Contacts of the helix formed by residues 348 - 364 (chain A) in PDB entry 5JQE
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 MET 348 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180A ALA* 4.3 4.9 - - - -
181A PHE* 3.5 20.4 - - + -
270A PHE* 4.9 2.0 - - + -
342A MET* 3.6 24.7 - - + -
343A PRO* 3.9 36.1 - - + +
345A ILE 3.2 12.2 + - - +
346A PRO 2.9 1.8 + - - -
347A GLN* 1.3 75.6 - - - +
349A SER* 1.3 59.0 + - - +
350A ALA 3.2 1.1 - - - -
351A PHE* 3.0 44.1 + - + +
352A TRP* 3.0 57.4 - - + +
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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
----------------------------------------------------------
346A PRO 3.1 16.5 + - - -
347A GLN* 5.0 0.2 - - - -
348A MET* 1.3 78.7 - - - +
350A ALA* 1.3 62.4 + - - +
352A TRP* 3.7 11.6 + - - +
353A TYR* 3.6 18.2 + - - +
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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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347A GLN* 3.6 7.5 + - - +
348A MET 3.2 0.4 - - - -
349A SER* 1.3 77.8 + - - +
351A PHE* 1.3 60.5 + - - +
352A TRP 3.4 0.2 - - - -
353A TYR* 3.9 3.2 - - - +
354A ALA* 3.0 31.9 + - - +
379A HIS* 4.0 12.8 + - + +
1001A MET* 3.5 17.2 - - + +
1004A SER* 3.7 32.8 - - - +
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Residues in contact with PHE 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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166A PRO* 5.6 0.4 - - + -
170A TRP* 3.6 44.4 - + - -
180A ALA* 3.8 17.9 - - + -
181A PHE* 5.0 2.7 - - + -
193A VAL* 5.1 0.7 - - + -
195A VAL* 3.7 15.7 - - + -
270A PHE* 3.5 26.5 - + - -
348A MET* 3.0 37.0 + - - +
350A ALA* 1.3 75.7 - - - +
352A TRP* 1.3 77.5 + + - +
354A ALA 3.4 0.3 + - - -
355A VAL* 2.9 58.9 + - + +
1001A MET* 3.4 22.8 - - + +
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Residues in contact with TRP 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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165A GLU* 5.8 1.1 - - - +
166A PRO* 4.0 21.3 - - + +
167A TYR* 4.0 27.6 - + + -
270A PHE* 3.6 39.3 - + - -
342A MET* 3.5 18.1 - - - -
348A MET* 3.0 57.5 + - + +
349A SER* 3.7 9.8 + - - +
351A PHE* 1.3 82.7 - + - +
353A TYR* 1.3 56.7 + - - +
356A ARG* 2.9 51.4 + - - +
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Residues in contact with TYR 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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349A SER 3.6 11.6 + - - +
350A ALA* 3.9 6.5 - - - +
351A PHE 3.3 0.2 - - - -
352A TRP* 1.3 79.1 - - - +
354A ALA* 1.3 58.1 + - - +
356A ARG* 3.6 19.9 - - - +
357A THR* 2.7 63.4 + - + +
379A HIS* 3.1 42.0 - + + -
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Residues in contact with ALA 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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350A ALA 3.0 19.7 + - - +
351A PHE 3.9 2.9 - - - +
353A TYR* 1.3 81.9 - - - +
355A VAL* 1.3 58.7 + - + +
357A THR* 3.0 13.5 + - - -
358A ALA* 3.0 22.3 + - - +
376A ALA* 3.6 36.4 - - + +
379A HIS* 4.2 9.6 - - + +
1001A MET* 4.1 11.2 - - + -
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Residues in contact with VAL 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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166A PRO* 3.7 24.2 - - + -
170A TRP* 4.0 24.7 - - + -
173A ILE* 5.2 1.1 - - + -
195A VAL* 4.4 13.9 - - + -
351A PHE* 2.9 48.9 + - + +
354A ALA* 1.3 78.2 - - + +
356A ARG* 1.3 61.0 + - - +
358A ALA* 3.5 6.2 - - + -
359A VAL* 2.8 41.6 + - + +
376A ALA* 5.1 0.7 - - + -
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Residues in contact with ARG 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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164A GLN 4.0 15.0 - - - +
165A GLU* 3.5 29.3 + - - -
166A PRO* 3.5 17.1 - - + +
