Contacts of the helix formed by residues 277 - 284 (chain A) in PDB entry 2IZV
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 ASP 277 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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275A VAL* 3.2 4.4 - - + -
276A PRO* 1.3 77.2 - - + +
278A LEU* 1.3 63.8 + - - +
279A LEU 3.3 2.2 - - - -
280A GLN* 2.8 45.9 + - - +
281A ILE* 3.0 33.2 + - + +
356A ASP* 3.8 17.5 - - - +
357A ILE* 3.1 15.6 + - - +
358A THR* 2.6 37.7 + - - -
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Residues in contact with LEU 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A LEU* 5.7 1.6 - - + -
275A VAL* 3.5 18.3 + - + +
276A PRO 3.3 3.4 + - - -
277A ASP* 1.3 76.1 - - - +
279A LEU* 1.3 56.5 + - - +
281A ILE* 3.6 8.6 + - + +
282A ASN* 3.0 50.3 + - - +
287A TYR* 6.0 0.2 - - - +
320A PHE* 4.5 13.0 - - + -
391A HIS* 5.8 0.4 - - + -
394A ARG* 5.1 3.6 - - - -
395A THR* 4.2 17.7 - - + +
398A CYS* 3.9 34.1 - - + -
399A ASN* 6.1 1.1 - - - +
422A TYR* 3.6 48.2 - - + +
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Residues in contact with LEU 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A ASP 3.1 0.8 + - - -
278A LEU* 1.3 74.5 - - - +
280A GLN* 1.3 66.8 + - - +
282A ASN* 3.1 4.5 + - + -
283A ASN* 2.9 49.7 + - - +
392A ILE* 6.3 0.7 - - + -
395A THR* 3.6 37.8 + - - +
396A VAL* 4.4 19.3 - - + +
399A ASN* 3.3 43.3 + - + +
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Residues in contact with GLN 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A ASP* 2.8 34.6 + - - +
279A LEU* 1.3 77.0 - - - +
281A ILE* 1.3 63.6 + - - +
283A ASN* 3.0 11.9 + - - +
284A ASN* 3.0 21.9 + - - +
356A ASP* 3.7 14.5 + - - -
358A THR* 3.8 24.2 + - - +
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Residues in contact with ILE 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A VAL* 4.0 10.5 - - + -
277A ASP* 3.0 45.3 + - + +
278A LEU* 3.7 8.7 - - + +
279A LEU 3.3 0.2 - - - -
280A GLN* 1.3 78.5 - - - +
282A ASN* 1.3 60.6 + - - +
284A ASN* 3.0 30.2 + - - +
287A TYR* 3.5 34.4 - - + +
310A LEU* 3.9 15.7 - - + -
320A PHE* 4.4 13.0 - - + -
357A ILE* 3.6 30.5 - - + -
358A THR* 4.5 4.9 - - - +
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Residues in contact with ASN 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A LEU* 3.0 39.3 + - - +
279A LEU* 3.1 4.0 + - + +
281A ILE* 1.3 80.6 - - - +
283A ASN* 1.3 61.8 + - - +
284A ASN 3.3 1.2 + - - -
287A TYR* 3.4 19.7 + - - -
383A ARG* 3.7 18.5 + - - -
387A PHE* 3.3 22.3 - - + -
391A HIS* 2.6 35.2 + - + -
395A THR* 3.6 20.1 - - + +
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Residues in contact with ASN 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A LEU* 2.9 45.5 + - - +
280A GLN* 3.5 8.9 - - - +
282A ASN* 1.3 77.8 - - - +
284A ASN* 1.3 60.3 + - - +
285A PRO* 3.6 7.4 - - - +
383A ARG* 5.5 0.4 - - - -
89C GLU* 5.7 0.2 - - - +
92C GLU* 3.4 45.8 + - + +
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Residues in contact with ASN 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A GLN 3.0 9.0 + - - +
281A ILE* 3.0 21.4 + - + +
283A ASN* 1.3 77.3 - - - +
285A PRO* 1.3 71.1 - - - +
286A CYS* 3.0 38.4 + - - +
287A TYR* 3.1 15.6 + - + +
310A LEU* 6.4 0.7 - - + -
358A THR* 4.9 13.3 + - - +
361A LEU* 4.9 7.9 - - - +
383A ARG* 4.0 6.4 + - - -
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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