Contacts of the helix formed by residues 335 - 353 (chain A) in PDB entry 5MQI
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 ALA 335 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A ASP* 3.3 8.2 + - - +
333A ARG 3.6 1.4 + - - -
334A SER* 1.3 74.8 - - - +
336A LEU* 1.3 67.0 + - - +
337A ASN* 3.5 8.3 - - - +
338A VAL* 3.0 11.7 + - + +
339A ARG* 2.9 19.6 + - - +
1602A SO4 3.3 27.1 - - - +
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Residues in contact with LEU 336 (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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335A ALA* 1.3 73.2 - - - +
337A ASN* 1.3 58.7 + - - +
339A ARG* 3.2 40.9 + - + +
340A LEU* 2.9 53.9 + - + +
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Residues in contact with ASN 337 (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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191A TRP* 3.2 40.7 - - + -
335A ALA* 3.5 5.5 - - - +
336A LEU* 1.3 76.9 - - - +
338A VAL* 1.3 64.5 + - - -
340A LEU* 4.0 11.5 - - + +
341A PHE* 3.2 14.9 + - - +
1602A SO4 3.0 45.9 + - - -
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Residues in contact with VAL 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A ASP* 3.9 38.6 - - + +
190A LEU* 3.8 33.4 - - + -
191A TRP* 4.1 15.7 - - + +
334A SER* 4.0 10.1 - - - -
335A ALA* 3.0 10.9 + - + +
337A ASN* 1.3 81.5 + - - +
339A ARG* 1.4 59.6 + - - +
341A PHE* 3.2 5.4 + - + +
342A LEU* 2.9 31.8 + - + +
1602A SO4 3.6 22.2 - - - +
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Residues in contact with ARG 339 (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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229A GLN* 4.5 11.0 - - - +
233A GLN* 5.7 1.6 - - - -
234A LEU* 3.5 22.6 - - + +
333A ARG* 3.5 47.6 - - - +
334A SER* 2.8 52.9 + - - +
335A ALA* 2.9 7.6 + - - +
336A LEU* 3.3 51.1 - - + +
338A VAL* 1.4 76.8 - - - +
340A LEU* 1.4 59.4 + - + +
342A LEU* 3.2 3.0 + - - -
343A ARG* 2.9 27.4 + - - +
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Residues in contact with LEU 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A LEU* 2.9 49.0 + - + +
337A ASN* 4.0 9.0 - - + +
338A VAL 3.3 0.2 - - - -
339A ARG* 1.4 73.5 - - - +
341A PHE* 1.3 66.8 + - - +
343A ARG* 3.4 31.2 + - - +
344A ASP* 2.9 35.4 + - - +
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Residues in contact with PHE 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A LEU* 3.5 29.4 - - + -
191A TRP* 4.2 12.1 - + + -
193A ILE* 4.6 0.7 - - + -
194A HIS* 3.3 37.5 - + + +
199A ASP* 3.5 32.1 - - + -
225A MET* 3.9 23.6 - - + -
337A ASN 3.2 13.4 + - - +
338A VAL* 3.2 13.2 + - - +
340A LEU* 1.3 77.2 - - - +
342A LEU* 1.3 77.5 + - + +
344A ASP* 3.1 9.7 + - + +
345A PHE* 2.8 37.7 + + + +
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Residues in contact with LEU 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A LEU* 3.8 24.7 - - + -
225A MET* 3.9 20.0 - - + +
226A PHE* 3.5 29.6 - - + -
229A GLN* 3.6 42.4 - - + +
234A LEU* 4.1 6.7 - - + -
338A VAL* 2.9 24.9 + - + +
339A ARG* 3.7 6.1 - - - +
340A LEU 3.2 0.2 - - - -
341A PHE* 1.3 93.6 - - + +
343A ARG* 1.3 56.0 + - - +
345A PHE* 4.3 2.5 - - + -
346A CYS* 2.8 32.7 + - - +
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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
----------------------------------------------------------
234A LEU* 3.2 35.7 - - + +
235A ALA* 4.6 13.5 + - - +
236A GLY* 5.0 3.8 - - - +
339A ARG 2.9 17.2 + - - +
340A LEU* 3.6 27.5 - - + +
342A LEU* 1.3 77.1 - - - +
344A ASP* 1.3 66.5 + - - +
346A CYS* 3.5 3.4 + - - +
347A SER* 2.9 33.8 + - - +
388A PHE* 4.2 11.1 - - + -
1601A SO4 3.4 36.6 + - - +
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Residues in contact with ASP 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A LEU* 2.9 25.5 + - - +
341A PHE* 3.5 8.6 - - + +
343A ARG* 1.3 84.3 + - - +
345A PHE* 1.3 66.8 + - - +
347A SER* 3.5 2.4 + - - -
348A GLU* 3.0 25.5 + - - +
1601A SO4 2.6 31.7 + - - +
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Residues in contact with PHE 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A ASP* 3.6 44.9 - - + -
