Contacts of the helix formed by residues 341 - 353 (chain A) in PDB entry 5A19
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 341 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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334A HIS* 3.9 2.9 - - - -
339A GLN 4.0 0.8 + - - -
340A LYS* 1.3 76.4 - - - +
342A GLU* 1.3 63.6 - - - +
343A ARG* 3.4 10.2 + - - +
344A GLU* 2.8 41.8 + - - +
345A LEU* 3.1 21.1 + - - +
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Residues in contact with GLU 342 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332A ILE* 3.4 29.5 - - + +
333A PHE* 3.4 14.0 - - - +
334A HIS* 3.1 52.3 + - + +
335A TYR 4.3 2.3 + - - -
336A GLY 5.2 0.5 + - - -
341A SER* 1.3 73.4 - - - +
343A ARG* 1.3 56.7 + - - +
345A LEU* 3.4 7.2 + - - +
346A LEU* 3.0 28.4 + - - +
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Residues in contact with ARG 343 (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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341A SER* 3.2 9.4 + - - +
342A GLU* 1.3 77.8 - - - +
344A GLU* 1.3 62.8 + - - +
346A LEU* 3.4 14.3 + - + +
347A GLU* 3.1 48.6 + - + +
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Residues in contact with GLU 344 (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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339A GLN 4.7 0.7 - - - +
340A LYS* 3.3 30.9 + - + +
341A SER* 2.8 46.6 + - - +
343A ARG* 1.3 75.0 - - + +
345A LEU* 1.3 65.2 + - - +
347A GLU* 3.3 18.7 + - - +
348A ILE* 3.1 29.4 + - + +
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Residues in contact with LEU 345 (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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305A LEU* 4.6 9.8 - - + +
310A LEU* 3.9 34.8 - - + -
311A CYS* 4.7 10.3 - - - -
332A ILE* 4.0 19.7 - - + -
334A HIS* 3.5 40.4 - - + -
338A SER* 4.1 14.6 - - - +
340A LYS* 4.2 14.1 - - + -
341A SER 3.1 14.3 + - - +
342A GLU 3.8 6.7 - - - +
343A ARG 3.4 0.2 - - - -
344A GLU* 1.3 76.1 - - - +
346A LEU* 1.3 57.3 + - - +
348A ILE* 3.3 6.7 + - + +
349A VAL* 3.0 34.4 + - - +
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Residues in contact with LEU 346 (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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330A ILE* 3.5 53.4 - - + +
331A SER* 4.7 2.5 - - - -
332A ILE* 3.9 17.1 - - + +
342A GLU 3.0 14.6 + - - +
343A ARG* 3.5 17.9 - - + +
345A LEU* 1.3 76.3 - - - +
347A GLU* 1.3 56.7 + - + +
349A VAL* 3.2 4.9 + - + +
350A LYS* 3.0 55.7 + - + +
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Residues in contact with GLU 347 (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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343A ARG* 3.1 45.4 + - + +
344A GLU* 3.3 18.3 + - - +
346A LEU* 1.3 74.4 - - + +
348A ILE* 1.3 57.9 + - + +
350A LYS* 3.5 12.0 + - + +
351A LYS* 3.0 56.0 + - - +
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Residues in contact with ILE 348 (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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305A LEU* 4.7 3.1 - - + -
310A LEU* 4.2 19.3 - - + -
340A LYS* 4.0 27.6 - - + +
344A GLU* 3.1 18.3 + - + +
345A LEU* 3.6 10.5 - - + +
346A LEU 3.3 0.2 - - - -
347A GLU* 1.3 74.3 - - + +
349A VAL* 1.3 66.4 + - - +
351A LYS* 3.5 10.2 + - - +
352A ASN* 2.7 44.4 + - + +
393A LEU* 4.2 21.5 - - + -
395A TYR* 4.0 33.0 - - + -
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Residues in contact with VAL 349 (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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301A VAL* 3.7 36.8 - - + -
305A LEU* 4.1 16.6 - - + -
316A VAL* 5.8 0.4 - - + -
330A ILE* 4.6 21.1 - - + -
332A ILE* 3.9 16.4 - - + -
345A LEU 3.0 19.6 + - - +
346A LEU* 3.5 8.5 - - + +
348A ILE* 1.3 75.7 - - - +
350A LYS* 1.3 57.0 + - - +
352A ASN 3.0 1.6 + - - -
353A PHE* 2.8 49.5 + - + +
355A LEU* 5.0 6.1 - - + -
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Residues in contact with LYS 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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330A ILE* 4.8 14.6 - - + -
346A LEU* 3.0 50.0 + - + +
347A GLU* 3.7 11.0 - - + +
349A VAL* 1.3 77.7 - - - +
351A LYS* 1.3 61.6 + - + +
353A PHE 3.5 15.5 - - - +
401A PEG 4.0 35.7 + - - -
404A EDO 3.7 14.4 + - - -
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Residues in contact with LYS 351 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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347A GLU* 3.0 45.1 + - - +
348A ILE* 3.9 12.4 - - + +
349A VAL 3.3 0.2 - - - -
350A LYS* 1.3 76.7 - - + +
352A ASN* 1.3 65.5 + - - +
394A LYS* 5.0 9.8 + - - +
395A TYR* 5.9 5.8 - - - +
404A EDO 3.8 15.9 + - - -
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Residues in contact with ASN 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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348A ILE* 2.7 35.2 + - - +
349A VAL 3.0 2.0 + - - -
351A LYS* 1.3 83.9 - - - +
353A PHE* 1.3 68.4 - - + +
391A LYS* 3.2 29.7 + - + +
392A LYS 4.4 2.1 - - - +
393A LEU* 3.6 20.7 - - + +
394A LYS* 2.9 57.7 + - - +
404A EDO 4.6 6.9 + - - -
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Residues in contact with PHE 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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300A TRP* 3.8 30.5 - + - -
301A VAL* 3.7 36.6 - - + -
304A SER* 3.8 25.6 - - - -
305A LEU* 5.9 0.7 - - + -
349A VAL* 2.8 35.3 + - + +
350A LYS* 3.5 17.2 - - - +
351A LYS 3.8 0.6 - - - -
352A ASN* 1.3 77.5 - - + +
354A ASP* 1.3 59.8 + - - +
355A LEU* 3.9 21.2 + - + +
391A LYS* 3.6 31.6 - - + +
393A LEU* 3.7 22.2 - - + -
404A EDO 4.2 6.1 + - - -
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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