Contacts of the helix formed by residues 340 - 354 (chain A) in PDB entry 3SRH
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 THR 340 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332A SER* 3.5 22.4 + - - +
339A PRO* 1.3 78.9 - - - +
341A ARG* 1.3 66.6 + - - +
342A ALA* 3.5 10.0 + - - +
343A GLU* 2.9 36.2 + - - +
344A GLY* 3.1 18.5 + - - -
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Residues in contact with ARG 341 (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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338A ARG* 6.1 0.8 - - - +
339A PRO 3.8 21.0 + - - -
340A THR* 1.3 72.1 - - - +
342A ALA* 1.3 59.9 + - - +
344A GLY* 3.5 2.2 + - - +
345A SER* 3.0 28.1 + - - -
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Residues in contact with ALA 342 (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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340A THR* 3.2 9.3 + - - +
341A ARG* 1.3 77.6 - - - +
343A GLU* 1.3 59.4 + - + +
345A SER* 3.4 7.9 + - - -
346A ASP* 2.9 28.6 + - - +
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Residues in contact with GLU 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A GLN 4.3 4.0 - - - +
329A MET 3.2 27.5 - - - +
330A LEU* 3.8 7.2 - - + -
331A GLU* 3.3 13.5 + - - +
332A SER* 2.6 50.4 + - - -
339A PRO* 3.4 14.1 - - + +
340A THR* 2.9 32.8 + - - +
341A ARG 3.2 0.2 - - - -
342A ALA* 1.3 76.7 - - + +
344A GLY* 1.3 65.8 + - - +
346A ASP* 3.2 5.2 + - - +
347A VAL* 3.2 23.6 + - - +
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Residues in contact with GLY 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 PRO* 4.7 5.4 - - - +
340A THR 3.1 13.3 + - - -
341A ARG* 3.5 4.0 + - - -
342A ALA 3.4 0.2 - - - -
343A GLU* 1.3 74.7 - - - +
345A SER* 1.3 61.8 + - - +
347A VAL 3.7 0.2 + - - -
348A ALA* 3.3 22.7 + - - +
380A ILE* 3.8 26.0 - - - +
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Residues in contact with SER 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A ARG 3.0 18.4 + - - -
342A ALA* 3.5 8.1 - - - -
344A GLY* 1.3 75.1 - - - +
346A ASP* 1.3 56.1 + - - +
348A ALA* 3.3 5.8 + - - +
349A ASN* 2.9 46.1 + - - +
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Residues in contact with ASP 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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293A ARG* 2.8 45.4 + - - -
309A GLN* 4.8 2.3 + - - +
325A CYS* 5.5 0.2 - - - -
328A GLN 4.7 0.6 - - - +
329A MET* 3.4 22.8 - - - +
342A ALA 2.9 17.1 + - - +
343A GLU* 3.2 10.3 + - - +
345A SER* 1.3 73.4 + - - +
347A VAL* 1.3 60.5 + - - +
349A ASN* 3.3 4.6 + - - +
350A ALA* 2.9 29.0 + - - +
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Residues in contact with VAL 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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329A MET* 4.1 19.5 - - + -
330A LEU* 3.6 30.3 - - + -
343A GLU 3.2 7.3 + - - +
344A GLY 4.2 0.4 - - - +
346A ASP* 1.3 75.4 - - - +
348A ALA* 1.3 62.8 + - - +
350A ALA* 3.3 6.6 + - - +
351A VAL* 3.2 27.0 + - + +
358A ILE* 4.8 12.7 - - + +
377A GLN* 3.9 29.4 - - - +
380A ILE* 3.8 28.9 - - + -
381A ALA 4.4 4.0 - - - +
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Residues in contact with ALA 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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344A GLY 3.3 16.3 + - - +
345A SER* 3.7 5.8 - - - +
346A ASP 3.3 0.4 - - - -
347A VAL* 1.3 78.0 - - - +
349A ASN* 1.3 60.7 + - - +
351A VAL 3.6 0.7 + - - -
352A LEU* 3.1 37.8 + - + +
380A ILE* 3.6 16.8 - - + +
384A ALA* 3.7 18.2 - - + +
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Residues in contact with ASN 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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309A GLN* 4.9 1.8 - - - +
310A LYS* 5.4 6.8 - - - +
345A SER* 2.9 37.1 + - - +
346A ASP* 3.9 4.7 - - - +
347A VAL 3.3 0.2 - - - -
348A ALA* 1.3 76.7 - - - +
350A ALA* 1.3 58.8 + - - +
352A LEU* 3.9 19.9 - - - +
353A ASP* 2.9 43.0 + - - +
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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
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309A GLN* 4.1 12.4 - - - +
313A ILE* 4.3 0.2 - - - +
325A CYS* 4.0 34.1 - - + -
329A MET* 4.9 2.0 - - - -
346A ASP* 2.9 16.7 + - - +
347A VAL* 3.6 7.4 - - - +
349A ASN* 1.3 77.8 - - - +
351A VAL* 1.3 62.3 + - - +
353A ASP* 3.3 4.9 + - - +
354A GLY 3.2 6.1 + - - -
355A ALA* 3.1 24.0 + - + +
358A ILE* 4.1 12.6 - - + -
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Residues in contact with VAL 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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44A THR* 3.6 36.3 - - + +
347A VAL* 3.2 15.5 + - + +
348A ALA 3.8 6.7 - - - +
350A ALA* 1.3 77.4 - - - +
352A LEU* 1.3 62.4 + - - +
354A GLY 3.1 4.0 + - - -
355A ALA 4.5 1.1 - - - +
358A ILE* 4.6 6.1 - - + -
381A ALA* 4.0 20.2 - - + +
384A ALA* 3.8 16.8 - - + -
385A GLU* 3.8 22.2 - - + +
388A ILE* 4.3 1.8 - - + -
466A ARG* 3.1 40.5 + - - +
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Residues in contact with LEU 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 ALA* 3.1 30.4 + - + +
349A ASN* 3.9 24.5 - - - +
351A VAL* 1.3 76.2 - - - +
353A ASP* 1.3 63.2 + - - +
354A GLY* 3.6 0.7 + - - -
384A ALA* 3.6 25.1 - - + +
387A ALA* 3.7 28.0 - - + +
388A ILE* 3.9 15.9 - - + +
466A ARG* 5.5 0.3 + - - -
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Residues in contact with ASP 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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309A GLN* 3.4 18.1 + - - -
310A LYS* 3.0 49.0 + - + +
313A ILE* 3.3 27.9 - - + +
314A GLY* 5.5 0.9 + - - -
317A ASN* 3.7 6.1 + - - -
349A ASN* 2.9 26.7 + - - +
350A ALA 3.6 5.2 - - - +
352A LEU* 1.3 81.1 - - - +
354A GLY* 1.3 56.7 + - - +
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Residues in contact with GLY 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A ILE* 3.6 5.8 - - - -
317A ASN* 3.1 30.3 - - - +
323A VAL* 3.9 1.9 - - - +
350A ALA 3.2 0.2 + - - -
351A VAL 3.1 11.8 + - - -
352A LEU 4.5 0.4 - - - -
353A ASP* 1.3 79.7 - - - +
355A ALA* 1.3 66.7 + - - +
356A ASP 3.4 0.5 + - - -
393A LEU* 6.5 0.2 - - - -
444A ARG* 3.1 19.7 + - - -
466A ARG* 3.4 5.8 - - - -
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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