Contacts of the helix formed by residues 349 - 360 (chain A) in PDB entry 1ACL
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 ARG 349 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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348A SER* 1.3 75.0 - - - +
350A GLU* 1.3 63.5 + - - +
352A PHE* 3.5 19.2 - - - +
353A MET* 3.2 43.4 + - - +
372A THR* 3.5 27.9 - - - +
376A THR* 3.5 21.2 - - - +
378A TRP* 4.4 9.1 - - - -
381A ASP* 2.9 45.1 + - - +
382A ASN* 3.8 19.0 - - + +
387A ASN* 3.2 25.4 - - - +
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Residues in contact with GLU 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348A SER* 2.9 10.8 - - - +
349A ARG* 1.3 82.4 - - - +
351A ASP* 1.3 62.5 + - - +
352A PHE 3.1 0.4 - - - -
353A MET* 3.4 3.9 + - - +
354A SER* 2.9 27.2 + - - +
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Residues in contact with ASP 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337A PRO* 3.4 37.7 - - + +
338A GLY* 3.9 12.8 - - - -
347A ILE* 4.0 12.6 - - + +
348A SER* 2.9 23.2 + - - +
350A GLU* 1.3 81.2 - - - +
352A PHE* 1.3 59.5 + - - +
354A SER* 3.5 11.8 + - - -
355A GLY* 2.9 24.1 + - - -
391A LEU* 4.4 2.6 - - - +
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Residues in contact with PHE 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347A ILE* 3.6 8.3 - - + +
348A SER 2.9 18.7 + - - +
349A ARG* 3.5 36.3 - - - +
350A GLU 3.1 0.2 - - - -
351A ASP* 1.3 74.4 - - - +
353A MET* 1.3 71.9 + - + +
354A SER 3.0 1.6 - - - -
355A GLY* 2.9 2.1 + - - -
356A VAL* 2.8 42.3 + - + +
372A THR* 4.0 14.8 - - + -
375A TYR* 4.9 10.5 - - + -
376A THR* 3.8 16.2 - - + -
387A ASN* 3.5 42.4 - - + -
390A GLY* 4.8 6.1 - - - -
391A LEU* 4.1 20.1 - - + +
394A ILE* 4.6 8.1 - - + -
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Residues in contact with MET 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349A ARG* 3.2 40.5 + - - +
350A GLU* 3.4 3.8 + - - +
352A PHE* 1.3 88.2 - - + +
354A SER* 1.3 60.0 + - - +
356A VAL* 3.5 14.6 - - + +
357A LYS* 3.4 28.9 + - - +
372A THR* 5.1 5.6 - - + +
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Residues in contact with SER 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A PRO* 3.8 18.6 - - - +
350A GLU* 2.9 22.4 + - - +
351A ASP* 3.5 14.1 + - - -
352A PHE 3.0 1.0 - - - -
353A MET* 1.3 75.5 - - - +
355A GLY* 1.3 67.9 + - - +
357A LYS* 3.2 24.3 + - - +
358A LEU* 3.2 17.6 + - - +
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Residues in contact with GLY 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332A LEU* 5.6 0.6 - - - +
336A ALA* 4.9 4.7 - - - -
337A PRO* 4.7 4.9 - - - +
351A ASP 2.9 15.6 + - - -
352A PHE 2.9 4.8 + - - -
354A SER* 1.3 74.1 - - - +
356A VAL* 1.3 65.4 + - - -
358A LEU* 2.8 25.8 + - - +
359A SER* 3.0 13.0 + - - -
391A LEU* 3.8 19.5 - - - -
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Residues in contact with VAL 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352A PHE* 2.8 31.8 + - + +
353A MET* 3.5 20.2 - - + +
355A GLY* 1.3 71.1 - - - -
357A LYS* 1.3 65.5 + - + +
359A SER* 3.7 7.9 - - - -
360A VAL* 3.1 25.7 + - + +
368A LEU* 3.8 21.7 - - + +
371A VAL* 5.0 7.6 - - + -
372A THR* 4.5 14.8 - - - +
391A LEU* 3.5 16.3 - - + +
394A ILE* 3.6 22.7 - - + -
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Residues in contact with LYS 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A ASP 4.3 3.0 - - - +
353A MET* 3.4 22.1 + - - +
354A SER* 3.2 19.5 + - - +
355A GLY 2.9 1.6 + - - -
356A VAL* 1.3 80.9 - - + +
358A LEU* 1.3 65.4 + - + +
359A SER 3.2 0.3 + - - -
360A VAL 3.5 6.2 + - - +
361A PRO* 3.6 15.6 - - - +
368A LEU* 3.8 33.2 - - + -
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Residues in contact with LEU 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A ASP* 3.6 47.6 - - + +
286A SER* 3.2 12.1 - - - +
287A ILE* 2.8 36.3 + - + +
335A GLY 3.3 27.6 - - - +
336A ALA* 3.9 7.6 - - + -
337A PRO* 3.9 23.1 - - + -
354A SER 3.2 11.0 + - - +
355A GLY 2.8 7.5 + - - +
357A LYS* 1.3 80.5 - - + +
359A SER* 1.3 61.0 + - - +
361A PRO* 3.7 6.1 - - - +
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Residues in contact with SER 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A ILE* 3.8 12.6 - - - +
289A ARG* 4.4 3.3 + - - -
332A LEU* 4.9 1.9 - - - +
355A GLY 3.0 14.7 + - - -
356A VAL* 3.7 8.3 - - - -
357A LYS 3.1 0.8 - - - -
358A LEU* 1.3 74.0 - - - +
360A VAL* 1.3 59.3 + - - +
361A PRO* 3.0 13.3 - - - +
391A LEU* 4.4 4.0 - - - +
394A ILE* 4.0 24.5 - - - -
395A VAL* 3.5 26.3 - - - +
398A HIS* 3.6 20.5 - - - -
399A ASN* 4.4 3.0 + - - +
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Residues in contact with VAL 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A VAL* 3.1 14.6 + - - +
357A LYS 3.8 3.4 - - - +
359A SER* 1.3 88.6 - - - +
361A PRO* 1.3 57.9 - - - +
362A HIS* 2.8 32.9 + - + +
363A ALA* 2.9 36.3 + - + +
368A LEU* 4.4 7.2 - - + +
371A VAL* 4.3 11.4 - - + -
394A ILE* 4.3 6.1 - - + -
398A HIS* 4.8 1.6 - - + -
524A TRP* 3.6 38.8 - - + -
528A LEU* 4.3 7.9 - - + -
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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