Contacts of the strand formed by residues 307 - 311 (chain K) in PDB entry 1ZUM
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 ARG 307 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272K LYS* 3.0 38.4 + - + +
273K SER 3.4 7.1 + - - +
274K PRO* 3.3 12.0 - - + +
275K ASN 2.8 25.2 + - - -
305K GLY 3.2 2.1 - - - -
306K SER* 1.3 83.2 - - - +
308K THR* 1.3 60.3 + - - +
309K PHE* 3.4 33.6 + - + -
391K ASP* 5.3 3.4 + - - -
396K ALA* 3.6 26.9 + - - +
406K GLN* 3.9 3.1 - - + -
408K LEU* 4.0 16.8 - - + -
419K ARG 3.0 24.0 + - - -
420K ALA 2.9 24.2 + - - -
422K ASN 4.2 6.5 + - - -
423K SER* 3.7 16.7 - - - -
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Residues in contact with THR 308 (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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275K ASN* 3.5 17.8 + - - +
277K ILE* 4.4 2.9 - - + -
290K ALA* 4.1 16.6 + - + +
305K GLY 3.7 14.2 + - - -
307K ARG* 1.3 68.5 - - - +
309K PHE* 1.3 59.7 + - - +
310K VAL* 3.7 3.9 + - + -
318K PHE* 3.8 33.4 - - + -
405K MET* 4.1 14.3 - - - +
406K GLN 2.9 19.0 + - - -
407K ILE* 3.4 11.2 - - + +
408K LEU* 2.8 28.2 + - - +
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Residues in contact with PHE 309 (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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274K PRO* 3.9 20.0 - - + -
275K ASN 2.9 9.3 + - - +
276K ILE* 4.3 7.2 - - + -
277K ILE* 2.8 31.0 + - - +
307K ARG* 3.4 48.0 + - + -
308K THR* 1.3 71.8 - - - +
310K VAL* 1.3 59.4 + - - +
391K ASP* 4.3 2.5 - - - -
408K LEU* 3.4 27.1 - - + -
410K PHE* 3.6 10.3 - + + -
416K VAL* 3.7 29.4 - - + -
419K ARG* 3.7 50.7 - - + -
420K ALA* 4.3 4.9 - - - -
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Residues in contact with VAL 310 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277K ILE* 3.7 10.5 - - + +
308K THR* 4.0 2.7 - - + +
309K PHE* 1.3 78.8 - - - +
311K GLN* 1.3 76.9 + - - +
312K GLU 3.4 0.5 + - - -
314K ILE* 3.8 17.0 - - + -
315K TYR* 3.7 24.9 - - + -
318K PHE* 3.5 42.8 - - + -
407K ILE* 3.8 16.2 - - + -
408K LEU 2.8 12.2 + - - +
409K LYS* 3.4 6.8 - - - +
410K PHE* 3.1 23.2 + - - -
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Residues in contact with GLN 311 (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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277K ILE 3.1 12.3 + - - +
278K MET* 3.7 27.2 - - - +
279K SER* 2.7 56.6 + - - +
310K VAL* 1.3 73.1 - - - +
312K GLU* 1.3 70.3 + - + +
313K ASP* 3.2 6.7 - - + +
314K ILE* 3.0 16.7 + - + +
315K TYR 3.1 8.7 + - - -
410K PHE* 3.1 18.5 - - + +
411K LYS* 3.0 29.2 + - - +
412K THR* 4.5 3.8 - - - +
413K ILE 4.7 0.6 - - - +
438K LYS* 5.2 2.1 + - - -
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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