Contacts of the strand formed by residues 433 - 436 (chain C) in PDB entry 4ZZ7
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 433 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281C MET* 3.5 24.9 - - + +
410C ASN* 3.0 35.0 + - - +
411C GLY* 3.3 3.9 - - - -
412C THR 2.9 26.7 + - - +
431C VAL* 3.4 1.7 - - - +
432C GLY* 1.3 81.4 - - - +
434C VAL* 1.3 62.8 + - - +
441C PRO* 3.7 19.7 - - + +
443C PRO* 3.4 34.8 - - + -
448C SER 5.1 0.2 - - - +
449C PHE* 3.6 14.1 - - + -
450C GLY 3.4 39.9 - - - +
476D THR* 3.5 9.4 - - - +
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Residues in contact with VAL 434 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412C THR* 3.5 4.9 - - + -
425C PHE* 3.5 34.1 - - + -
426C SER* 3.9 18.6 - - - +
429C ILE* 3.8 21.5 - - + -
431C VAL 3.8 13.2 - - - +
433C MET* 1.3 76.8 - - - +
435C GLY* 1.3 64.3 + - - +
436C ILE* 4.7 0.4 - - + -
441C PRO* 3.5 7.8 - - - +
475D LYS* 3.8 20.6 - - + -
476D THR 3.1 4.9 + - - +
477D VAL* 3.5 12.2 - - + -
478D THR 2.9 26.6 + - - -
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Residues in contact with GLY 435 (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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412C THR 2.7 13.5 + - - -
413C CYS* 3.3 1.6 - - - -
414C ILE* 3.0 24.6 + - - +
425C PHE* 4.0 2.4 - - - -
434C VAL* 1.3 74.7 - - - +
436C ILE* 1.3 69.1 + - - +
437C ASN 3.9 0.7 - - - -
438C ILE* 3.5 15.0 - - - -
441C PRO* 3.5 15.2 - - - +
478D THR 3.3 6.7 - - - -
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Residues in contact with ILE 436 (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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414C ILE* 3.7 22.9 - - + +
416C THR* 5.2 1.1 - - + -
422C ALA* 3.6 31.6 - - + +
425C PHE* 4.4 5.2 - - + -
426C SER* 4.4 8.3 - - - +
434C VAL* 4.7 0.9 - - + -
435C GLY* 1.3 74.8 - - - +
437C ASN* 1.3 83.0 + - - +
438C ILE* 3.1 3.4 + - - +
133D TRP* 5.7 0.2 - - + -
477D VAL* 4.2 11.0 - - + -
478D THR 2.9 12.4 + - - +
479D GLN* 3.8 25.1 - - + +
480D ARG 3.0 24.9 + - - +
481D TRP* 3.9 25.8 - - + -
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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