 4.3 0.2 - - - +
527F ALA 3.9 0.5 - - - +
529F GLN* 3.1 70.7 + - + +
531F ALA* 4.7 15.0 - - + -
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Residues in contact with ILE 487 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550C LEU* 3.5 20.0 - - + -
332F SER* 6.0 0.5 - - - -
333F ALA* 3.4 34.1 - - + +
485F VAL* 3.8 13.9 - - + -
486F LEU* 1.3 78.4 - - - +
488F ASN* 1.3 71.5 + - + +
489F GLY 3.2 0.4 - - - -
490F GLU* 3.0 22.0 + - - +
492F VAL* 4.2 8.4 - - + +
495F LEU* 4.8 5.6 - - + -
515F MET* 5.1 4.3 - - + -
519F ILE* 3.8 22.4 - - + -
526F ILE* 4.2 7.6 - - + -
527F ALA 3.2 10.1 - - - +
528F ILE* 3.8 25.4 - - + -
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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