Contacts of the helix formed by residues 350 - 361 (chain Q) in PDB entry 1HI0
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 ALA 350 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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348Q GLY 3.9 0.6 + - - -
349Q TYR* 1.3 70.6 - - - +
351Q PRO* 1.3 72.8 - - + +
352Q TRP* 3.1 39.9 - - + +
353Q TRP* 3.0 5.7 + - + +
354Q VAL* 3.0 22.0 + - - +
660Q SER 3.8 8.5 - - - +
661Q VAL* 3.1 20.2 + - - +
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Residues in contact with PRO 351 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179Q ASN* 5.7 0.2 - - - +
182Q LEU* 4.0 20.7 - - + +
345Q LEU* 3.8 22.1 - - + +
349Q TYR 3.3 7.6 - - - +
350Q ALA* 1.3 84.2 - - + +
352Q TRP* 1.3 56.3 + - + +
354Q VAL* 3.1 3.6 + - - +
355Q LYS* 2.7 35.2 + - - +
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Residues in contact with TRP 352 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174Q ALA* 3.9 8.1 - - + -
175Q GLU* 3.2 64.1 + - + +
178Q GLY* 3.6 4.1 - - - -
179Q ASN* 3.5 35.0 - - - +
182Q LEU* 3.7 10.6 - - - +
350Q ALA* 3.1 21.0 - - + +
351Q PRO* 1.3 81.5 - - + +
353Q TRP* 1.3 95.4 + + + +
355Q LYS* 3.3 4.0 + - - +
356Q LEU* 3.0 28.2 + - + +
657Q PHE* 3.9 13.7 - + - -
660Q SER* 3.4 36.3 + - - -
661Q VAL* 3.3 21.3 - - + -
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Residues in contact with TRP 353 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135Q PHE* 4.7 6.1 - + - -
282Q PRO* 3.1 24.7 + - + +
283Q ILE* 4.2 10.2 - - + +
286Q VAL* 3.3 40.5 - - + +
344Q LEU* 4.1 19.5 - - + -
349Q TYR* 4.2 12.8 - + - -
350Q ALA* 3.0 11.0 + - + +
352Q TRP* 1.3 98.4 - + + +
354Q VAL* 1.3 78.8 + - + +
356Q LEU* 3.1 12.3 + - + +
357Q PHE* 2.9 60.0 + + + -
657Q PHE* 3.8 9.6 - + - -
661Q VAL* 3.6 32.8 - - + -
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Residues in contact with VAL 354 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341Q CYS* 3.5 43.7 - - + +
344Q LEU* 4.3 10.1 - - + -
345Q LEU* 3.7 24.5 - - + -
349Q TYR* 3.7 25.4 - - + -
350Q ALA 3.0 14.5 + - - +
351Q PRO 3.5 5.2 - - - +
353Q TRP* 1.3 86.8 - - + +
355Q LYS* 1.3 58.6 - - - +
357Q PHE* 3.2 3.7 + - + +
358Q GLU* 2.8 28.3 + - + +
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Residues in contact with LYS 355 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178Q GLY 4.3 1.3 - - - +
181Q MET* 3.6 40.4 - - + -
182Q LEU* 3.5 31.6 - - + +
186Q PHE* 4.1 17.0 - - - -
351Q PRO 2.7 14.8 + - - +
352Q TRP* 3.4 9.4 - - - +
353Q TRP 3.1 0.2 - - - -
354Q VAL* 1.3 77.2 - - - +
356Q LEU* 1.3 52.5 + - - +
358Q GLU* 3.1 34.4 + - - +
359Q THR* 2.6 40.0 + - - +
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Residues in contact with LEU 356 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174Q ALA* 3.7 29.8 - - + +
