Contacts of the helix formed by residues 277 - 284 (chain A) in PDB entry 2I91
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 PRO 277 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170A LYS* 4.3 1.6 - - - +
254A VAL* 4.1 27.4 - - + -
275A ASP 3.7 3.6 - - - +
276A MET* 1.3 94.2 - - + +
278A LEU* 1.3 60.2 + - - +
279A THR 3.5 0.4 - - - -
280A ALA* 3.3 6.7 + - + +
281A LEU* 2.8 25.5 + - - +
13D C 3.1 29.2 - - - +
14D A 3.2 48.2 - - - +
15D A 3.7 2.5 - - - +
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Residues in contact with LEU 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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276A MET 3.6 0.2 + - - -
277A PRO* 1.3 69.1 - - - +
279A THR* 1.3 61.7 + - - +
281A LEU* 3.3 17.4 + - + +
282A LEU* 2.8 30.0 + - - +
307A ARG* 3.7 41.7 - - + +
308A LEU* 4.8 8.8 - - + +
313A LEU* 3.5 43.3 - - + +
314A LEU* 3.8 19.1 - - + +
317A ALA* 3.7 15.5 - - + -
319A ILE* 3.8 8.9 - - + +
15D A 3.2 15.1 + - - +
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Residues in contact with THR 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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277A PRO 3.5 0.4 - - - -
278A LEU* 1.3 74.4 - - - +
280A ALA* 1.3 67.6 + - - +
282A LEU* 3.1 7.5 + - + +
283A ARG* 2.8 40.3 + - + +
317A ALA* 4.6 1.2 + - - +
319A ILE* 3.3 20.9 - - - +
323A HIS* 5.9 6.5 - - + -
12D U 3.6 24.7 - - - +
13D C 3.5 30.1 + - - -
15D A 4.9 1.8 + - - -
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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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254A VAL* 6.5 0.2 - - + -
255A ARG* 4.3 9.4 - - + +
276A MET* 3.7 17.7 - - + -
277A PRO* 3.4 13.7 - - + +
278A LEU 3.2 0.2 - - - -
279A THR* 1.3 79.1 - - - +
281A LEU* 1.3 63.1 + - - +
283A ARG 3.3 0.2 + - - -
284A ASN* 2.8 32.2 + - - +
12D U 3.2 25.1 - - - +
13D C 3.0 16.7 + - - +
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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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273A LEU* 3.8 24.5 - - + -
276A MET* 3.7 17.0 - - + -
277A PRO 2.8 17.0 + - - +
278A LEU* 3.6 21.1 - - + +
280A ALA* 1.3 77.2 - - - +
282A LEU* 1.3 62.5 + - - +
284A ASN 3.4 8.8 + - - -
285A LEU* 3.4 22.9 + - + +
288A MET* 4.8 6.1 - - + -
304A VAL* 3.8 27.4 - - + -
307A ARG* 4.0 30.7 - - + +
308A LEU* 4.5 11.0 - - + -
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Residues in contact with LEU 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 LEU 2.8 21.1 + - - +
279A THR* 3.5 7.9 - - + +
281A LEU* 1.3 77.2 - - - +
283A ARG* 1.3 54.2 + - + +
284A ASN 3.3 0.9 + - - -
285A LEU* 3.6 9.9 - - + +
308A LEU* 3.8 13.9 - - + -
319A ILE* 4.0 15.3 - - + -
323A HIS* 3.9 24.5 - - + +
324A ILE* 3.7 26.9 - - + -
327A ALA* 4.1 12.8 - - + -
353A LEU* 3.3 34.8 - - + -
9D U 2.7 31.4 + - - +
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Residues in contact with ARG 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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279A THR* 2.8 32.2 + - + +
280A ALA 4.0 0.2 - - - +
282A LEU* 1.3 73.2 - - + +
284A ASN* 1.3 62.7 + - - +
287A LYS 5.7 0.2 + - - -
7D G 5.2 0.6 + - - -
8D C 4.9 20.2 + - - +
9D U 3.3 51.7 + - + +
10D U 3.8 19.7 - - - -
11D U 3.0 46.5 + - - +
12D U 3.4 64.3 + - + +
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Residues in contact with ASN 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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255A ARG* 3.9 17.3 + - - +
269A TRP* 3.9 32.6 - - + -
276A MET* 5.1 1.4 - - - -
280A ALA* 2.8 27.8 + - - +
281A LEU 3.4 4.0 + - - +
282A LEU 3.2 0.6 - - - -
283A ARG* 1.3 82.2 - - - +
285A LEU* 1.3 63.9 + - - +
286A GLY 3.3 2.0 - - - +
287A LYS* 3.6 13.0 + - + +
288A MET* 3.2 32.1 + - + +
7D G 5.1 10.0 + - - +
12D U 3.4 23.1 + - - +
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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