352A TRP* 2.9 42.3 + - - +
353A TYR* 3.6 34.2 + - - +
355A VAL* 1.3 77.5 - - - +
357A THR* 1.3 67.9 + - + +
359A VAL* 3.3 3.3 - - - +
360A ILE* 3.1 38.1 + - + +
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Residues in contact with THR 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 TYR* 2.7 58.2 + - + +
354A ALA* 3.0 10.4 + - - -
356A ARG* 1.3 83.6 - - + +
358A ALA* 1.3 55.7 + - - +
360A ILE* 4.0 7.0 - - - -
361A ASN* 2.8 42.0 + - - +
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Residues in contact with ALA 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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204A LEU* 4.1 2.6 - - - +
354A ALA 3.0 20.8 + - - +
355A VAL* 3.0 8.2 + - + +
357A THR* 1.3 77.0 - - - +
359A VAL* 1.3 62.0 + - + +
361A ASN* 5.0 0.7 - - - +
362A ALA* 3.3 26.2 + - - +
367A GLN* 5.8 0.2 - - - -
372A ALA* 3.3 34.5 - - - +
373A LEU* 4.4 7.9 - - + -
376A ALA* 3.8 10.5 - - + -
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Residues in contact with VAL 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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163A LEU 4.6 6.7 - - - +
166A PRO* 5.3 4.7 - - + -
169A THR* 4.2 19.3 - - + +
173A ILE* 3.7 30.7 - - + -
204A LEU* 4.2 14.7 - - + +
207A LEU* 5.3 3.1 - - + -
355A VAL* 2.8 26.6 + - + +
356A ARG* 3.3 14.8 - - - +
358A ALA* 1.3 77.1 - - + +
360A ILE* 1.3 75.7 + - + +
361A ASN 3.3 0.4 - - - -
362A ALA* 4.4 4.0 - - - -
363A ALA* 3.0 34.9 + - + +
373A LEU* 5.9 0.2 - - + -
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Residues in contact with ILE 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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163A LEU 4.0 15.9 - - - +
164A GLN* 4.3 27.4 - - - +
356A ARG* 3.1 33.4 + - + +
357A THR* 4.1 7.4 - - - +
359A VAL* 1.3 89.2 - - + +
361A ASN* 1.3 69.5 + - - +
363A ALA* 4.5 1.9 - - - +
364A SER* 3.2 26.7 + - - -
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Residues in contact with ASN 361 (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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357A THR* 2.8 28.7 + - - +
358A ALA* 4.6 3.1 - - - +
359A VAL 3.3 0.4 - - - -
360A ILE* 1.3 87.4 - - - +
362A ALA* 1.3 62.5 + - - +
363A ALA 3.4 0.2 - - - -
364A SER* 3.3 4.8 + - - -
366A ARG* 3.2 37.9 + - - +
367A GLN* 3.0 56.6 + - + +
372A ALA* 4.9 0.7 - - + -
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Residues in contact with ALA 362 (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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204A LEU* 3.6 23.1 - - + -
208A VAL* 3.5 26.8 - - + +
212A LYS* 4.0 1.6 + - - -
358A ALA 3.3 20.1 + - - +
359A VAL 4.1 2.0 - - - +
361A ASN* 1.3 79.0 - - - +
363A ALA* 1.3 60.9 + - - +
365A GLY 3.6 6.4 + - - -
367A GLN 3.7 15.7 - - - +
369A VAL* 4.2 9.3 - - + +
372A ALA* 3.9 11.4 - - + +
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Residues in contact with ALA 363 (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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163A LEU* 6.5 0.2 - - + -
204A LEU* 6.0 0.7 - - + -
207A LEU* 5.8 4.7 - - + -
208A VAL* 3.9 15.4 - - + +
211A ILE* 3.6 45.6 - - + +
212A LYS* 4.8 6.8 + - - +
218A ALA* 4.8 6.1 - - + +
359A VAL* 3.0 19.4 + - + +
360A ILE* 4.6 2.7 - - - +
362A ALA* 1.3 76.7 - - - +
364A SER* 1.3 61.5 + - - +
365A GLY 3.2 1.4 + - - -
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Residues in contact with SER 364 (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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212A LYS* 5.1 0.7 - - - -
218A ALA* 5.7 4.3 - - - -
360A ILE* 3.2 20.0 + - - -
361A ASN* 3.3 1.6 + - - -
363A ALA* 1.3 77.4 - - - +
365A GLY* 1.3 56.8 + - - +
366A ARG* 3.1 30.5 + - - +
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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