Contacts of the helix formed by residues 276 - 284 (chain A) in PDB entry 5AM1
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 276 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A LEU* 3.5 27.1 - - + +
229A PRO* 3.4 35.8 - - + +
230A THR 3.7 10.9 - - - +
231A SER* 3.9 17.3 - - - -
273A SER 5.2 2.0 + - - -
274A TRP 3.2 1.0 - - - -
275A ARG* 1.4 106.4 - - + +
277A GLN* 1.3 66.1 + - - +
278A ILE 3.7 0.2 - - - -
279A PRO* 4.3 0.9 - - - +
280A ALA* 3.8 5.5 - - - +
441A MET 4.6 2.1 + - - -
446A GLU* 3.7 10.5 + - - -
527A GLN 4.1 9.0 - - - -
528A MET* 4.3 13.9 - - + -
531A PRO* 3.5 31.4 - - + -
535A ASN* 3.0 19.8 + - - -
1550A SO4 3.5 22.7 + - - -
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Residues in contact with GLN 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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263A LEU* 4.5 5.4 - - + -
273A SER 3.9 0.2 - - - +
274A TRP* 2.9 33.7 + - + +
276A TYR* 1.3 86.1 + - - +
278A ILE* 1.3 56.1 + - - +
279A PRO 3.6 0.2 - - - -
280A ALA* 3.4 1.2 + - - +
281A LEU* 2.8 48.3 + - + +
527A GLN* 3.2 42.0 + - - +
531A PRO 3.8 6.9 + - - -
534A VAL* 3.7 27.8 - - + +
535A ASN* 2.9 28.4 + - - +
538A LEU* 4.5 7.6 - - + -
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Residues in contact with ILE 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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232A CYS* 3.8 6.1 - - - -
237A MET* 4.1 12.3 - - + -
253A VAL* 4.4 6.7 - - + -
255A LEU* 3.7 29.8 - - + +
263A LEU* 4.2 0.7 - - + -
271A TRP* 3.8 26.5 - - + -
274A TRP* 3.0 33.3 + - + +
277A GLN* 1.3 74.9 - - - +
279A PRO* 1.4 68.2 - - + +
282A ALA* 3.1 23.7 + - - +
288A VAL* 3.9 28.4 - - + +
290A ALA* 3.7 24.5 - - + -
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Residues in contact with PRO 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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145A MET* 5.6 7.4 - - + -
230A THR* 3.6 29.4 - - + +
231A SER 3.4 25.1 - - - +
232A CYS* 3.7 7.4 - - - -
255A LEU* 3.7 17.0 - - + +
275A ARG 3.2 20.6 - - - +
276A TYR 4.3 0.4 - - - -
277A GLN 3.9 0.9 - - - -
278A ILE* 1.4 86.2 - - + +
280A ALA* 1.4 56.7 + - - +
282A ALA* 3.5 1.6 + - - +
283A GLN* 2.9 32.4 + - - +
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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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229A PRO* 5.3 3.1 - - + -
230A THR 5.3 0.6 + - - -
276A TYR 3.8 3.3 + - - +
277A GLN 3.4 6.2 + - - +
278A ILE 3.3 0.6 - - - -
279A PRO* 1.4 79.4 - - - +
281A LEU* 1.4 56.6 + - + +
283A GLN* 3.3 6.7 + - - +
284A ALA* 3.0 27.9 + - - +
535A ASN* 3.3 37.7 - - + +
539A ILE* 3.9 11.1 - - + +
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Residues in contact with LEU 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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261A VAL* 4.1 25.4 - - + -
263A LEU* 4.3 21.1 - - + -
277A GLN* 2.8 32.1 + - + +
280A ALA* 1.4 71.8 - - + +
282A ALA* 1.4 64.9 + - - +
284A ALA* 3.3 13.5 + - - +
285A GLY 3.4 0.9 + - - -
286A TYR* 3.2 23.9 + - + +
288A VAL* 3.6 15.5 - - + -
332A ILE* 4.5 5.2 - - + -
535A ASN* 4.8 4.9 - - - +
538A LEU* 4.4 16.2 - - + -
539A ILE* 3.6 25.6 - - + -
542A LEU* 4.1 18.2 - - + -
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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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255A LEU* 3.6 41.1 - - + +
256A GLY* 3.8 10.2 - - - -
257A SER 4.9 1.4 + - - +
278A ILE 3.1 19.0 + - - +
279A PRO 3.8 1.6 - - - +
281A LEU* 1.4 74.6 - - - +
283A GLN* 1.3 62.2 + - - +
285A GLY* 3.2 14.4 + - - -
286A TYR 3.3 13.7 + - - +
288A VAL* 3.7 1.6 - - - +
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Residues in contact with GLN 283 (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 14.5 + - - +
142A GLU* 3.3 60.2 + - + +
145A MET* 4.1 10.4 - - - +
279A PRO 2.9 19.5 + - - +
280A ALA* 3.6 7.4 - - - +
282A ALA* 1.3 76.3 - - - +
284A ALA* 1.3 57.0 + - - +
285A GLY* 3.2 4.1 + - - -
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Residues in contact with ALA 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 ALA 3.0 16.4 + - - +
281A LEU 3.3 8.0 + - - +
283A GLN* 1.3 74.7 - - - +
285A GLY* 1.3 57.8 + - - +
286A TYR* 3.6 16.6 - - + -
539A ILE* 3.7 37.9 - - + -
543A ASP* 4.1 7.9 - - - +
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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