Contacts of the helix formed by residues 271 - 278 (chain A) in PDB entry 3V98
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 271 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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259A THR* 3.6 20.2 - - - -
266A LEU* 4.2 0.2 - - - -
269A GLN 4.3 0.2 + - - -
270A LEU* 1.3 77.7 - - - +
272A LEU* 1.3 65.7 + - - +
273A GLU* 3.6 12.4 + - - +
274A GLN* 3.0 25.1 + - - +
275A GLU* 3.0 19.8 + - - +
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Residues in contact with LEU 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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251A LEU* 3.7 27.8 - - + -
257A VAL* 3.7 28.0 - - + +
258A THR 4.2 5.2 - - - -
259A THR* 2.9 23.9 + - - +
262A VAL* 4.2 24.2 - - + -
266A LEU* 3.8 12.2 - - + +
271A SER* 1.3 70.3 - - - +
273A GLU* 1.3 65.8 + - - +
275A GLU* 3.1 4.6 + - + +
276A VAL* 3.0 24.2 + - + +
281A ILE* 3.7 29.6 - - + -
311A LEU* 4.4 6.5 - - + -
323A ILE* 4.5 7.2 - - + -
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Residues in contact with GLU 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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251A LEU* 4.7 16.5 - - + +
257A VAL 5.2 3.3 - - - +
258A THR* 5.3 1.2 - - - -
259A THR* 3.2 24.3 + - - -
271A SER* 3.6 11.8 + - - +
272A LEU* 1.3 76.9 - - - +
274A GLN* 1.3 60.8 + - - +
276A VAL* 3.4 12.0 + - - +
277A GLN* 3.3 25.1 + - - +
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Residues in contact with GLN 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 LEU* 3.8 36.6 - - + +
271A SER* 3.0 21.3 + - - +
273A GLU* 1.3 77.4 - - - +
275A GLU* 1.3 65.4 + - - +
276A VAL 3.2 0.2 - - - -
277A GLN* 3.3 8.9 + - + +
278A GLN* 3.1 37.4 + - + +
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Residues in contact with GLU 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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266A LEU* 4.4 10.6 - - + +
267A GLU 4.6 0.7 + - - -
268A ARG* 3.5 18.1 + - - +
270A LEU* 3.8 21.9 - - + +
271A SER 3.0 19.0 + - - +
272A LEU* 3.1 9.6 + - - +
274A GLN* 1.3 74.5 - - - +
276A VAL* 1.3 64.6 + - - +
278A GLN* 3.2 4.8 + - - +
279A GLY 3.2 4.0 + - - -
280A ASN* 3.0 56.7 + - + +
281A ILE* 3.9 18.4 - - + -
313A TYR* 2.7 35.1 + - + -
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Residues in contact with VAL 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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248A CYS* 3.6 14.3 - - - +
249A THR* 3.5 35.4 - - - +
250A GLU* 3.7 8.5 - - - +
251A LEU* 4.0 29.6 - - + +
272A LEU* 3.0 19.7 + - + +
273A GLU* 3.4 10.3 - - - +
275A GLU* 1.3 76.8 - - - +
277A GLN* 1.3 63.1 + - - +
279A GLY* 3.0 18.9 + - - -
281A ILE* 3.7 25.6 - - + -
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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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249A THR 3.8 19.8 + - - -
250A GLU* 5.4 2.0 - - - +
273A GLU 3.3 14.3 + - - +
274A GLN* 3.7 12.8 - - + +
275A GLU 3.3 0.6 - - - -
276A VAL* 1.3 81.8 - - - +
278A GLN* 1.3 68.8 + - - +
279A GLY 3.2 1.2 + - - -
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Residues in contact with GLN 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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270A LEU* 4.2 18.2 - - + -
274A GLN* 3.1 34.5 + - + +
275A GLU* 3.7 2.7 - - - +
276A VAL 3.2 0.6 - - - -
277A GLN* 1.3 83.1 + - - +
279A GLY* 1.3 61.5 + - - +
280A ASN* 3.4 24.0 + - - +
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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