Contacts of the helix formed by residues 350 - 361 (chain P) 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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348P GLY 3.9 0.8 + - - -
349P TYR* 1.3 69.9 - - - +
351P PRO* 1.3 72.4 - - + +
352P TRP* 3.1 39.0 - - + +
353P TRP* 3.0 5.3 + - + +
354P VAL* 3.0 22.2 + - - +
660P SER 3.8 9.0 - - - +
661P VAL* 3.1 20.6 + - - +
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Residues in contact with PRO 351 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179P ASN* 5.7 0.2 - - - +
182P LEU* 4.0 21.1 - - + +
345P LEU* 3.8 22.6 - - + +
349P TYR 3.1 8.3 - - - +
350P ALA* 1.3 83.7 - - + +
352P TRP* 1.3 55.6 + - + +
354P VAL* 3.1 3.5 + - - +
355P LYS* 2.7 35.9 + - - +
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Residues in contact with TRP 352 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174P ALA* 3.9 8.5 - - + -
175P GLU* 3.2 63.8 + - + +
178P GLY* 3.6 4.5 - - - -
179P ASN* 3.5 35.9 - - - +
182P LEU* 3.7 10.4 - - - +
350P ALA* 3.1 21.9 - - + +
351P PRO* 1.3 82.7 - - + +
353P TRP* 1.3 96.1 + + + +
355P LYS* 3.3 3.6 + - - +
356P LEU* 3.0 28.0 + - + +
657P PHE* 3.9 13.7 - + - -
660P SER* 3.4 35.0 + - - -
661P VAL* 3.3 20.9 - - + -
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Residues in contact with TRP 353 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135P PHE* 4.7 6.7 - + - -
282P PRO* 3.1 24.1 + - + +
283P ILE* 4.2 11.4 - - + +
286P VAL* 3.3 39.1 - - + +
344P LEU* 4.1 20.0 - - + -
349P TYR* 4.2 12.8 - + - -
350P ALA* 3.0 10.8 + - + +
352P TRP* 1.3 97.4 - + + +
354P VAL* 1.3 78.6 + - + +
356P LEU* 3.1 12.3 + - + +
357P PHE* 2.9 58.8 + + + -
657P PHE* 3.8 10.3 - + - -
661P VAL* 3.6 31.4 - - + -
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Residues in contact with VAL 354 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341P CYS* 3.5 44.0 - - + +
344P LEU* 4.3 9.2 - - + -
345P LEU* 3.7 24.5 - - + -
349P TYR* 3.7 25.1 - - + -
350P ALA 3.0 15.8 + - - +
351P PRO 3.5 4.7 - - - +
353P TRP* 1.3 86.0 - - + +
355P LYS* 1.3 58.9 + - - +
357P PHE* 3.2 3.0 + - + +
358P GLU* 2.8 28.5 + - + +
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Residues in contact with LYS 355 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178P GLY 4.3 1.6 - - - +
181P MET* 3.6 39.9 - - + -
182P LEU* 3.5 31.4 - - + +
186P PHE* 4.1 17.2 - - - -
351P PRO 2.7 13.6 + - - +
352P TRP* 3.4 8.7 - - - +
354P VAL* 1.3 78.9 - - - +
356P LEU* 1.3 52.5 + - - +
358P GLU* 3.1 34.4 + - - +
359P THR* 2.6 39.6 + - - +
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Residues in contact with LEU 356 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174P ALA* 3.7 29.2 - - + +
178P GLY* 3.9 10.8 - - - +
181P MET* 2.9 40.6 - - + -
195P MET* 4.0 16.8 - - - -
279P LEU* 4.0 16.2 - - + +
282P PRO* 4.4 13.0 - - + -
283P ILE* 4.7 5.8 - - + -
352P TRP* 3.0 33.5 + - + +
353P TRP* 3.3 12.1 - - + +
355P LYS* 1.3 74.2 - - - +
357P PHE* 1.3 65.5 + - - +
359P THR* 3.2 3.5 + - - -
360P SER* 2.9 24.9 + - - -
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Residues in contact with PHE 357 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135P PHE* 5.2 7.9 - + - -
283P ILE* 4.1 21.0 - - + +
337P ARG* 5.3 1.6 - - - -
340P ILE* 4.4 17.0 - - + -
341P CYS* 4.0 15.7 - - - -
344P LEU* 4.9 4.7 - - + -
353P TRP* 2.9 47.2 + + + +
354P VAL* 3.4 8.1 - - - +
356P LEU* 1.3 77.4 - - - +
358P GLU* 1.3 63.4 + - - +
360P SER* 2.7 24.1 + - - -
361P LEU* 3.5 23.5 + - + +
395P GLN* 3.7 18.4 - - - -
397P ALA* 4.4 9.6 - - + -
401P MET* 3.6 34.3 - - + -
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Residues in contact with GLU 358 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186P PHE* 5.8 0.2 - - - -
337P ARG* 3.7 13.4 - - - +
338P ASP* 4.4 6.1 - - - +
341P CYS* 3.5 29.7 - - - +
354P VAL 2.8 16.7 + - - +
355P LYS* 3.1 37.4 + - - +
357P PHE* 1.3 73.5 - - - +
359P THR* 1.3 61.3 + - - +
361P LEU* 2.8 22.3 + - - +
362P LYS* 3.2 43.5 + - + +
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Residues in contact with THR 359 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181P MET* 3.5 29.7 - - + -
186P PHE* 3.8 20.2 - - + -
196P GLY* 5.7 2.2 - - - -
279P LEU* 5.3 4.3 - - + -
355P LYS* 2.6 29.2 + - - +
356P LEU 3.5 4.3 - - - -
358P GLU* 1.3 79.4 + - - +
360P SER* 1.3 62.8 + - - +
361P LEU 2.9 1.8 + - - -
362P LYS* 3.0 19.5 + - - +
363P LEU* 3.3 23.8 + - + +
385P PRO* 3.9 19.1 - - + -
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Residues in contact with SER 360 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199P TYR* 2.7 36.2 + - - -
279P LEU* 4.0 19.7 - - - +
280P ASN* 4.9 1.3 - - - -
283P ILE* 3.4 25.7 - - - +
356P LEU 2.9 7.9 + - - -
357P PHE 2.7 16.5 + - - -
359P THR* 1.3 78.1 - - - +
361P LEU* 1.3 57.0 + - - +
362P LYS 3.4 0.2 - - - -
363P LEU* 4.4 2.0 - - - -
392P SER* 5.0 0.2 - - - -
395P GLN* 2.8 28.4 + - - +
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Residues in contact with LEU 361 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199P TYR* 6.0 0.2 - - - -
332P TRP* 4.5 8.9 - - + -
337P ARG* 3.1 37.7 + - + -
357P PHE* 3.8 28.5 - - + +
358P GLU 2.8 10.5 + - - +
360P SER* 1.3 80.3 + - - +
362P LYS* 1.3 58.1 + - - +
363P LEU 3.8 0.4 - - - -
387P LEU 4.3 1.6 - - - +
388P GLU* 5.6 1.2 - - - -
389P VAL* 5.6 4.4 + - - +
390P GLY 4.7 15.4 - - - +
391P LEU* 4.2 20.6 - - + -
392P SER* 4.9 7.4 - - - +
395P GLN* 3.5 43.5 - - + +
401P MET* 4.3 12.8 - - + -
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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