Contacts of the helix formed by residues 358 - 371 (chain I) in PDB entry 6ASX
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 ASP 358 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211I ARG* 4.6 9.7 - - - +
356I THR* 5.1 0.2 + - - -
357I ASN* 1.3 90.0 + - + +
359I ARG* 1.3 60.9 + - + +
360I LEU* 3.6 17.0 + - - +
361I SER* 2.8 33.0 + - - -
362I ALA* 2.9 28.5 + - - +
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Residues in contact with ARG 359 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211I ARG* 4.1 21.0 + - - +
212I ALA* 4.3 14.4 + - - +
214I ASN* 4.1 35.5 - - - +
358I ASP* 1.3 78.1 - - + +
360I LEU* 1.3 56.7 + - - +
362I ALA* 3.4 4.1 + - - +
363I LEU* 2.9 45.9 + - + +
378I ARG* 4.4 12.7 - - - +
382I GLU* 2.9 34.6 + - - +
385I PHE* 6.3 1.0 - - - -
386I GLU* 5.1 8.7 + - - +
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Residues in contact with LEU 360 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358I ASP* 3.3 15.4 + - - +
359I ARG* 1.3 79.7 - - - +
361I SER* 1.3 58.2 + - - +
363I LEU* 3.2 14.6 + - + +
364I VAL* 2.9 44.1 + - + +
377I THR 5.5 0.2 - - - -
378I ARG* 3.4 65.2 - - + +
381I ALA* 5.9 0.7 - - + -
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Residues in contact with SER 361 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356I THR* 3.3 23.6 - - - +
357I ASN* 3.9 9.0 - - - -
358I ASP* 2.8 31.0 + - - -
360I LEU* 1.3 70.4 - - - +
362I ALA* 1.3 60.2 + - - +
364I VAL* 3.3 9.9 + - - +
365I GLU* 2.9 28.4 + - - +
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Residues in contact with ALA 362 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208I ILE* 3.6 41.8 - - + +
211I ARG* 4.1 5.8 - - + -
212I ALA* 4.1 14.4 - - + +
356I THR* 4.7 1.9 - - - +
358I ASP 2.9 18.1 + - - +
359I ARG 3.6 5.6 - - - +
360I LEU 3.3 0.2 - - - -
361I SER* 1.3 76.6 - - - +
363I LEU* 1.3 56.6 + - - +
365I GLU* 3.3 2.3 + - - +
366I ILE* 3.0 36.3 + - - +
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Residues in contact with LEU 363 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212I ALA* 4.9 11.0 - - + +
359I ARG* 2.9 44.5 + - + +
360I LEU* 3.2 17.5 + - + +
362I ALA* 1.3 75.3 - - + +
364I VAL* 1.3 57.4 + - - +
366I ILE* 3.5 6.1 + - + +
367I TYR* 2.9 30.7 + - - +
378I ARG* 6.0 0.4 - - - +
381I ALA* 3.7 22.9 - - + +
382I GLU* 3.7 29.2 - - + +
385I PHE* 3.8 38.1 - - + -
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Residues in contact with VAL 364 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360I LEU* 2.9 32.6 + - + +
361I SER* 3.5 12.6 - - - +
362I ALA 3.3 0.2 - - - -
363I LEU* 1.3 77.5 - - + +
365I GLU* 1.3 58.6 + - - +
367I TYR* 3.3 5.7 + - - +
368I ARG* 2.9 39.7 + - + +
376I PRO* 3.8 32.7 - - + +
377I THR 5.9 1.8 - - - +
381I ALA* 5.1 1.8 - - + -
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Residues in contact with GLU 365 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202I ARG* 3.2 26.8 + - - -
204I LEU* 4.0 19.0 - - + +
205I PRO* 6.3 0.2 - - + -
208I ILE* 3.7 28.5 - - + -
355I PRO* 5.8 4.6 - - + +
356I THR* 4.6 8.8 - - + +
361I SER 2.9 17.1 + - - +
362I ALA 3.3 0.4 + - - +
364I VAL* 1.3 79.9 - - - +
366I ILE* 1.3 56.9 + - - +
368I ARG* 2.6 34.0 + - - +
369I MET* 2.9 28.5 + - - +
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Residues in contact with ILE 366 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198I ILE* 5.0 9.0 - - + -
204I LEU* 4.4 16.2 - - + -
208I ILE* 4.6 11.2 - - + +
209I ILE* 4.7 10.1 - - + -
212I ALA* 3.8 27.8 - - + -
362I ALA 3.0 21.4 + - - +
363I LEU* 3.9 7.6 - - + +
365I GLU* 1.3 75.9 - - - +
367I TYR* 1.3 58.3 + - - +
369I MET* 3.3 11.5 + - + +
370I MET* 2.9 40.3 + - + +
384I LEU* 5.2 4.0 - - + -
385I PHE* 4.3 29.2 - - + -
388I LEU* 5.0 5.4 - - + -
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Residues in contact with TYR 367 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363I LEU 2.9 19.1 + - - +
364I VAL* 3.7 5.6 - - - +
366I ILE* 1.3 77.8 - - - +
368I ARG* 1.3 57.5 + - - +
371I ARG* 2.9 49.4 + - + +
374I GLU* 3.2 39.4 + - + -
375I PRO 4.0 7.2 + - - -
376I PRO* 3.6 33.9 - - + -
380I ALA* 3.9 31.5 - - + +
381I ALA* 3.7 21.5 - - + -
384I LEU* 3.6 28.3 - - + -
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Residues in contact with ARG 368 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202I ARG* 4.6 11.3 + - - +
364I VAL* 2.9 26.6 + - + +
365I GLU* 2.6 39.8 + - - +
367I TYR* 1.3 75.2 - - + +
369I MET* 1.3 66.1 + - - +
371I ARG 3.7 12.6 - - - +
372I PRO* 3.8 15.6 - - + +
373I GLY 5.5 3.6 - - - +
374I GLU 5.7 4.7 - - - +
376I PRO* 6.0 5.8 - - + -
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Residues in contact with MET 369 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197I ARG* 5.9 0.2 - - - -
198I ILE* 3.8 35.9 - - + +
201I ARG* 3.7 40.6 + - + +
202I ARG* 3.8 36.4 + - + +
204I LEU* 3.7 37.5 - - + -
365I GLU 2.9 18.6 + - - +
366I ILE* 3.3 6.0 + - + +
368I ARG* 1.3 79.9 - - - +
370I MET* 1.3 78.9 + - + +
372I PRO* 5.0 2.6 - - - +
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Residues in contact with MET 370 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198I ILE* 4.1 15.0 - - + -
199I ASP* 4.7 11.0 - - - +
201I ARG* 3.9 42.7 + - - +
366I ILE* 2.9 21.4 + - + +
369I MET* 1.3 101.4 - - + +
371I ARG* 1.3 63.8 + - + +
372I PRO* 3.3 10.7 - - - +
384I LEU* 3.8 24.7 - - + -
388I LEU* 4.5 27.8 - - + -
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Residues in contact with ARG 371 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367I TYR* 2.9 53.3 + - + +
368I ARG* 3.7 6.7 - - - +
370I MET* 1.3 81.0 - - + +
372I PRO* 1.3 68.2 - - - +
374I GLU* 3.3 34.2 + - + +
380I ALA 5.9 0.2 + - - -
384I LEU* 4.2 24.9 - - + +
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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