Contacts of the strand formed by residues 274 - 277 (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 PRO 274 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272K LYS 3.5 6.7 - - - +
273K SER* 1.3 84.2 - - - +
275K ASN* 1.3 59.0 + - - +
276K ILE* 3.9 4.1 - - + +
307K ARG* 3.3 19.3 - - + +
309K PHE* 3.9 26.2 - - + -
420K ALA* 3.9 24.9 - - + +
428K ALA 3.4 13.7 - - - +
429K ALA* 3.3 14.8 - - + +
430K ALA 3.0 24.9 + - - +
446K LEU* 5.0 2.2 - - + -
456K TYR* 4.9 1.6 - - - -
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Residues in contact with ASN 275 (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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273K SER 3.8 0.4 + - - -
274K PRO* 1.3 71.8 - - - +
276K ILE* 1.3 62.0 + - - +
277K ILE* 3.7 7.0 + - - +
290K ALA* 3.5 34.1 + - - +
293K ALA* 4.0 5.2 - - - +
305K GLY* 4.6 10.5 - - - +
307K ARG 2.8 11.2 + - - +
308K THR* 3.5 12.5 + - + +
309K PHE 2.9 26.6 + - - +
430K ALA* 3.5 11.0 - - - +
432K PHE* 3.5 33.4 - - - -
456K TYR* 4.3 17.0 - - + -
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Residues in contact with ILE 276 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274K PRO* 4.7 6.5 - - + -
275K ASN* 1.3 72.9 - - - +
277K ILE* 1.3 60.4 + - - +
278K MET* 3.8 26.5 + - - -
309K PHE* 3.7 11.9 - - + -
410K PHE* 4.0 13.7 - - + -
416K VAL* 3.9 32.5 - - + -
420K ALA* 4.1 8.5 - - + -
430K ALA 2.7 17.1 + - - +
431K VAL* 3.3 4.2 - - + +
432K PHE 2.8 31.2 + - - +
442K LEU* 4.4 10.5 - - + -
446K LEU* 3.9 35.4 - - + -
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Residues in contact with ILE 277 (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* 3.9 18.6 - - - +
276K ILE* 1.3 73.4 - - - +
278K MET* 1.3 71.7 + - - +
281K ALA* 4.1 4.3 - - + -
283K MET* 6.1 0.2 - - - -
286K ALA* 4.0 29.4 - - + +
308K THR* 4.4 2.5 - - + -
309K PHE 2.8 17.9 + - - +
310K VAL* 3.7 7.5 - - + -
311K GLN 3.1 24.9 + - - -
314K ILE* 3.8 15.0 - - + -
318K PHE* 3.9 28.5 - - + -
410K PHE* 3.7 2.8 - - - -
432K PHE* 3.8 32.5 - - + -
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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