Contacts of the strand formed by residues 274 - 277 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272J LYS 3.4 6.7 - - - +
273J SER* 1.3 82.7 - - - +
275J ASN* 1.3 59.3 + - - +
276J ILE* 3.9 4.0 - - + +
307J ARG* 3.4 16.6 - - + +
309J PHE* 3.9 15.7 - - + -
420J ALA* 3.8 35.9 - - + +
426J GLY* 6.6 0.4 - - - -
428J ALA 3.3 13.5 - - - +
429J ALA* 3.2 17.7 - - + -
430J ALA 3.0 24.1 + - - +
446J LEU* 4.9 2.7 - - + -
456J TYR* 4.8 1.4 - - - -
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Residues in contact with ASN 275 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274J PRO* 1.3 71.4 - - - +
276J ILE* 1.3 61.6 + - - +
277J ILE* 3.7 6.0 + - - +
290J ALA* 3.5 33.1 - - - +
293J ALA* 4.0 6.4 - - - +
305J GLY* 4.6 9.9 - - - +
307J ARG 2.8 12.2 + - - +
308J THR* 3.5 11.3 + - + +
309J PHE 2.9 26.3 + - - +
430J ALA* 3.4 10.9 - - - +
432J PHE* 3.2 36.8 - - - -
456J TYR* 4.2 16.2 - - + -
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Residues in contact with ILE 276 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274J PRO* 4.6 3.4 - - + -
275J ASN* 1.3 76.1 - - - +
277J ILE* 1.3 60.2 + - - +
278J MET* 3.8 25.3 + - - -
309J PHE* 3.6 11.7 - - + -
410J PHE* 3.9 7.0 - - + -
416J VAL* 3.9 40.2 - - + -
420J ALA* 4.0 8.5 - - + -
430J ALA 2.8 16.3 + - - +
431J VAL* 3.3 5.7 - - + +
432J PHE* 2.8 31.4 + - - -
442J LEU* 4.5 8.7 - - + -
446J LEU* 3.8 38.6 - - + -
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Residues in contact with ILE 277 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275J ASN* 3.8 20.2 - - - +
276J ILE* 1.3 75.5 - - - +
278J MET* 1.3 66.3 + - - +
281J ALA* 4.1 5.6 - - + -
283J MET* 6.3 0.2 - - - -
286J ALA* 3.9 28.9 - - + +
290J ALA* 4.7 0.2 - - + -
308J THR* 4.3 2.0 - - + -
309J PHE 2.7 18.8 + - - +
310J VAL* 4.2 9.9 - - + -
311J GLN 3.1 24.9 + - - -
314J ILE* 3.8 19.8 - - + +
318J PHE* 4.0 27.6 - - + -
410J PHE* 3.6 3.5 - - - -
432J PHE* 3.8 27.1 - - + -
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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