Contacts of the helix formed by residues 280 - 290 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278D ILE* 3.3 4.1 - - - +
279D TYR* 1.3 96.3 + - + +
281D PRO* 1.3 63.2 - - - +
282D ASP* 2.5 39.3 + - - -
283D LYS* 3.1 48.1 + - + +
284D PHE* 2.8 26.9 + - - +
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Residues in contact with PRO 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D LEU* 3.8 17.3 - - + +
243D ILE* 3.5 23.1 - - + -
244D HIS 3.8 19.5 - - - +
245D GLY 5.7 2.7 - - - +
278D ILE* 3.9 9.1 - - + +
279D TYR 3.4 11.0 - - - +
280D ARG* 1.3 87.5 - - - +
282D ASP* 1.3 64.2 + - + +
284D PHE* 3.0 25.1 - - + +
285D LEU* 3.1 16.3 + - - +
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Residues in contact with ASP 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280D ARG* 2.5 41.5 + - - -
281D PRO* 1.3 81.7 - - + +
283D LYS* 1.3 84.1 + - - +
284D PHE 3.3 0.2 + - - -
285D LEU* 3.4 10.5 + - - +
286D GLN* 3.3 37.1 + - - +
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Residues in contact with LYS 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280D ARG* 3.1 52.1 + - + +
282D ASP* 1.3 90.8 + - - +
284D PHE* 1.3 64.8 + - - +
286D GLN* 3.1 16.8 + - - +
287D CYS* 3.0 30.6 + - - -
295D SER* 4.3 28.0 - - - +
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Residues in contact with PHE 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D LEU* 5.3 5.4 - - + -
135D PHE* 3.5 39.5 - + - -
207D MET* 4.5 13.9 - - + -
241D TRP* 3.9 20.2 - + - -
278D ILE* 4.0 31.0 - - + -
280D ARG 2.8 14.7 + - - +
281D PRO* 3.0 17.5 - - + +
283D LYS* 1.3 76.4 - - - +
285D LEU* 1.3 72.5 + - + +
287D CYS* 3.0 16.9 + - + +
288D VAL* 3.1 26.6 + - + +
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Residues in contact with LEU 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D LEU* 3.5 29.8 - - + -
134D GLN* 3.7 24.9 - - + +
135D PHE* 4.0 32.5 - - + +
138D VAL* 4.1 15.0 - - + +
281D PRO 3.1 12.6 + - - +
282D ASP* 3.8 10.1 - - - +
283D LYS 3.4 0.2 - - - -
284D PHE* 1.3 89.2 - - + +
286D GLN* 1.3 64.1 + - + +
288D VAL* 3.1 16.3 + - + +
289D LYS* 3.1 15.2 + - - +
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Residues in contact with GLN 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282D ASP* 3.3 32.2 + - - +
283D LYS* 3.1 17.7 + - - +
285D LEU* 1.3 77.1 - - + +
287D CYS* 1.3 61.2 + - - +
289D LYS* 3.5 11.2 + - - +
290D ASN* 2.9 29.3 + - - +
293D ASP* 5.3 9.3 - - - +
295D SER* 5.4 6.1 - - - -
296D CYS* 4.9 0.4 - - - -
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Residues in contact with CYS 287 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283D LYS* 3.0 22.2 + - - +
284D PHE* 3.0 9.6 + - + +
286D GLN* 1.3 77.0 - - - +
288D VAL* 1.3 61.5 + - + +
289D LYS 3.2 0.2 - - - -
290D ASN 3.9 1.3 - - - -
291D PRO* 2.9 32.4 - - - +
295D SER* 4.2 6.3 - - - -
296D CYS* 2.0 58.3 - - + -
297D THR 5.0 0.9 - - - -
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Residues in contact with VAL 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D PHE* 3.8 25.1 - - + -
138D VAL* 3.8 15.7 - - + +
139D GLN* 3.2 43.6 - - + +
284D PHE* 3.2 31.2 - - + +
285D LEU* 3.1 9.8 + - + +
287D CYS* 1.3 79.0 - - + +
289D LYS* 1.3 63.8 + - - +
291D PRO* 3.8 10.9 - - - +
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Residues in contact with LYS 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D VAL* 3.4 30.4 - - + +
285D LEU 3.1 9.3 + - - +
286D GLN* 3.7 13.0 - - - +
288D VAL* 1.3 79.4 - - - +
290D ASN* 1.3 61.7 + - + +
291D PRO* 3.0 10.0 - - - +
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Residues in contact with ASN 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286D GLN 2.9 15.0 + - - +
287D CYS* 3.3 6.2 - - - +
289D LYS* 1.3 80.6 - - + +
291D PRO* 1.3 64.8 - - - +
292D GLU* 3.3 23.9 + - - +
293D ASP* 3.2 26.6 + - + +
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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