Contacts of the helix formed by residues 349 - 359 (chain A) in PDB entry 4D10
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 SER 349 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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307A LEU* 4.4 5.5 + - - +
344A ARG 4.3 3.2 + - - -
345A ASN* 3.4 27.7 + - - -
346A VAL 3.7 10.4 - - - +
347A ILE 3.2 6.6 - - - +
348A SER* 1.3 77.1 + - - +
350A SER* 1.3 58.4 + - - +
351A SER* 3.8 7.3 + - - -
352A PHE* 3.5 21.3 + - - +
353A LYS* 3.3 24.6 + - - +
248B GLU* 4.7 0.4 - - - -
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Residues in contact with SER 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 3.3 5.3 + - - -
349A SER* 1.3 71.9 - - - +
351A SER* 1.3 69.1 + - - +
353A LYS* 3.5 13.1 + - - +
354A LEU* 4.2 12.6 + - - +
215B LYS* 6.1 0.2 - - - -
248B GLU* 3.8 33.5 - - - +
250B GLU* 5.4 5.2 - - - -
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Residues in contact with SER 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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307A LEU 4.4 10.8 - - - -
308A LEU 5.2 4.6 + - - -
309A ALA 4.4 8.0 - - - +
310A SER* 4.9 10.4 - - - +
311A PHE 4.5 3.9 + - - +
349A SER* 3.8 6.6 + - - -
350A SER* 1.3 83.6 + - - +
352A PHE* 1.3 59.1 + - - +
354A LEU* 4.3 12.2 + - - +
355A PHE* 3.4 22.0 - - - -
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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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306A LEU 3.9 16.4 - - - -
307A LEU* 3.6 44.2 - - + +
309A ALA 5.3 0.2 - - - -
325A VAL* 3.9 12.1 - - + -
326A ALA* 3.7 31.9 - - - -
329A GLY* 4.1 3.6 - - - -
330A GLY* 3.8 18.4 - - - -
346A VAL* 4.7 5.4 - - + +
349A SER* 3.5 19.0 + - - +
351A SER* 1.3 75.4 - - - +
353A LYS* 1.3 53.4 + - - +
354A LEU 3.3 2.9 - - - -
355A PHE* 3.0 24.0 + + + +
356A LEU* 2.8 62.5 + - + +
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Residues in contact with LYS 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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347A ILE 4.2 15.9 - - - +
349A SER 3.3 19.5 + - - +
350A SER* 3.5 13.9 - - - +
351A SER 3.4 0.4 - - - -
352A PHE* 1.3 76.0 - - - +
354A LEU* 1.3 51.7 + - + +
356A LEU* 3.1 20.3 + - + +
357A GLU* 2.8 55.5 + - + +
363A ARG* 5.4 1.6 - - - +
367A PHE* 4.6 20.9 - - + -
215B LYS* 5.9 0.9 - - - +
247B ARG 5.3 4.9 + - - -
248B GLU* 3.7 33.0 - - - +
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Residues in contact with LEU 354 (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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311A PHE* 3.7 52.6 - - + -
350A SER 4.2 13.5 - - - +
351A SER* 4.4 6.1 - - - +
352A PHE 3.3 0.8 - - - -
353A LYS* 1.3 74.8 - - + +
355A PHE* 1.3 65.4 + - - +
357A GLU* 3.1 11.5 + - - +
358A LEU* 3.0 24.1 + - - +
212B LYS* 4.9 24.0 - - + +
215B LYS* 6.3 4.0 - - + -
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Residues in contact with PHE 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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309A ALA* 3.4 24.5 - - + -
310A SER 3.8 8.7 - - - -
311A PHE* 3.7 33.7 - + - -
313A HIS* 4.7 8.7 - + - -
322A PRO* 3.3 40.2 - - + -
325A VAL* 3.7 23.8 - - + -
326A ALA* 3.3 30.4 - - + +
351A SER 3.4 20.4 - - - -
352A PHE* 3.0 25.2 + + + +
354A LEU* 1.3 76.4 - - - +
356A LEU* 1.3 58.5 + - - +
358A LEU* 3.0 20.7 + - - +
359A GLU 3.3 5.5 + - - -
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Residues in contact with LEU 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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326A ALA* 5.0 2.7 - - + +
346A VAL* 3.9 19.5 - - + +
347A ILE* 5.4 1.1 - - - +
352A PHE* 2.8 42.1 + - + +
353A LYS* 3.1 27.1 + - + +
355A PHE* 1.3 76.3 - - - +
357A GLU* 1.3 56.9 + - - +
359A GLU 3.0 23.7 - - - +
360A PRO* 3.9 1.0 - - - +
362A VAL* 4.7 4.0 - - + -
363A ARG* 3.4 45.0 - - + +
366A ILE* 3.7 30.5 - - + -
367A PHE* 5.4 7.4 - - + -
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Residues in contact with GLU 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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353A LYS* 2.8 37.0 + - + +
354A LEU* 3.1 12.5 + - - +
356A LEU* 1.3 74.9 - - - +
358A LEU* 1.3 64.2 + - - +
359A GLU 3.5 0.2 - - - -
360A PRO* 4.5 7.5 - - - +
363A ARG* 3.2 37.1 + - - +
212B LYS* 3.4 41.7 + - - +
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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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311A PHE* 3.5 32.8 - - + -
322A PRO* 3.8 26.7 - - + +
323A SER* 4.0 22.0 - - - +
354A LEU 3.0 14.3 + - - +
355A PHE* 3.0 9.1 + - - +
357A GLU* 1.3 79.9 - - - +
359A GLU* 1.3 65.6 + - + +
360A PRO* 3.4 9.8 - - - +
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Residues in contact with GLU 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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87A TYR* 5.6 1.4 + - - -
323A SER* 3.7 40.0 - - - +
326A ALA* 4.5 4.5 - - + -
327A ILE* 3.8 22.3 - - + +
355A PHE 3.3 5.9 + - - +
356A LEU* 3.0 15.3 - - - +
358A LEU* 1.3 82.4 - - - +
360A PRO* 1.3 68.5 - - - +
361A GLN* 3.3 18.8 + - - +
362A VAL* 3.7 19.9 + - + +
363A ARG* 3.5 11.3 + - - +
384A MET* 5.0 4.2 - - - +
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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