Contacts of the helix formed by residues 268 - 277 (chain A) in PDB entry 7A62
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 SER 268 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A PHE* 3.8 33.6 - - - +
171A GLU* 4.6 1.8 + - - -
266A GLN 3.6 1.1 + - - -
267A SER* 1.3 74.3 + - - +
269A VAL* 1.3 59.3 + - - +
270A PHE 3.5 0.9 - - - -
271A GLN* 3.6 4.3 + - - +
272A CYS* 2.8 30.8 + - - +
299A MET* 3.0 35.5 - - - +
300A PRO* 5.4 0.5 - - - +
303A HIS* 4.1 11.7 + - - +
307A LEU* 4.4 7.9 - - - +
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Residues in contact with VAL 269 (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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23A PHE* 4.0 13.2 - - + -
170A VAL* 5.7 6.3 - - + -
171A GLU* 3.3 34.1 - - - +
174A ALA* 3.9 31.6 - - + -
178A ILE* 4.8 0.4 - - + -
207A LEU* 5.3 4.7 - - + -
267A SER* 3.1 8.0 + - - +
268A SER* 1.3 76.8 - - - +
270A PHE* 1.3 85.0 + - + +
272A CYS* 3.3 8.6 + - - +
273A PHE* 3.2 34.7 - - + -
342A LEU* 5.8 2.2 - - + -
502A HEM 5.5 4.5 - - + -
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Residues in contact with PHE 270 (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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170A VAL* 6.2 2.0 - - + -
214A PHE* 5.0 4.3 - + - -
267A SER* 6.5 0.2 - - - -
268A SER 3.5 0.2 - - - -
269A VAL* 1.3 89.2 - - + +
271A GLN* 1.3 59.8 + - - +
273A PHE* 3.3 4.0 + - - +
274A ASP* 2.9 30.7 + - - -
339A LEU* 4.3 16.0 - - + +
342A LEU* 4.0 44.4 - - + -
343A ARG* 3.3 33.3 + - + +
346A HIS* 4.6 13.7 - + + -
502A HEM 3.1 74.6 - + + +
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Residues in contact with GLN 271 (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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267A SER 5.1 3.9 + - - +
268A SER 3.6 8.1 + - - +
269A VAL 3.3 0.4 - - - -
270A PHE* 1.3 76.2 - - + +
272A CYS* 1.3 66.3 + - - +
274A ASP* 3.4 14.1 - - + +
275A VAL* 3.0 27.9 + - - +
281A GLN* 6.4 0.7 - - + -
282A THR* 4.6 2.5 + - - -
292A LEU* 3.0 51.2 + - + +
295A MET* 4.5 4.0 - - - +
296A ARG* 2.6 40.2 + - - +
299A MET* 3.8 21.9 - - + +
307A LEU* 4.1 12.1 - - + -
502A HEM 5.3 2.9 - - + +
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Residues in contact with CYS 272 (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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23A PHE* 4.2 13.0 - - + -
178A ILE* 4.5 4.7 - - - -
181A ILE* 3.7 27.8 - - - -
268A SER 2.8 21.1 + - - +
269A VAL* 3.4 6.7 - - - +
271A GLN* 1.3 77.1 - - - +
273A PHE* 1.3 71.8 + - + +
275A VAL* 3.3 5.0 - - - +
276A LEU* 3.1 23.6 + - - +
306A PHE* 3.9 18.4 - - - -
307A LEU* 3.6 16.7 - - + +
310A LEU* 3.9 1.6 - - - +
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Residues in contact with PHE 273 (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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174A ALA* 4.9 2.2 - - + -
177A ALA* 3.6 25.1 - - + -
178A ILE* 4.0 23.1 - - + -
181A ILE* 4.3 7.6 - - + -
203A ILE* 3.9 25.8 - - + -
207A LEU* 4.1 25.4 - - + -
269A VAL* 3.2 32.1 - - + +
270A PHE 3.3 2.5 + - - +
271A GLN 3.2 0.4 - - - -
272A CYS* 1.3 88.2 - - + +
274A ASP* 1.3 66.5 + - - +
275A VAL 3.3 0.2 - - - -
276A LEU* 3.9 24.7 - - + -
277A LEU* 3.0 33.1 + - + +
339A LEU* 4.0 23.8 - - + -
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Residues in contact with ASP 274 (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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270A PHE 2.9 14.6 + - - +
271A GLN* 3.4 19.7 - - + +
273A PHE* 1.3 78.1 - - - +
275A VAL* 1.3 65.2 + - + +
277A LEU 3.2 0.3 + - - -
278A GLY 3.1 3.3 + - - -
279A ILE* 2.9 47.0 + - - +
281A GLN* 3.2 30.8 + - + +
292A LEU* 5.4 1.0 - - - +
339A LEU* 3.7 8.2 - - - +
343A ARG* 3.0 36.9 + - - -
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Residues in contact with VAL 275 (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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271A GLN* 3.0 11.6 + - - +
272A CYS* 3.3 13.7 - - - +
274A ASP* 1.3 76.2 - - + +
276A LEU* 1.3 69.6 + - - +
278A GLY* 3.2 11.7 + - - +
279A ILE 4.7 4.5 - - - +
282A THR* 6.3 1.1 - - - -
296A ARG* 3.7 25.4 - - - +
307A LEU* 4.2 12.1 - - + +
310A LEU* 3.7 34.6 - - + +
311A GLU* 4.1 25.7 - - + +
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Residues in contact with LEU 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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181A ILE* 4.0 23.1 - - + -
184A VAL* 4.8 8.3 - - + -
185A PHE* 3.9 27.9 - - + -
200A LEU* 5.6 3.6 - - + -
203A ILE* 4.2 23.3 - - + -
272A CYS 3.1 14.5 + - - +
273A PHE* 3.7 29.8 - - + +
275A VAL* 1.3 86.0 - - - +
277A LEU* 1.3 71.5 + - + +
278A GLY 3.5 0.5 + - - -
310A LEU* 4.7 8.1 - - + -
316A VAL* 3.6 30.4 + - + +
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Residues in contact with LEU 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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200A LEU* 5.1 4.5 - - + -
207A LEU* 6.0 0.7 - - + -
273A PHE* 3.0 24.7 + - + +
274A ASP 3.2 0.2 + - - -
276A LEU* 1.3 93.9 - - + +
278A GLY* 1.3 62.7 + - - +
279A ILE* 3.1 14.5 + - + +
316A VAL* 4.9 4.9 - - + -
317A ARG* 3.7 6.7 - - - +
332A TYR* 2.6 55.3 + - + +
335A CYS* 3.8 44.6 - - + +
336A VAL* 3.9 11.4 - - + +
339A LEU* 4.3 12.6 - - + -
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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