Contacts of the strand formed by residues 501 - 504 (chain C) in PDB entry 4Z2C
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 LEU 501 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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429C LEU* 3.4 41.7 - - + +
431C ILE* 3.9 30.5 - - + -
479C LEU* 4.7 4.9 - - + -
483C MET* 4.2 20.0 - - + -
498C TYR* 5.1 1.3 + - + +
499C GLN 4.1 0.2 - - - -
500C LYS* 1.3 70.2 - - - +
502C VAL* 1.3 56.6 + - - +
503C LEU* 3.7 8.1 + - + +
522C ILE* 5.9 5.2 - - + -
526C MET* 4.9 10.5 - - + -
529C ILE* 4.9 10.1 - - + -
534C TYR* 2.7 17.4 + - + +
535C VAL* 3.6 19.9 - - + +
536C TYR 2.7 31.0 + - - +
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Residues in contact with VAL 502 (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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428C GLU* 4.7 3.6 - - + -
429C LEU 2.9 9.4 + - - +
430C PHE* 3.4 45.3 - - + -
431C ILE* 2.9 29.3 + - - +
500C LYS* 4.2 15.0 - - + +
501C LEU* 1.3 72.6 - - - +
503C LEU* 1.3 66.1 + - - +
504C MET 3.5 0.2 + - - -
536C TYR* 3.2 5.2 - - + +
538C ALA* 3.8 21.8 - - + +
607C MET* 3.6 39.0 - - + -
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Residues in contact with LEU 503 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431C ILE* 3.7 29.8 - - + -
501C LEU* 4.8 9.2 - - + -
502C VAL* 1.3 70.9 - - - +
504C MET* 1.3 59.5 + - - +
505C THR* 3.6 7.9 + - + +
515C ARG* 4.6 11.2 - - + +
518C LEU* 4.2 29.4 - - + -
519C LEU* 3.7 35.4 - - + +
535C VAL* 4.4 9.9 - - + -
536C TYR 2.7 18.7 + - - +
537C ILE* 3.9 22.7 - - + +
538C ALA* 3.2 22.2 + - - +
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Residues in contact with MET 504 (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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430C PHE* 3.5 34.1 - - + -
431C ILE 2.9 24.5 + - - +
432C VAL* 3.9 21.7 - - + -
433C GLU 4.1 0.9 + - - -
441C ALA* 5.4 1.1 - - - -
502C VAL 3.5 0.6 + - - -
503C LEU* 1.3 71.6 - - - +
505C THR* 1.3 64.7 + - - +
538C ALA* 4.0 15.9 - - + -
540C PRO* 5.8 3.1 - - + -
587C LEU* 3.3 23.7 - - + +
595C LEU* 3.6 20.2 - - + -
599C THR* 3.2 38.6 - - + +
600C MET* 3.7 17.9 - - + +
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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