Contacts of the helix formed by residues 348 - 361 (chain H) in PDB entry 1F9E
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 TRP 348 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340H TYR* 3.0 57.2 + + + +
342H ASN* 5.3 2.7 - - + -
346H GLY 4.9 3.8 - - - -
347H THR* 1.3 72.7 - - - +
349H TYR* 1.3 62.8 + - - +
351H GLN* 4.2 1.8 - - - +
352H SER* 3.1 27.7 + - - -
377H VAL* 4.0 9.0 - - + +
381H LYS* 3.4 88.2 - - + +
383H GLY 4.6 0.4 - - - -
385H GLN* 3.6 42.0 - - + +
4401T ASP* 3.2 37.2 + - + -
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Residues in contact with TYR 349 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281G PHE* 3.8 15.8 - + + -
282G ILE 4.4 3.8 - - - -
283G GLN* 3.2 17.3 - - + +
330H GLY* 3.4 37.8 + - - -
331H MET 3.7 11.9 + - - -
332H ALA* 3.3 29.4 - - + -
347H THR* 3.2 1.0 - - - -
348H TRP* 1.3 80.0 - - - +
350H ILE* 1.3 72.7 + - + +
352H SER* 3.5 1.7 - - - -
353H LEU* 2.8 37.4 + - + +
370H LEU* 3.6 21.3 - - + +
373H VAL* 3.8 24.7 - - + -
377H VAL* 4.5 4.0 - - - -
385H GLN* 3.8 8.9 - - - +
387H PRO* 4.1 15.3 - - + -
389H PRO* 5.8 1.3 - - + +
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Residues in contact with ILE 350 (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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185G ASP* 3.3 34.5 - - + +
189G LEU* 3.7 29.2 - - + -
235G LEU* 4.1 12.3 - - + -
281G PHE* 4.9 8.7 - - + -
283G GLN* 3.8 24.9 - - + +
347H THR* 3.1 20.1 + - - +
349H TYR* 1.3 86.0 - - + +
351H GLN* 1.3 67.1 + - - +
353H LEU* 3.0 17.5 + - + +
354H CYS* 2.8 26.4 + - - -
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Residues in contact with GLN 351 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184G LEU* 3.7 22.0 + - - +
185G ASP* 3.2 22.4 + - - +
188G ALA* 3.9 13.9 - - - +
345H GLU* 3.0 29.9 + - + +
346H GLY* 4.0 2.5 - - - +
347H THR 3.1 18.4 + - - +
348H TRP* 4.2 2.2 - - - +
350H ILE* 1.3 76.8 - - - +
352H SER* 1.3 59.1 + - - +
354H CYS* 3.2 3.8 + - - +
355H GLN* 2.9 46.0 + - - +
358H ARG* 5.5 3.8 + - - -
381H LYS* 6.4 1.1 - - - -
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Residues in contact with SER 352 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348H TRP 3.1 19.4 + - - -
349H TYR 3.5 2.9 - - - -
351H GLN* 1.3 78.9 - - - +
353H LEU* 1.3 62.3 + - - +
355H GLN* 3.2 14.9 + - - +
356H SER* 2.8 27.9 + - - -
373H VAL* 3.5 21.1 - - - +
376H GLU* 3.8 23.8 - - - +
377H VAL* 4.0 6.7 - - - +
381H LYS* 5.3 5.6 - - - +
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Residues in contact with LEU 353 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189G LEU* 4.9 7.9 - - + -
281G PHE* 3.4 54.7 - - + -
349H TYR* 2.8 24.5 + - + +
350H ILE* 3.0 23.5 + - + +
352H SER* 1.3 71.5 - - - +
354H CYS* 1.3 56.3 + - - +
356H SER* 3.4 1.6 + - - -
357H LEU* 2.8 63.8 + - + +
366H ILE* 5.3 1.1 - - + -
369H ILE* 4.9 3.8 - - + -
370H LEU* 4.4 15.0 - - + -
373H VAL* 4.1 15.8 - - + +
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Residues in contact with CYS 354 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188G ALA* 3.6 33.0 - - + -
189G LEU* 3.7 23.8 - - - -
192G THR* 3.4 27.1 - - - +
350H ILE* 2.8 16.1 + - - +
351H GLN* 3.7 6.7 - - - +
353H LEU* 1.3 74.8 - - - +