202A LEU* 4.4 7.2 - - + -
203A LEU* 3.7 29.2 - - + +
222A VAL* 4.2 29.4 - - + -
225A MET* 4.1 20.0 - - + -
226A PHE* 3.6 27.4 - + + -
341A PHE* 2.8 32.5 + + + +
342A LEU* 3.7 6.1 - - - +
344A ASP* 1.3 73.0 - - - +
346A CYS* 1.3 59.7 + - - +
348A GLU* 3.3 7.2 + - - +
349A PHE* 2.8 36.0 + + + +
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Residues in contact with CYS 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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226A PHE* 3.7 15.0 - - + -
234A LEU* 4.7 0.4 - - + -
342A LEU 2.8 17.9 + - - +
343A ARG* 3.7 4.3 - - - +
345A PHE* 1.3 77.6 - - - +
347A SER* 1.3 56.6 + - - +
349A PHE* 3.5 6.8 - - - +
350A LEU* 2.9 31.2 + - - +
384A PHE* 4.5 4.5 - - - -
385A PHE* 3.6 28.3 - - - -
388A PHE* 3.5 42.2 - - + -
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Residues in contact with SER 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A ARG* 2.9 19.5 + - - +
344A ASP* 3.7 5.8 - - - -
345A PHE 3.3 0.2 - - - -
346A CYS* 1.3 77.3 - - - +
348A GLU* 1.3 56.8 + - - +
350A LEU* 3.9 1.7 - - - +
351A GLU* 3.0 29.7 + - - +
388A PHE* 4.1 7.6 - - - -
394A PHE* 3.7 31.3 - - - -
1601A SO4 3.4 27.4 + - - -
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Residues in contact with GLU 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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200A ASP* 4.8 6.4 - - - +
203A LEU* 3.5 38.0 - - + +
344A ASP 3.0 16.9 + - - +
345A PHE* 3.8 3.3 - - - +
347A SER* 1.3 75.0 - - - +
349A PHE* 1.3 66.0 + - - +
351A GLU* 3.3 5.1 + - - -
352A ASN* 3.0 43.5 + - + +
353A CYS* 4.2 0.3 - - - -
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Residues in contact with PHE 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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203A LEU* 4.0 15.4 - - + +
206A ALA* 4.2 5.4 - - + -
219A LEU* 4.6 5.2 - - + -
222A VAL* 4.2 22.7 - - + -
345A PHE* 2.8 26.9 + + + +
346A CYS* 3.5 5.6 - - - +
347A SER 3.3 0.2 - - - -
348A GLU* 1.3 73.3 - - - +
350A LEU* 1.4 57.8 + - - +
353A CYS* 2.7 52.6 + - + -
354A TYR* 2.9 43.8 + + + -
357A LEU* 3.7 32.3 - - + -
358A MET* 5.7 0.4 - - + -
385A PHE* 3.7 40.2 - + - -
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Residues in contact with LEU 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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346A CYS* 2.9 25.7 + - - +
347A SER 4.0 3.4 - - - +
349A PHE* 1.4 74.1 - - + +
351A GLU* 1.3 64.6 + - - +
352A ASN 3.4 0.3 + - - -
353A CYS 4.2 1.7 + - - -
354A TYR* 4.0 20.9 + - + -
355A ASN* 5.4 0.7 + - - -
385A PHE* 3.9 26.7 - - + +
388A PHE* 3.6 31.0 - - + -
389A ASN* 3.8 20.9 - - - +
394A PHE* 4.1 6.7 - - + -
398A LEU* 3.7 28.8 - - + +
399A VAL* 3.7 30.1 - - + -
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Residues in contact with GLU 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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347A SER 3.0 19.2 + - - +
348A GLU* 3.3 7.2 + - - +
350A LEU* 1.3 77.8 - - - +
352A ASN* 1.3 73.5 + - - +
394A PHE* 5.7 2.6 - - - -
395A ARG* 4.1 20.7 + - - -
398A LEU* 3.6 26.4 - - - +
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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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207A SER* 3.6 19.1 - - - +
348A GLU* 3.0 35.8 + - + +
350A LEU 4.7 0.2 - - - -
351A GLU* 1.3 94.2 - - - +
353A CYS* 1.3 67.7 + - - +
356A ARG* 5.1 3.6 - - - +
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Residues in contact with CYS 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A LEU* 3.6 38.1 - - - -
206A ALA* 3.5 22.7 - - + +
207A SER* 3.9 10.8 - - - +
348A GLU* 4.2 1.1 - - - -
349A PHE* 2.7 37.1 + - + +
350A LEU 4.2 0.4 + - - -
351A GLU 3.9 0.2 - - - -
352A ASN* 1.3 86.0 - - - +
354A TYR* 1.3 58.9 + - - +
355A ASN 3.4 2.2 - - - -
356A ARG* 3.3 6.2 + - - +
357A LEU* 2.9 30.4 + - - +
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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
------------------------------------------------------------
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