178Q GLY* 3.9 11.4 - - - +
181Q MET* 2.9 41.1 - - + -
195Q MET* 4.0 16.6 - - - -
279Q LEU* 4.0 15.9 - - + +
282Q PRO* 4.4 12.8 - - + -
283Q ILE* 4.7 6.1 - - + -
352Q TRP* 3.0 34.6 + - + +
353Q TRP* 3.3 12.1 - - + +
355Q LYS* 1.3 73.8 - - - +
357Q PHE* 1.3 64.1 + - - +
359Q THR* 3.2 4.0 + - - -
360Q SER* 2.9 24.3 + - - -
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Residues in contact with PHE 357 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135Q PHE* 5.2 8.1 - + - -
283Q ILE* 4.1 22.1 - - + +
337Q ARG* 5.3 2.0 - - - -
340Q ILE* 4.4 16.4 - - + -
341Q CYS* 4.0 16.8 - - - -
344Q LEU* 4.9 4.5 - - + -
353Q TRP* 2.9 46.7 + + + +
354Q VAL* 3.4 7.9 - - - +
356Q LEU* 1.3 76.4 - - - +
358Q GLU* 1.3 62.0 + - - +
360Q SER* 2.7 23.5 + - - -
361Q LEU* 3.5 24.2 + - + +
395Q GLN* 3.7 17.3 - - - -
397Q ALA* 4.4 9.6 - - + -
401Q MET* 3.6 35.0 - - + -
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Residues in contact with GLU 358 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186Q PHE* 5.8 0.3 - - - -
337Q ARG* 3.7 13.1 - - - +
338Q ASP* 4.4 5.9 - - - +
341Q CYS* 3.5 28.3 - - + +
354Q VAL 2.8 16.5 + - - +
355Q LYS* 3.1 37.7 + - - +
357Q PHE* 1.3 73.4 - - - +
359Q THR* 1.3 63.4 + - - +
361Q LEU* 2.8 22.0 + - - +
362Q LYS* 3.2 43.4 + - + +
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Residues in contact with THR 359 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181Q MET* 3.5 29.5 - - + -
186Q PHE* 3.8 21.2 - - + -
196Q GLY* 5.7 2.5 - - - -
279Q LEU* 5.3 3.4 - - + -
355Q LYS* 2.6 29.4 + - - +
356Q LEU 3.5 4.0 - - - -
358Q GLU* 1.3 79.2 + - - +
360Q SER* 1.3 63.1 + - - +
361Q LEU 3.0 0.9 + - - -
362Q LYS* 3.0 19.2 + - - +
363Q LEU* 3.3 22.2 + - + +
385Q PRO* 3.9 18.2 - - + -
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Residues in contact with SER 360 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199Q TYR* 2.7 36.5 + - - -
279Q LEU* 4.0 20.1 - - - +
280Q ASN* 4.9 1.1 - - - -
283Q ILE* 3.4 25.5 - - - +
356Q LEU 2.9 8.6 + - - -
357Q PHE 2.7 16.3 + - - -
359Q THR* 1.3 76.0 - - - +
361Q LEU* 1.3 57.1 + - - +
362Q LYS 3.4 0.2 - - - -
363Q LEU* 4.4 2.0 - - - -
392Q SER* 5.0 0.3 - - - -
395Q GLN* 2.8 29.0 + - - +
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Residues in contact with LEU 361 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332Q TRP* 4.5 8.9 - - + -
337Q ARG* 3.1 38.1 + - + -
357Q PHE* 3.8 27.4 - - + +
358Q GLU 2.8 11.1 + - - +
360Q SER* 1.3 80.9 + - - +
362Q LYS* 1.3 59.1 + - - +
363Q LEU 3.8 0.7 - - - -
387Q LEU 4.3 1.2 - - - +
388Q GLU* 5.6 1.2 - - - -
389Q VAL* 5.6 4.6 + - - +
390Q GLY 4.7 15.3 - - - +
391Q LEU* 4.2 20.6 - - + -
392Q SER* 4.9 7.0 - - - +
395Q GLN* 3.5 43.1 - - + +
401Q MET* 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