Contacts of the helix formed by residues 268 - 280 (chain H) in PDB entry 1W88
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 ILE 268 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133H GLU* 4.2 6.5 - - + +
134H GLY* 4.1 7.9 - - - +
137H ALA* 3.8 29.6 - - + -
209H TYR* 3.5 25.9 + - + +
235H LEU* 3.6 30.5 - - + -
238H VAL* 3.9 22.2 - - + +
241H LEU* 4.3 5.2 - - + -
258H VAL* 5.6 0.2 - - + -
260H GLN* 3.2 2.6 + - - -
267H GLY* 1.3 78.6 - - - +
269H ALA* 1.3 65.9 + - - +
270H ALA* 3.3 3.1 - - - -
271H ASN* 3.1 30.9 + - + +
272H VAL* 3.3 18.7 + - + -
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Residues in contact with ALA 269 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209H TYR* 5.2 0.8 - - - -
258H VAL* 3.7 28.4 - - + +
260H GLN* 2.8 30.1 + - + +
266H ALA 4.8 0.8 + - - +
267H GLY 3.7 0.6 - - - -
268H ILE* 1.3 78.4 - - - +
270H ALA* 1.3 60.6 + - - +
272H VAL* 3.3 3.1 + - - +
273H VAL* 3.0 27.0 + - - +
290H ARG* 3.8 24.2 - - + -
292H ALA* 6.0 0.4 - - + -
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Residues in contact with ALA 270 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270F ALA* 3.7 10.1 - - + +
271F ASN* 3.4 39.3 - - - +
274F ALA* 4.2 13.0 - - + -
264H ARG 5.8 0.9 - - - +
266H ALA 5.6 1.9 + - - +
268H ILE 3.3 1.5 - - - -
269H ALA* 1.3 78.1 - - - +
271H ASN* 1.3 57.0 + - - +
273H VAL* 3.8 1.0 - - - +
274H ALA* 2.9 30.1 + - - +
290H ARG* 4.1 12.9 - - - +
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Residues in contact with ASN 271 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264F ARG 5.5 1.9 - - - +
265F GLN* 4.9 15.4 + - - +
270F ALA* 3.4 20.9 - - - +
290F ARG* 5.1 3.8 + - - +
137H ALA* 5.1 3.4 + - - +
138H GLN* 5.6 6.0 + - - +
238H VAL 5.7 0.8 + - - -
239H GLN* 4.6 14.9 - - - +
241H LEU* 4.6 11.7 - - + -
268H ILE* 3.1 33.5 + - + +
270H ALA* 1.3 77.7 - - - +
272H VAL* 1.3 62.9 + - - +
274H ALA* 3.4 1.9 + - - +
275H GLU* 3.0 31.3 + - + +
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Residues in contact with VAL 272 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207H ILE* 4.0 18.6 - - + -
235H LEU* 4.3 4.3 - - + -
241H LEU* 4.1 21.8 - - + -
246H ILE* 4.5 14.3 - - + +
258H VAL* 4.0 26.5 - - + -
268H ILE* 3.3 34.7 + - + +
269H ALA 3.3 5.8 + - - +
271H ASN* 1.3 75.1 - - - +
273H VAL* 1.3 62.5 + - - +
275H GLU* 3.2 4.1 + - - +
276H ILE* 3.0 34.4 + - + +
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Residues in contact with VAL 273 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273F VAL 5.3 0.2 - - - -
274F ALA* 3.7 20.2 - - + -
277F ASN* 3.4 35.0 - - + +
258H VAL* 4.0 12.1 - - + -
269H ALA 3.0 22.0 + - - +
270H ALA 3.8 4.3 - - - +
272H VAL* 1.3 74.3 - - - +
274H ALA* 1.3 65.2 + - - +
276H ILE* 3.2 10.1 + - - +
277H ASN* 3.0 22.7 + - - +
288H VAL* 4.0 15.7 - - + +
290H ARG* 3.8 28.5 - - + +
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Residues in contact with ALA 274 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270F ALA* 3.8 25.1 - - + +
273F VAL* 3.8 22.4 - - + -
274F ALA* 4.9 0.2 - - - +
