Contacts of the helix formed by residues 350 - 361 (chain R) 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 R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348R GLY 3.9 0.6 + - - -
349R TYR* 1.3 69.7 - - - +
351R PRO* 1.3 72.5 - - + +
352R TRP* 3.1 39.3 - - + +
353R TRP* 3.0 5.2 + - + +
354R VAL* 3.0 22.4 + - - +
660R SER 3.8 8.3 - - - +
661R VAL* 3.1 20.8 + - - +
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Residues in contact with PRO 351 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179R ASN* 5.7 0.2 - - - +
182R LEU* 4.0 20.3 - - + +
345R LEU* 3.8 22.3 - - + +
349R TYR 3.3 7.4 - - - +
350R ALA* 1.3 82.9 - - + +
352R TRP* 1.3 55.5 + - + +
354R VAL* 3.1 3.6 + - - +
355R LYS* 2.7 36.0 + - - +
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Residues in contact with TRP 352 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174R ALA* 3.9 8.3 - - + -
175R GLU* 3.2 63.6 + - + +
178R GLY* 3.6 5.3 - - - -
179R ASN* 3.5 36.3 - - - +
182R LEU* 3.7 10.6 - - - +
350R ALA* 3.1 22.1 - - + +
351R PRO* 1.3 81.9 - - + +
353R TRP* 1.3 95.2 + + + +
355R LYS* 3.3 3.9 + - - +
356R LEU* 3.0 27.8 + - + +
657R PHE* 3.9 12.6 - + - -
660R SER* 3.4 35.4 + - - -
661R VAL* 3.3 21.8 - - + -
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Residues in contact with TRP 353 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135R PHE* 4.7 6.1 - + - -
282R PRO* 3.1 24.4 + - + -
283R ILE* 4.2 11.6 - - + +
286R VAL* 3.3 39.2 - - + +
344R LEU* 4.1 19.5 - - + -
349R TYR* 4.2 13.0 - + - -
350R ALA* 3.0 11.8 + - + +
352R TRP* 1.3 97.4 - + + +
354R VAL* 1.3 78.4 + - + +
356R LEU* 3.1 12.3 + - + +
357R PHE* 2.9 59.2 + + + -
657R PHE* 3.8 10.5 - + - -
661R VAL* 3.6 32.1 - - + -
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Residues in contact with VAL 354 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341R CYS* 3.5 44.0 - - + +
344R LEU* 4.3 9.2 - - + -
345R LEU* 3.7 23.8 - - + -
349R TYR* 3.7 24.9 - - + -
350R ALA 3.0 15.4 + - - +
351R PRO 3.5 5.4 - - - +
353R TRP* 1.3 86.0 - - + +
355R LYS* 1.3 57.4 + - - +
357R PHE* 3.2 3.3 + - + +
358R GLU* 2.8 28.5 + - + +
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Residues in contact with LYS 355 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178R GLY 4.3 2.0 - - - +
181R MET* 3.6 40.4 - - + -
182R LEU* 3.5 31.4 - - + +
186R PHE* 4.1 17.2 - - - -
351R PRO 2.7 13.8 + - - +
352R TRP 3.4 8.7 - - - +
353R TRP 3.1 0.2 - - - -
354R VAL* 1.3 77.9 - - - +
356R LEU* 1.3 52.4 + - - +
358R GLU* 3.1 35.2 + - - +
359R THR* 2.6 38.8 + - - +
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Residues in contact with LEU 356 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174R ALA* 3.7 29.8 - - + +
178R GLY* 3.9 11.9 - - - +
181R MET* 2.9 41.1 - - + -
195R MET* 4.0 16.2 - - - -
279R LEU* 4.0 15.6 - - + +
282R PRO* 4.4 12.8 - - + -
283R ILE* 4.7 5.8 - - + -
352R TRP* 3.0 34.4 + - + +
353R TRP* 3.1 11.2 + - + +
355R LYS* 1.3 74.4 - - - +
357R PHE* 1.3 64.9 + - - +
359R THR* 3.2 3.8 + - - -
360R SER* 2.9 24.5 + - - -
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Residues in contact with PHE 357 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135R PHE* 5.2 7.9 - + - -
283R ILE* 4.1 21.7 - - + +
337R ARG* 5.3 1.8 - - - -
340R ILE* 4.4 16.8 - - + -
341R CYS* 4.0 16.4 - - - -
344R LEU* 4.9 4.3 - - + -
353R TRP* 2.9 46.7 + + + +
354R VAL* 3.4 7.9 - - - +
356R LEU* 1.3 76.8 - - - +
358R GLU* 1.3 63.8 + - - +
360R SER* 2.7 23.6 + - - -
361R LEU* 3.5 23.5 + - + +
395R GLN* 3.7 17.9 - - - -
397R ALA* 4.4 9.6 - - + -
401R MET* 3.6 34.5 - - + -
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Residues in contact with GLU 358 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186R PHE* 5.8 0.2 - - - -
337R ARG* 4.1 12.3 - - - +
338R ASP* 4.4 6.9 - - - +
341R CYS* 3.5 28.7 - - - +
354R VAL* 2.8 16.9 + - + +
355R LYS* 3.1 36.8 + - - +
357R PHE* 1.3 73.7 - - - +
359R THR* 1.3 61.1 + - - +
361R LEU* 2.8 22.5 + - - +
362R LYS* 3.2 43.0 + - + +
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Residues in contact with THR 359 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181R MET* 3.5 28.5 - - + -
186R PHE* 3.8 21.3 - - + -
196R GLY* 5.7 2.5 - - - -
279R LEU* 5.3 3.1 - - + -
355R LYS* 2.6 28.6 + - - +
356R LEU* 3.5 4.7 - - - -
358R GLU* 1.3 79.2 + - - +
360R SER* 1.3 62.7 + - - +
361R LEU 2.9 1.4 + - - -
362R LYS* 3.0 18.9 + - - +
363R LEU* 3.3 23.5 + - + +
385R PRO* 3.9 19.1 - - + -
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Residues in contact with SER 360 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199R TYR* 2.7 36.9 + - - -
279R LEU* 4.0 20.1 - - - +
280R ASN* 4.9 0.9 - - - -
283R ILE* 3.4 26.0 - - - +
356R LEU 2.9 8.1 + - - -
357R PHE 2.7 16.4 + - - -
359R THR* 1.3 77.6 - - - +
361R LEU* 1.3 57.7 + - - +
362R LYS 3.4 0.4 + - - -
363R LEU* 4.4 2.2 - - - -
392R SER* 5.0 0.3 - - - -
395R GLN* 2.8 28.7 + - - +
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Residues in contact with LEU 361 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332R TRP* 4.5 8.2 - - + -
337R ARG* 3.1 37.6 + - + -
357R PHE* 3.8 27.6 - - + +
358R GLU 2.8 10.3 + - - +
360R SER* 1.3 80.7 + - - +
362R LYS* 1.3 60.0 + - - +
363R LEU 3.8 0.4 - - - -
387R LEU 4.3 1.6 - - - +
388R GLU* 5.6 1.0 - - - -
389R VAL* 5.6 4.2 + - - +
390R GLY 4.7 15.3 - - - +
391R LEU* 4.2 20.9 - - + -
392R SER* 4.9 7.6 - - - +
395R GLN* 3.5 42.0 - - + +
401R MET* 4.3 13.5 - - + -
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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