Contacts of the helix formed by residues 394 - 403 (chain A) in PDB entry 1AMI
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 GLU 394 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142A GLY 4.1 4.9 - - - +
143A SER* 3.0 21.5 + - - +
393A SER* 1.3 69.4 - - - +
395A GLN* 1.3 60.8 - - - +
397A ARG* 2.7 46.1 + - - +
398A ALA* 2.8 32.2 + - - +
419A ASN* 3.3 15.9 + - - +
512A PRO 4.0 2.5 - - - +
513A GLY* 3.5 3.6 - - - -
514A GLN* 3.0 56.4 + - + +
516A THR* 4.8 5.2 - - + +
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Residues in contact with GLN 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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152A GLU* 3.9 27.9 - - - +
153A ASN* 6.4 0.2 - - - -
283A THR* 4.7 6.4 - - - +
393A SER* 3.3 8.4 + - - +
394A GLU* 1.3 77.6 - - - +
396A ILE* 1.3 56.8 + - - +
399A THR* 2.8 34.7 + - - -
510A PHE* 3.7 39.4 - - + +
511A ASP 3.2 16.5 - - - +
512A PRO* 3.7 30.7 + - - +
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Residues in contact with ILE 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A GLN* 3.6 21.5 - - + +
152A GLU* 3.1 25.8 - - - +
361A SER 3.5 27.4 - - - +
362A SER* 4.0 8.7 - - - -
363A TYR* 4.2 11.0 - - + +
366A MET* 4.4 7.9 - - + -
391A PRO* 4.4 6.3 - - + -
392A GLY 4.3 6.3 - - - +
393A SER* 3.2 16.1 + - - +
395A GLN* 1.3 77.9 - - - +
397A ARG* 1.3 56.5 + - - +
399A THR* 3.3 5.2 + - - -
400A ILE* 2.9 47.9 + - + +
510A PHE* 4.9 12.1 - - + -
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Residues in contact with ARG 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A PRO* 3.9 16.1 - - + +
393A SER 2.9 8.9 + - - +
394A GLU* 2.7 45.6 + - - +
396A ILE* 1.3 73.4 - - - +
398A ALA* 1.3 79.0 + - - +
400A ILE* 3.5 10.4 - - + +
401A GLU* 3.1 51.4 + - - +
416A VAL* 5.2 9.4 - - + -
417A LEU 6.2 0.2 - - - -
419A ASN* 3.7 26.9 - - - +
513A GLY* 4.7 1.4 - - - -
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Residues in contact with ALA 398 (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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394A GLU 2.8 20.8 + - - +
397A ARG* 1.3 87.4 - - - +
399A THR* 1.3 57.0 + - - +
401A GLU* 3.4 2.8 - - - +
402A ARG* 3.0 28.4 + - - +
511A ASP* 3.7 22.6 - - - +
513A GLY* 3.6 26.5 - - - +
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Residues in contact with THR 399 (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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363A TYR* 3.7 27.1 - - + -
395A GLN 2.8 19.0 + - - -
396A ILE* 3.9 2.7 - - - -
398A ALA* 1.3 73.6 - - - +
400A ILE* 1.3 58.6 + - - +
402A ARG* 3.3 27.6 + - - +
403A ASP* 2.8 32.2 + - - +
506A PRO* 4.0 10.3 - - + -
510A PHE* 3.7 17.2 - - + -
511A ASP* 2.9 23.0 + - - -
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Residues in contact with ILE 400 (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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363A TYR* 4.0 16.4 - - + -
366A MET* 3.8 37.5 - - + -
389A ILE* 5.2 4.7 - - + -
391A PRO* 4.3 21.8 - - + -
396A ILE* 2.9 30.7 + - + +
397A ARG* 3.5 7.9 - - + +
399A THR* 1.3 72.4 - - - +
401A GLU* 1.3 63.3 + - - +
403A ASP* 4.3 0.4 - - - +
404A GLY 3.2 1.7 + - - -
405A TYR* 2.9 59.5 + - + -
406A ALA* 3.1 22.8 + - + +
409A LEU* 5.4 1.8 - - + -
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Residues in contact with GLU 401 (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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397A ARG* 3.1 43.0 + - - +
398A ALA* 3.4 7.4 - - - +
400A ILE* 1.3 77.6 - - - +
402A ARG* 1.3 62.8 + - - +
404A GLY* 3.2 13.3 + - - -
406A ALA* 3.6 10.0 + - + +
407A GLN* 4.5 2.9 + - - +
410A ARG* 2.6 46.4 + - - -
416A VAL* 5.8 1.9 - - - +
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Residues in contact with ARG 402 (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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398A ALA 3.0 17.3 + - - +
399A THR* 3.6 12.9 - - - +
401A GLU* 1.3 77.0 - - - +
403A ASP* 1.3 106.8 + - - +
404A GLY* 3.1 4.5 + - - -
506A PRO* 4.2 1.8 - - - +
508A ALA* 3.8 21.1 - - - +
509A GLU* 2.6 32.9 + - - +
510A PHE 3.9 1.0 + - - -
511A ASP* 3.6 29.9 + - - +
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Residues in contact with ASP 403 (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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363A TYR* 2.9 36.3 + - + +
399A THR* 2.8 18.3 + - - +
400A ILE* 4.7 2.2 - - - +
402A ARG* 1.3 115.4 + - - +
404A GLY* 1.3 59.7 + - - +
405A TYR* 3.5 16.9 + - + -
506A PRO* 3.7 4.9 - - - +
507A ARG 5.2 1.2 + - - -
508A ALA* 5.5 0.9 + - - +
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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