Contacts of the helix formed by residues 354 - 361 (chain A) in PDB entry 5M8L
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 354 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339A VAL* 3.7 0.9 - - - -
341A LEU 4.1 2.2 - - - -
342A PHE 3.3 1.3 + - - -
343A ASP* 2.4 36.3 + - - -
344A THR* 3.5 19.1 - - - -
351A SER* 3.7 13.2 + - - -
352A THR* 3.0 0.6 - - - +
353A ASN* 1.3 77.6 - - - +
355A PHE* 1.3 54.7 + - - +
357A ASN* 3.2 18.6 + - - +
358A THR* 2.5 38.7 + - - -
363A SER* 5.5 0.6 + - - -
367A GLY 4.8 0.2 + - - -
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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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221A LEU* 3.8 20.4 - - + -
336A CYS* 3.3 42.6 - - + -
337A LEU* 4.4 1.8 - - + -
339A VAL* 3.4 13.4 - - - +
341A LEU 2.9 23.6 + - - +
342A PHE* 3.8 12.1 - + - +
354A SER* 1.3 68.7 - - - +
356A ARG* 1.3 69.8 + - - +
358A THR* 3.1 2.0 + - - -
359A VAL* 3.0 35.0 + - + +
410A VAL* 4.1 15.7 - - + -
411A PHE* 4.3 9.0 - + - -
414A TRP* 3.4 58.8 - + + +
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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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216A GLU* 3.9 2.2 - - - +
217A GLY 3.0 37.1 + - - +
218A PRO* 3.9 15.7 - - + +
220A PHE* 3.9 5.1 - - + -
221A LEU* 4.1 21.1 - - + -
342A PHE* 2.8 37.1 + - + +
343A ASP* 3.0 32.3 + - - +
347A PHE 3.9 0.2 - - - -
348A TYR 2.8 33.9 + - - +
351A SER* 3.8 0.6 + - - -
354A SER* 3.9 1.1 - - - +
355A PHE* 1.3 74.9 - - - +
357A ASN* 1.3 82.9 + - - +
359A VAL* 3.7 1.6 - - - +
360A GLU* 2.7 64.3 + - - +
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Residues in contact with ASN 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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348A TYR 3.4 12.6 - - - +
349A SER* 3.1 27.7 + - - -
350A ASN* 4.5 0.2 - - - +
351A SER* 3.1 14.6 + - - +
354A SER* 3.2 19.6 + - - +
356A ARG* 1.3 105.7 + - - +
358A THR* 1.3 63.4 + - - +
360A GLU* 4.3 1.1 - - - -
361A GLY 3.1 15.8 + - - -
362A TYR* 3.1 30.3 + - - +
363A SER* 3.1 23.6 + - - +
369A TYR* 4.7 0.6 - - - -
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Residues in contact with THR 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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336A CYS* 3.6 18.4 - - + -
339A VAL* 4.2 5.2 - - + +
354A SER 2.5 23.7 + - - -
355A PHE* 3.1 7.1 + - - -
357A ASN* 1.3 78.1 - - - +
359A VAL* 1.3 62.2 + - - +
361A GLY* 3.2 14.7 + - - -
363A SER* 4.0 8.4 - - - -
364A ASP 3.5 14.4 - - - +
365A PRO* 3.3 30.7 - - + +
367A GLY* 3.6 18.2 - - - +
375A SER* 3.7 3.5 + - - -
376A LEU* 3.5 9.4 - - + +
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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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220A PHE* 4.8 0.4 - - - -
221A LEU* 3.8 31.4 - - + -
336A CYS* 4.3 6.5 - - - +
355A PHE* 3.0 34.2 + - + +
356A ARG 3.7 5.2 - - - +
358A THR* 1.3 74.8 - - - +
360A GLU* 1.3 69.5 + - - +
376A LEU* 3.7 14.8 - - + +
377A HIS* 3.1 27.4 + - + +
407A THR* 4.3 15.9 - - + +
410A VAL* 4.0 30.5 - - + -
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Residues in contact with GLU 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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215A HIS* 3.6 11.6 - - - +
216A GLU 2.7 27.0 + - - -
220A PHE* 3.6 40.5 - - + +
356A ARG* 2.7 51.3 + - - +
357A ASN* 4.0 4.7 - - - +
359A VAL* 1.3 76.1 - - - +
361A GLY* 1.3 58.8 + - - +
362A TYR* 3.5 22.7 - - + -
377A HIS* 2.9 23.6 + - + +
378A ASN* 3.0 16.6 + - - +
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Residues in contact with GLY 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 ASN 3.1 4.8 + - - -
358A THR 3.5 11.0 - - - -
359A VAL 3.1 1.6 - - - -
360A GLU* 1.3 77.2 - - - +
362A TYR* 1.3 62.2 + - - +
363A SER 3.4 1.6 - - - -
374A ARG* 3.5 9.7 - - - -
375A SER* 3.0 42.7 + - - -
378A ASN* 3.3 13.7 + - - -
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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