Contacts of the helix formed by residues 347 - 361 (chain A) in PDB entry 4L0D
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 GLY 347 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335A ALA* 3.9 2.8 - - - +
346A CYS* 1.3 80.1 - - - +
348A GLY* 1.3 65.2 + - - -
349A SER 3.2 2.5 - - - -
350A ALA* 3.3 17.9 - - - +
351A GLY 3.4 3.1 + - - -
376A ASP* 2.5 22.9 + - - -
377A SER 3.8 0.9 - - - -
381A TYR* 3.4 27.8 - - - -
385A PHE* 4.3 2.2 - - - -
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Residues in contact with GLY 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A VAL* 4.4 6.7 - - - -
331A ALA* 3.7 4.1 - - - +
332A PHE* 4.3 23.1 - - - -
335A ALA* 4.1 12.3 - - - -
347A GLY* 1.3 71.7 - - - -
349A SER* 1.3 59.6 + - - +
351A GLY* 2.8 17.2 + - - -
352A SER* 2.9 17.9 + - - -
381A TYR* 3.7 10.5 - - - -
385A PHE* 3.9 5.1 - - - -
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Residues in contact with SER 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A SER* 3.4 2.8 + - - -
303A VAL* 4.3 9.0 - - - +
304A GLU 4.4 6.8 + - - -
306A ILE* 3.4 10.5 - - - +
348A GLY* 1.3 76.6 - - - +
350A ALA* 1.3 62.6 + - - +
352A SER* 3.1 12.4 + - - -
353A THR* 2.9 25.7 + - - -
375A PRO* 3.3 10.8 - - - +
376A ASP* 4.2 3.1 - - - -
381A TYR* 5.2 1.6 - - - -
601A PLP 2.5 50.9 + - - -
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Residues in contact with ALA 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A LEU* 4.5 1.8 - - + -
346A CYS* 3.7 19.7 - - + -
347A GLY 3.3 14.2 + - - +
349A SER* 1.3 78.7 - - - +
351A GLY* 1.3 62.8 - - - +
353A THR* 3.1 4.8 + - - -
354A VAL* 2.9 29.0 + - - +
374A LEU* 3.5 33.7 - - + -
375A PRO* 3.6 13.2 - - + +
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Residues in contact with GLY 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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331A ALA* 3.3 22.2 - - - -
334A PHE* 3.4 8.1 - - - +
335A ALA* 3.8 17.2 - - - +
338A LEU* 5.0 1.1 - - - +
347A GLY 3.4 2.4 + - - -
348A GLY 2.8 10.7 + - - -
350A ALA* 1.3 79.0 - - - +
352A SER* 1.3 61.2 + - - +
354A VAL* 3.9 1.5 - - - -
355A ALA* 2.9 25.1 + - - +
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Residues in contact with SER 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A SER* 5.1 0.4 - - - -
280A VAL* 4.4 5.8 - - - -
303A VAL* 4.1 5.7 - - - +
306A ILE* 3.9 21.5 - - - +
326A SER* 3.8 23.1 + - - -
331A ALA* 3.2 26.4 - - - +
348A GLY 2.9 7.8 + - - -
349A SER 3.2 8.2 + - - -
351A GLY* 1.3 74.1 - - - +
353A THR* 1.3 65.0 + - - +
355A ALA* 3.1 6.9 + - - +
356A VAL* 2.9 25.6 + - - +
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Residues in contact with THR 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A VAL* 3.6 27.8 - - + +
253A ALA* 4.3 4.3 - - - -
254A SER* 3.3 20.5 + - - +
280A VAL* 4.4 8.5 - - - -
349A SER 2.9 14.6 + - - -
350A ALA* 3.1 8.0 + - - -
352A SER* 1.3 77.1 - - - +
354A VAL* 1.3 58.8 + - - +
356A VAL* 3.3 5.4 + - - +
357A ALA* 2.9 24.3 + - - +
372A VAL* 3.5 23.6 - - + -
373A ILE 3.6 17.8 + - - +
375A PRO* 4.6 0.2 - - - +
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Residues in contact with VAL 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ILE* 5.8 5.2 - - + -
95A ILE* 4.6 7.9 - - + -
105A LEU* 5.1 10.8 - - + -
107A ALA* 6.0 0.7 - - + -
334A PHE* 3.9 19.3 - - + -
338A LEU* 4.1 28.5 - - + -
350A ALA 2.9 16.9 + - - +
351A GLY 4.1 2.2 - - - +
353A THR* 1.3 74.1 - - - +
