Contacts of the helix formed by residues 274 - 282 (chain A) in PDB entry 1ZD4
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 TYR 274 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226A LEU* 3.6 32.8 - - + +
227A PRO* 3.6 33.8 - - + +
228A THR 4.0 7.3 - - - +
229A SER* 3.8 20.2 + - - -
271A SER 5.7 0.4 - - - -
272A TRP 2.7 5.7 + - - -
273A ARG* 1.3 107.2 - - + +
275A GLN* 1.3 65.6 + - - +
276A ILE 3.7 0.2 - - - -
277A PRO* 4.1 2.0 - - - +
278A ALA* 3.9 6.1 - - - +
440A MET 4.4 7.6 + - - -
445A GLU* 3.5 19.0 + - - -
526A GLN* 3.7 20.4 - - + -
527A MET* 4.5 11.2 - - + -
530A PRO* 3.5 22.7 - - + -
534A ASN* 3.0 17.7 - - - +
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Residues in contact with GLN 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A LEU* 5.0 1.3 - - + -
271A SER 3.7 3.8 - - - +
272A TRP* 2.7 41.4 + - + +
274A TYR* 1.3 85.0 - - - +
276A ILE* 1.3 56.1 + - - -
277A PRO 3.3 2.2 - - - -
278A ALA 4.0 0.2 - - - -
279A LEU* 2.8 52.5 + - + +
526A GLN* 2.8 38.6 - - - +
530A PRO* 3.9 5.9 + - - +
533A VAL* 4.1 11.1 - - + +
534A ASN* 2.5 43.7 - - - +
537A LEU* 5.1 4.7 - - + -
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Residues in contact with ILE 276 (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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230A CYS* 4.0 5.8 - - - -
235A MET* 4.0 12.1 - - + -
251A VAL* 4.4 4.9 - - + +
253A LEU* 3.8 26.2 - - + +
261A LEU* 4.3 0.2 - - + -
269A TRP* 3.6 33.7 - - + +
272A TRP* 2.9 28.3 + - + +
275A GLN* 1.3 79.0 - - - +
277A PRO* 1.3 71.6 - - + +
280A ALA* 3.2 18.9 + - - +
286A VAL* 3.7 22.7 - - + +
288A ALA* 3.4 29.8 - - + -
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Residues in contact with PRO 277 (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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145A MET* 5.2 6.7 - - + -
228A THR* 3.4 39.9 - - + +
230A CYS* 3.9 21.5 - - + +
253A LEU* 4.1 13.7 - - + -
273A ARG 3.2 17.9 - - - +
274A TYR 4.1 1.3 - - - -
275A GLN 3.6 1.8 - - - -
276A ILE* 1.3 94.4 - - + +
278A ALA* 1.3 58.8 + - - +
280A ALA* 2.9 5.2 + - + +
281A GLN* 2.8 31.1 + - - +
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Residues in contact with ALA 278 (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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227A PRO* 5.5 3.8 - - + -
274A TYR 3.9 6.0 + - - +
275A GLN 3.5 1.8 + - - +
277A PRO* 1.3 80.3 - - - +
279A LEU* 1.3 56.9 + - - +
281A GLN* 3.2 8.7 + - - +
282A ALA* 2.9 27.5 + - - +
534A ASN* 3.3 38.1 - - + +
538A ILE* 4.1 10.2 - - + +
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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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259A VAL* 4.2 20.4 - - + -
261A LEU* 4.3 13.9 - - + -
275A GLN* 2.8 38.5 + - + +
278A ALA* 1.3 72.6 - - + +
280A ALA* 1.3 64.7 + - - +
282A ALA* 3.0 18.1 + - - +
284A TYR* 3.3 17.8 + - + -
286A VAL* 3.4 21.1 - - + -
330A ILE* 4.6 5.4 - - + -
534A ASN* 5.0 3.6 - - - +
537A LEU* 4.3 16.2 - - + -
538A ILE* 3.6 25.8 - - + -
541A LEU* 3.7 20.9 - - + -
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Residues in contact with ALA 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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253A LEU* 3.7 31.4 - - + +
254A GLY* 3.9 11.4 - - - -
255A SER 5.3 0.7 + - - -
276A ILE 3.2 13.5 + - - +
277A PRO 2.9 9.2 + - - +
279A LEU* 1.3 77.5 - - - +
281A GLN* 1.3 55.1 + - - +
283A GLY* 2.6 27.4 + - - -
284A TYR 3.3 17.4 + - - +
286A VAL* 3.8 1.3 - - - +
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Residues in contact with GLN 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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138A GLN* 4.7 12.3 + - - +
141A CYS* 5.4 2.1 - - - +
142A GLU* 3.1 54.6 + - - +
145A MET* 5.0 7.1 - - - +
277A PRO 2.8 16.5 + - - +
278A ALA* 3.6 10.8 - - - +
280A ALA* 1.3 72.7 - - - +
282A ALA* 1.3 59.0 + - - +
283A GLY* 3.1 1.6 + - - -
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Residues in contact with ALA 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 ALA 2.9 13.3 + - - +
279A LEU* 3.1 15.3 - - - +
280A ALA 2.8 0.6 + - - -
281A GLN* 1.3 76.3 - - - +
283A GLY* 1.3 58.4 + - - +
284A TYR* 3.5 19.6 - - + -
538A ILE* 3.9 34.3 - - + -
542A ASP* 4.3 4.9 - - - +
546A ARG* 4.3 3.1 + - - -
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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