Contacts of the strand formed by residues 433 - 436 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476J THR* 3.5 9.9 - - - +
281K MET* 3.6 27.6 - - + +
410K ASN* 3.0 19.2 + - - +
411K GLY* 3.3 4.4 - - - -
412K THR 3.0 24.9 + - - -
431K VAL* 3.4 1.5 - - - +
432K GLY* 1.3 79.9 - - - +
434K VAL* 1.3 62.1 + - - +
441K PRO* 3.5 21.3 - - + +
443K PRO* 3.4 34.1 - - + -
448K SER 5.2 0.4 - - - +
449K PHE* 3.7 17.5 - - + -
450K GLY 3.6 42.0 - - - +
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Residues in contact with VAL 434 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475J LYS* 4.0 21.5 - - + -
476J THR 3.0 7.1 + - - +
477J VAL* 3.4 7.9 - - + +
478J THR 2.9 26.5 + - - -
412K THR* 3.5 6.1 - - + -
425K PHE* 3.6 34.1 - - + -
426K SER* 4.0 17.3 - - - +
429K ILE* 3.9 20.6 - - + -
431K VAL 3.9 12.8 - - - +
433K MET* 1.3 75.4 - - - +
435K GLY* 1.3 65.6 + - - +
436K ILE* 4.5 2.0 - - + -
441K PRO* 3.4 8.2 - - - +
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Residues in contact with GLY 435 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478J THR 3.4 6.3 - - - -
412K THR 2.7 14.5 + - - -
413K CYS* 3.4 2.2 - - - -
414K ILE 3.3 19.6 + - - -
434K VAL* 1.3 78.5 - - - +
436K ILE* 1.3 69.8 + - - +
437K ASN 4.0 0.9 - - - -
438K ILE* 3.4 24.5 - - - -
441K PRO* 3.3 8.1 - - - +
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Residues in contact with ILE 436 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133J TRP* 5.5 0.2 - - + -
477J VAL* 4.2 12.3 - - + -
478J THR 2.9 10.3 + - - +
479J GLN* 3.9 23.3 - - + +
480J ARG 3.1 21.9 + - - +
481J TRP* 3.9 26.5 - - + -
414K ILE* 3.6 27.1 - - + +
416K THR* 5.0 1.6 - - + -
422K ALA* 3.7 31.0 - - + +
425K PHE* 4.4 2.7 - - + -
426K SER* 4.3 11.7 - - - -
434K VAL* 4.5 1.3 - - + -
435K GLY* 1.3 75.0 - - - +
437K ASN* 1.3 80.4 + - - +
438K ILE* 3.0 4.9 + - - +
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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