355A ALA* 1.3 59.6 + - - +
357A ALA* 2.8 25.8 + - + +
358A VAL* 2.9 24.6 + - + +
372A VAL* 3.8 23.8 - - + -
374A LEU* 4.0 9.2 - - + -
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Residues in contact with ALA 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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326A SER* 5.6 0.2 - - - -
330A GLU* 4.1 29.1 - - + +
334A PHE* 3.6 34.5 - - + -
351A GLY 2.9 19.2 + - - +
352A SER* 3.2 10.1 - - - +
354A VAL* 1.3 77.4 - - - +
356A VAL* 1.3 58.2 + - + +
358A VAL* 3.1 18.4 - - - +
359A LYS* 4.1 9.4 + - - +
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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
----------------------------------------------------------
252A VAL* 3.9 9.6 - - + -
278A ILE* 4.1 8.5 - - + -
280A VAL* 3.5 41.1 - - + -
324A PHE* 3.6 40.2 - - + +
325A LYS 4.8 2.7 - - - +
326A SER* 4.4 10.5 - - - -
330A GLU* 5.6 2.2 - - - +
352A SER 2.9 8.9 + - - +
353A THR 3.5 7.2 - - - +
355A ALA* 1.3 77.6 - - - +
357A ALA* 1.3 67.6 + - - +
359A LYS* 2.9 18.3 + - - +
360A ALA* 2.9 14.7 + - + -
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Residues in contact with ALA 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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101A LEU* 4.8 1.3 - - - -
105A LEU* 4.6 11.2 - - + -
252A VAL* 4.1 16.4 - - + -
353A THR 2.9 9.4 + - - +
354A VAL* 2.8 14.6 + - + +
356A VAL* 1.3 77.3 - - - +
358A VAL* 1.3 56.7 + - + +
360A ALA* 4.6 1.1 - - - +
361A ALA* 2.9 36.2 + - - +
370A CYS* 4.8 1.3 - - - -
372A VAL* 3.5 31.9 - - + -
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Residues in contact with VAL 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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95A ILE* 4.4 13.0 - - + +
99A PHE* 3.8 36.5 - - + +
101A LEU* 3.4 34.6 - - + +
105A LEU* 5.4 2.9 - - + -
334A PHE* 3.8 25.4 - - + -
354A VAL* 2.9 17.0 + - + +
355A ALA 3.1 21.5 - - - +
357A ALA* 1.3 73.1 - - + +
359A LYS* 1.3 72.2 + - - +
362A GLN* 3.5 11.4 + - - +
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Residues in contact with LYS 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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99A PHE* 4.9 12.5 - - - -
324A PHE* 4.3 17.0 - - + -
330A GLU* 5.6 5.5 + - - +
334A PHE* 5.4 2.8 - - - -
355A ALA 4.1 10.4 + - - +
356A VAL* 2.9 9.1 + - - +
358A VAL* 1.3 92.6 + - - +
360A ALA* 1.3 65.8 + - - +
361A ALA 3.1 1.6 - - - -
362A GLN* 3.0 28.8 + - + +
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Residues in contact with ALA 360 (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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250A MET* 3.6 27.9 - - + +
252A VAL* 5.2 0.7 - - + -
278A ILE* 4.2 15.5 - - + -
324A PHE* 3.7 33.4 - - + -
356A VAL* 2.9 13.8 + - + +
357A ALA* 4.3 2.9 - - - +
359A LYS* 1.3 80.0 - - - +
361A ALA* 1.3 60.8 + - - +
362A GLN 3.2 1.1 + - - -
363A GLU* 3.8 12.8 + - - +
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Residues in contact with ALA 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LEU* 3.9 23.9 - - + +
102A LYS 5.8 0.3 + - - -
103A CYS* 4.2 12.2 - - - -
250A MET* 3.8 11.0 - - - -
357A ALA 2.9 19.2 + - - +
359A LYS 3.1 0.2 + - - -
360A ALA* 1.3 74.4 - - - +
362A GLN* 1.3 64.8 + - - +
363A GLU 3.1 3.1 - - - -
364A LEU* 3.0 30.7 + - + +
370A CYS* 4.2 15.3 - - + -
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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