Contacts of the strand formed by residues 480 - 487 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372C TYR* 4.2 8.5 - - + +
390C LEU* 5.6 0.5 - - - +
399C LEU* 3.4 35.6 - - + +
401C GLU* 3.3 36.8 - - + +
426C ARG* 4.0 1.3 - - - -
448C ALA* 5.9 0.4 - - - -
478C SER* 3.0 45.7 + - - +
479C ASP* 1.3 75.0 + - - +
481C VAL* 1.3 62.9 + - - +
498C ILE* 3.3 27.1 - - + -
499C THR* 3.3 9.0 - - - +
500C HIS* 3.5 28.0 - - - -
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Residues in contact with VAL 481 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390C LEU* 5.5 0.9 - - - -
480C MET* 1.3 77.0 - - - +
482C ARG* 1.3 59.8 + - - +
483C VAL* 3.9 2.3 + - + -
497C LEU 3.9 0.2 - - - +
498C ILE* 3.4 5.9 - - - -
499C THR* 2.7 44.9 + - + +
501C ARG* 3.4 54.3 - - + +
504C SER* 3.6 31.4 - - - +
532C ILE* 4.4 20.0 - - + -
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Residues in contact with ARG 482 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387C PRO* 3.1 36.6 + - + +
388C SER* 3.9 18.3 + - - +
390C LEU* 4.1 34.4 + - + +
391C PRO 5.1 4.0 + - - -
392C ALA* 5.8 2.6 - - - +
481C VAL* 1.3 73.7 - - - +
483C VAL* 1.3 62.8 + - - +
484C ASP* 2.9 37.3 + - - +
491C ARG* 3.4 23.8 - - - +
493C ASP* 5.7 0.2 + - - -
496C ALA* 4.9 0.4 - - + +
497C LEU 3.5 9.6 - - - +
498C ILE* 4.6 2.2 - - + +
531C ALA 3.8 7.1 - - - +
532C ILE* 4.0 17.9 - - - +
533C GLY 4.8 0.9 + - - -
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Residues in contact with VAL 483 (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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481C VAL* 3.9 1.1 + - + +
482C ARG* 1.3 75.0 - - - +
484C ASP* 1.3 64.8 + - - +
485C VAL* 4.8 1.2 - - - +
496C ALA* 3.3 6.4 - - - +
497C LEU* 2.9 54.9 + - + +
499C THR* 4.6 4.3 - - + -
504C SER* 4.3 23.6 - - - +
508C GLY* 4.2 9.6 - - - -
511C LEU* 4.6 7.9 - - + -
530C ALA* 3.8 27.4 - - + -
531C ALA 3.3 9.9 - - - +
532C ILE* 3.9 20.4 - - + -
537C ILE* 4.5 1.8 - - + -
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Residues in contact with ASP 484 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388C SER* 5.4 0.5 - - - -
482C ARG* 2.9 46.8 + - - +
483C VAL* 1.3 75.2 - - - +
485C VAL* 1.3 63.2 + - - +
486C LEU* 4.1 8.5 + - + -
491C ARG* 3.7 32.9 + - + +
493C ASP* 5.7 0.3 - - - +
496C ALA* 4.1 10.6 - - - +
529C GLN 3.8 0.7 - - - +
530C ALA* 3.4 4.0 - - - -
531C ALA* 2.9 38.5 + - + +
533C GLY* 4.7 12.0 + - - +
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Residues in contact with VAL 485 (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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483C VAL* 4.8 0.4 - - + +
484C ASP* 1.3 78.2 - - - +
486C LEU* 1.3 62.9 + - - +
487C ILE* 3.9 22.9 - - + -
491C ARG* 3.9 1.7 - - - +
492C VAL* 2.8 34.4 + - + +
495C LEU* 3.9 33.2 - - + +
496C ALA* 4.8 0.8 - - - +
511C LEU* 3.5 44.4 - - + -
512C VAL* 5.9 1.8 - - + -
515C MET* 4.8 1.8 - - + -
528C ILE* 4.6 7.2 - - + -
529C GLN 3.4 12.3 - - - +
530C ALA* 5.2 4.0 - - + -
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Residues in contact with LEU 486 (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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484C ASP* 4.5 9.0 - - + +
485C VAL* 1.3 75.6 - - - +
487C ILE* 1.3 60.7 + - - +
489C GLY* 4.2 21.2 + - - +
490C GLU 3.1 20.0 - - - +
491C ARG* 4.1 13.5 - - + +
527C ALA 3.5 1.7 - - - +
529C GLN* 3.0 73.3 + - + +
531C ALA* 4.2 22.4 - - + -
536C ILE* 6.0 0.2 - - + -
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Residues in contact with ILE 487 (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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333C ALA* 3.3 35.5 - - + +
334C LEU* 5.8 0.7 - - + -
485C VAL* 3.9 14.2 + - + -
486C LEU* 1.3 75.5 - - - +
488C ASN* 1.3 71.5 + - - +
489C GLY 3.4 0.2 - - - -
490C GLU* 3.1 18.5 + - - +
492C VAL* 3.9 9.3 - - + +
495C LEU* 5.4 1.3 - - + -
515C MET* 4.3 13.9 - - + -
519C ILE* 3.8 26.0 - - + -
526C ILE* 4.8 2.7 - - + -
527C ALA 3.2 4.7 - - - +
528C ILE* 3.6 37.7 - - + -
550F LEU* 3.9 11.6 - - + +
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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