355H GLN* 1.3 66.6 + - - +
357H LEU* 3.0 8.2 + - - +
358H ARG* 2.8 36.0 + - - +
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Residues in contact with GLN 355 (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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351H GLN* 2.9 43.5 + - + +
352H SER* 3.6 16.0 - - - +
354H CYS* 1.3 72.2 - - - +
356H SER* 1.3 64.5 + - - +
358H ARG* 3.2 21.7 + - - +
359H GLU* 3.3 21.9 + - - +
381H LYS* 5.6 7.7 - - - +
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Residues in contact with SER 356 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352H SER* 2.8 17.4 + - - -
353H LEU 3.7 3.4 - - - -
355H GLN* 1.3 78.2 - - - +
357H LEU* 1.3 64.5 + - - +
359H GLU* 3.4 5.2 + - - +
360H ARG* 2.9 30.1 + - - +
369H ILE* 3.2 27.5 + - - +
372H GLU* 2.8 29.9 + - - +
373H VAL* 4.2 10.3 - - - -
376H GLU* 6.5 0.9 - - - -
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Residues in contact with LEU 357 (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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192G THR* 3.8 17.7 - - + -
193G PHE* 3.7 29.4 - - + -
196G LEU* 4.6 3.4 - - + +
281G PHE* 5.2 1.3 - - + -
353H LEU* 2.8 50.3 + - + +
354H CYS* 3.0 6.3 + - - +
356H SER* 1.3 73.6 - - - +
358H ARG* 1.3 62.8 + - - +
360H ARG* 4.7 0.4 - - - -
361H CYS* 3.0 56.0 + - - +
366H ILE* 5.1 5.4 - - + -
369H ILE* 3.9 19.3 - - + -
400H PHE* 4.5 14.1 - - + -
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Residues in contact with ARG 358 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188G ALA* 4.8 11.2 - - - +
191G THR* 4.3 17.6 - - - +
192G THR* 3.8 27.1 + - + +
195G GLU* 3.8 29.7 + - - +
351H GLN* 5.5 3.2 + - - -
354H CYS* 2.8 33.4 + - - +
355H GLN* 3.7 14.8 - - - +
357H LEU* 1.3 73.2 - - - +
359H GLU* 1.3 56.9 + - - +
362H PRO* 2.9 24.9 - - - +
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Residues in contact with GLU 359 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355H GLN* 3.3 20.5 + - - +
356H SER* 3.6 7.7 - - - +
358H ARG* 1.3 75.2 - - - +
360H ARG* 1.3 64.1 + - + +
362H PRO* 3.0 41.8 + - - +
372H GLU* 3.7 18.0 - - - +
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Residues in contact with ARG 360 (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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149E LEU 5.1 2.0 + - - -
150E ASP* 2.8 36.8 + - - +
356H SER* 2.9 23.6 + - - +
359H GLU* 1.3 79.3 + - + +
361H CYS* 1.3 58.2 + - - +
362H ARG* 2.8 50.9 + - - +
363H GLY 3.2 6.6 + - - -
364H ASP* 2.8 44.9 + - + +
368H THR* 3.7 16.4 - - - +
369H ILE* 3.7 23.1 - - + +
372H GLU* 2.4 45.0 + - - +
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Residues in contact with CYS 361 (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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196G LEU* 4.0 15.9 - - + -
357H LEU* 3.0 43.4 + - - +
360H ARG* 1.3 76.0 - - - +
362H PRO* 1.3 72.4 - - + +
363H GLY* 2.8 15.7 + - - +
364H ASP 4.5 8.1 - - - +
369H ILE* 3.8 9.9 - - - -
399H VAL* 5.2 0.4 - - - +
400H PHE* 3.4 43.5 - - - +
401H PRO* 4.7 6.1 - - - +
402H SER* 4.7 1.2 + - - -
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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