Contacts of the helix formed by residues 386 - 395 (chain A) in PDB entry 3M8S
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 386 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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374A MET* 3.3 5.2 - - - -
385A THR* 1.3 93.9 + - - +
387A PRO* 1.3 71.0 - - - +
388A GLU* 3.5 13.8 + - - +
389A GLY* 3.1 20.1 + - - -
390A VAL* 3.0 27.4 + - - +
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Residues in contact with PRO 387 (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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351A LEU* 4.8 7.7 - - + +
352A LEU* 4.6 17.3 - - + -
374A MET* 3.6 23.9 - - + -
385A THR 4.8 0.7 - - - +
386A THR* 1.3 81.4 - - - +
388A GLU* 1.3 79.4 + - - +
390A VAL* 3.9 2.2 - - + +
391A ALA* 2.9 27.7 + - - +
398A TRP* 3.8 47.8 - - + +
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Residues in contact with GLU 388 (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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386A THR* 3.5 13.6 - - - +
387A PRO* 1.3 94.4 - - - +
389A GLY* 1.3 61.3 + - - +
391A ALA* 3.8 2.3 - - - +
392A ARG* 3.2 26.3 + - - +
398A TRP* 3.8 36.9 + - + +
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Residues in contact with GLY 389 (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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384A ASN* 5.1 3.8 - - - -
386A THR* 3.1 12.5 + - - -
388A GLU* 1.3 78.1 - - - +
390A VAL* 1.3 65.0 + - - +
392A ARG* 3.2 7.0 + - - +
393A ARG* 3.0 25.7 + - - +
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Residues in contact with VAL 390 (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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351A LEU* 5.1 1.1 - - + -
373A PRO 4.8 1.1 - - - +
374A MET* 3.6 27.1 - - + -
377A ALA* 3.8 26.2 - - + -
384A ASN* 3.8 21.5 - - + +
386A THR 3.0 21.7 + - - +
387A PRO 4.2 1.6 - - - +
389A GLY* 1.3 75.0 - - - +
391A ALA* 1.3 58.5 + - - +
393A ARG* 3.3 1.3 + - - -
394A TYR* 2.9 47.7 + - + +
412A LEU* 4.0 18.3 - - + +
416A LEU* 4.3 7.2 - - + -
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Residues in contact with ALA 391 (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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387A PRO 2.9 21.7 + - - +
388A GLU 3.8 2.7 - - - +
390A VAL* 1.3 77.1 - - - +
392A ARG* 1.3 63.2 + - - +
395A GLY 3.0 8.7 + - - -
396A GLY 2.9 24.1 + - - +
397A GLU* 3.9 9.4 - - - +
398A TRP 3.7 24.5 - - - +
408A LEU* 3.9 13.9 - - + -
412A LEU* 4.0 12.8 - - + +
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Residues in contact with ARG 392 (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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388A GLU 3.2 16.9 + - - +
389A GLY* 3.2 6.7 + - - +
391A ALA* 1.3 80.1 - - - +
393A ARG* 1.3 61.2 + - + +
395A GLY* 4.4 2.6 + - - -
396A GLY 3.2 11.7 + - - -
397A GLU* 3.2 48.6 + - - +
398A TRP 5.9 0.2 - - - +
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Residues in contact with ARG 393 (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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381A ASP* 3.1 31.7 + - - +
383A SER* 4.0 5.7 + - - -
384A ASN* 3.1 28.9 + - - +
389A GLY 3.0 17.0 + - - +
391A ALA 3.1 0.2 - - - -
392A ARG* 1.3 79.8 - - - +
394A TYR* 1.3 98.0 + - + +
395A GLY 3.7 0.7 - - - -
419A ARG* 4.8 5.0 + - - -
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Residues in contact with TYR 394 (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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377A ALA* 4.1 3.4 - - + -
380A LEU* 4.4 14.3 - - + +
381A ASP* 4.9 0.5 - - - +
384A ASN* 3.0 34.9 + - - -
390A VAL* 2.9 32.2 + - + +
393A ARG* 1.3 117.1 + - + +
395A GLY* 1.3 55.3 + - - +
411A ARG* 5.5 0.5 - - - +
412A LEU* 3.3 21.8 - - + +
415A ASN* 3.0 30.9 + - + +
416A LEU* 3.5 36.6 - - + -
419A ARG* 3.9 35.7 - - + +
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Residues in contact with GLY 395 (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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391A ALA 3.0 3.6 + - - -
392A ARG 4.4 2.2 + - - -
393A ARG 3.7 1.8 + - - -
394A TYR* 1.3 80.8 - - - +
396A GLY* 1.3 59.4 + - - +
408A LEU* 4.2 1.9 - - - +
411A ARG* 3.3 25.6 + - - +
412A LEU* 4.1 5.9 - - - +
415A ASN* 5.1 0.7 - - - -
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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