Contacts of the helix formed by residues 280 - 290 (chain C) in PDB entry 1ZVM
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 280 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278C ILE* 3.3 4.3 - - - +
279C TYR* 1.3 95.6 - - + +
281C PRO* 1.3 63.1 - - - +
282C ASP* 2.5 45.1 + - - -
283C LYS* 3.1 46.8 + - + +
284C PHE* 2.8 26.5 + - - +
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Residues in contact with PRO 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C LEU* 4.2 15.5 - - + +
243C ILE* 3.7 21.8 - - + -
244C HIS 3.8 20.6 - - - +
245C GLY 6.0 0.4 - - - +
278C ILE* 3.9 8.7 - - + +
279C TYR 3.4 11.7 - - - +
280C ARG* 1.3 86.3 - - - +
282C ASP* 1.3 64.6 + - + +
284C PHE* 3.2 22.2 - - + +
285C LEU* 3.2 17.2 + - - +
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Residues in contact with ASP 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280C ARG* 2.5 36.5 + - - -
281C PRO* 1.3 82.1 - - + +
283C LYS* 1.3 86.7 + - - +
284C PHE 3.2 0.5 + - - -
285C LEU* 3.3 10.4 + - - +
286C GLN* 3.3 36.0 + - - +
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Residues in contact with LYS 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280C ARG* 3.1 51.4 + - + +
282C ASP* 1.3 90.5 + - - +
284C PHE* 1.3 63.2 + - - +
286C GLN* 3.3 17.6 + - - +
287C CYS* 3.1 30.0 + - - -
295C SER* 4.5 26.5 - - - +
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Residues in contact with PHE 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C LEU* 5.0 6.1 - - + -
135C PHE* 3.7 39.9 - + - -
207C MET* 4.7 8.1 - - + -
241C TRP* 4.0 20.2 - + - -
243C ILE* 5.6 0.2 - - + -
278C ILE* 3.9 34.3 - - + -
280C ARG 2.8 12.7 + - - +
281C PRO* 3.2 17.0 - - + +
283C LYS* 1.3 76.1 - - - +
285C LEU* 1.3 72.9 + - + +
287C CYS* 3.0 16.5 + - + +
288C VAL* 3.1 25.3 + - + +
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Residues in contact with LEU 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C LEU* 3.9 25.4 - - + -
134C GLN* 3.7 31.9 - - + +
135C PHE* 3.9 36.6 - - + +
138C VAL* 4.4 11.3 - - + +
281C PRO 3.2 12.6 + - - +
282C ASP* 3.3 9.4 + - - +
284C PHE* 1.3 85.3 - - + +
286C GLN* 1.3 63.4 + - + +
288C VAL* 3.0 18.0 + - + +
289C LYS* 3.1 14.9 + - - +
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Residues in contact with GLN 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282C ASP* 3.3 31.5 + - - +
283C LYS* 3.3 18.4 + - - +
284C PHE 3.2 0.4 - - - -
285C LEU* 1.3 78.8 - - + +
287C CYS* 1.3 60.4 + - - +
289C LYS* 3.5 11.9 + - - +
290C ASN* 3.0 28.8 + - - +
293C ASP* 5.2 8.8 - - - +
295C SER* 5.3 6.6 - - - -
296C CYS* 4.9 0.4 - - - -
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Residues in contact with CYS 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283C LYS* 3.1 18.9 + - - +
284C PHE* 3.0 12.4 + - + +
286C GLN* 1.3 77.2 - - - +
288C VAL* 1.3 61.8 + - + +
289C LYS 3.2 1.8 - - - -
290C ASN 4.0 1.1 - - - -
291C PRO* 3.0 30.2 - - - +
293C ASP* 5.0 1.1 - - - -
295C SER* 4.3 6.1 - - - -
296C CYS* 2.0 59.5 - - + -
297C THR 4.8 2.9 - - - +
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Residues in contact with VAL 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C PHE* 3.9 24.7 - - + -
138C VAL* 3.7 20.1 - - + +
139C GLN* 3.4 40.8 - - + +
284C PHE* 3.2 31.0 - - + +
285C LEU* 3.0 10.2 + - + +
287C CYS* 1.3 79.4 - - - +
289C LYS* 1.3 63.3 + - - +
291C PRO* 3.7 10.4 - - - +
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Residues in contact with LYS 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C VAL* 3.4 34.9 - - + +
285C LEU 3.1 9.0 + - - +
286C GLN* 3.6 13.5 - - - +
288C VAL* 1.3 80.5 - - - +
290C ASN* 1.3 61.5 + - + +
291C PRO* 3.1 9.2 - - - +
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Residues in contact with ASN 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286C GLN 3.0 12.4 + - - +
287C CYS 3.5 4.5 - - - +
289C LYS* 1.3 78.8 - - + +
291C PRO* 1.3 64.0 - - - +
292C GLU* 3.4 22.7 + - - +
293C ASP* 3.3 25.5 + - + +
296C CYS* 3.8 4.2 - - - -
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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