290F ARG* 3.9 18.2 + - - -
270H ALA 2.9 18.8 + - - +
271H ASN 3.6 4.9 - - - +
272H VAL 3.3 0.2 - - - -
273H VAL* 1.3 77.0 - - - +
275H GLU* 1.3 56.8 + - - +
277H ASN* 3.1 21.7 + - - -
278H GLU* 3.1 11.8 + - - +
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Residues in contact with GLU 275 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264F ARG* 5.1 6.7 + - - +
290F ARG* 3.9 19.6 + - - +
354G ASN* 6.0 1.4 - - - +
241H LEU* 4.3 10.7 - - + +
243H ILE* 4.1 24.3 - - + +
246H ILE* 6.3 1.6 - - + -
247H ILE* 4.5 1.8 - - + -
271H ASN* 3.0 23.0 + - + +
272H VAL* 3.7 5.2 - - - +
273H VAL 3.2 0.2 - - - -
274H ALA* 1.3 72.6 - - - +
276H ILE* 1.3 66.8 + - + +
278H GLU* 3.2 7.1 + - - +
279H ARG* 2.9 67.1 + - - +
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Residues in contact with ILE 276 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207H ILE* 3.6 31.2 - - + -
246H ILE* 3.8 18.2 - - + -
247H ILE* 3.9 10.7 - - + +
250H VAL* 4.1 27.8 - - + -
256H ALA* 4.5 0.4 - - + -
272H VAL* 3.0 26.4 + - + +
273H VAL 3.2 5.8 + - - +
275H GLU* 1.3 75.0 - - - +
277H ASN* 1.3 56.8 + - - +
278H GLU 3.1 0.3 + - - -
279H ARG 3.1 0.2 + - - -
280H ALA* 2.7 39.4 + - + -
284H LEU* 4.2 8.5 - - + -
288H VAL* 3.6 37.5 - - + -
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Residues in contact with ASN 277 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273F VAL* 3.3 18.2 - - + +
277F ASN* 4.8 19.3 - - + +
281F ILE* 6.1 0.4 - - + -
284F LEU* 4.8 2.3 - - - +
287F PRO* 3.2 17.0 - - - +
288F VAL* 3.1 46.4 + - - +
273H VAL 3.0 15.2 + - - +
274H ALA 3.1 11.3 + - - -
276H ILE* 1.3 77.7 - - - +
278H GLU* 1.3 65.7 + - - +
281H ILE* 3.4 30.1 - - + +
284H LEU* 4.9 3.6 - - + -
288H VAL* 5.5 0.8 - - + +
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Residues in contact with GLU 278 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264F ARG* 2.9 31.8 + - - -
287F PRO* 4.3 14.9 - - - +
288F VAL 5.2 0.7 - - - +
289F LEU* 3.7 24.3 - - + +
290F ARG* 3.1 23.9 + - - -
324F PHE* 5.9 0.9 - - - -
274H ALA 3.1 12.8 + - - +
275H GLU* 3.4 16.2 - - - +
276H ILE 3.1 1.0 - - - -
277H ASN* 1.3 86.7 + - - +
279H ARG* 1.3 76.2 + - + +
281H ILE* 5.0 1.1 + - - +
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Residues in contact with ARG 279 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264F ARG* 5.8 1.6 - - - +
353G PHE* 4.2 1.8 - - - -
357G GLU* 2.8 43.4 + - - -
243H ILE* 3.7 40.3 - - - +
247H ILE* 3.8 22.8 - - + +
251H GLU* 4.9 3.6 - - - +
275H GLU* 2.9 50.0 + - - +
278H GLU* 1.3 96.4 + - + +
280H ALA* 1.3 58.7 + - - +
281H ILE 3.9 0.9 - - - -
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Residues in contact with ALA 280 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247H ILE* 4.0 25.8 - - + -
250H VAL* 4.5 17.3 - - + -
251H GLU* 4.6 5.6 - - + -
276H ILE 2.7 19.8 + - - +
279H ARG* 1.3 75.7 - - - +
281H ILE* 1.3 63.5 + - - +
282H LEU* 3.2 4.0 - - - +
283H SER* 3.2 23.0 + - - +
284H LEU* 3.6 15.2 + - - +
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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