Contacts of the helix formed by residues 389 - 398 (chain A) in PDB entry 3PDC
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 GLY 389 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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388A PRO* 1.3 71.0 - - - +
390A VAL* 1.3 64.7 + - - +
391A ALA 3.6 0.9 - - - -
392A GLU* 2.9 30.7 + - - +
393A ALA* 3.2 21.3 + - - +
459A ARG* 6.1 0.2 - - - +
466A ARG* 3.3 1.8 - - - +
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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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384A TYR* 3.5 36.0 + - + +
387A GLU* 3.3 39.6 + - + +
388A PRO 3.3 3.3 - - - +
389A GLY* 1.3 78.1 - - - +
391A ALA* 1.3 63.4 + - - +
392A GLU 3.1 0.6 + - - -
393A ALA* 3.5 10.5 + - - +
394A GLU* 3.8 7.1 + - - +
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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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384A TYR* 3.6 28.0 - - + +
385A PHE* 3.7 33.4 - - + +
387A GLU 4.4 1.6 + - - -
390A VAL* 1.3 79.1 - - - +
392A GLU* 1.3 60.7 + - - +
394A GLU* 3.7 2.1 + - - +
395A LEU* 3.0 45.0 + - + +
462A LEU* 4.0 8.1 - - + -
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Residues in contact with GLU 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A PRO* 4.2 0.2 - - - +
389A GLY* 2.9 24.9 + - - +
390A VAL 3.1 0.6 - - - -
391A ALA* 1.3 79.3 + - - +
393A ALA* 1.3 58.1 + - - +
395A LEU* 3.2 2.4 + - - -
396A GLU* 2.8 61.1 + - - +
458A PHE* 4.7 0.2 - - - -
459A ARG* 3.7 27.5 - - + +
462A LEU* 3.1 23.2 - - + +
466A ARG* 2.8 43.2 + - - -
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Residues in contact with ALA 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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389A GLY 3.2 13.1 + - - +
390A VAL* 3.5 5.8 + - - +
392A GLU* 1.3 79.0 - - - +
394A GLU* 1.3 57.2 + - - +
396A GLU* 3.9 4.1 - - - +
397A GLN* 3.0 30.4 + - - +
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Residues in contact with GLU 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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384A TYR* 2.7 35.4 + - - +
390A VAL 3.8 3.5 + - - +
391A ALA* 3.7 6.9 + - - +
392A GLU 3.1 0.4 - - - -
393A ALA* 1.3 77.9 - - - +
395A LEU* 1.3 69.1 + - - +
397A GLN* 3.0 35.1 + - - +
398A ASN 4.1 0.2 + - - -
402A THR* 3.9 6.4 + - - -
425A GLY 4.9 0.2 - - - +
426A GLY* 3.4 6.7 - - - -
427A LEU* 2.9 32.1 + - - +
428A PHE* 3.0 36.5 + - + +
429A VAL* 4.1 4.2 + - - +
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Residues in contact with LEU 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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1A ZYI 5.8 0.7 - - + -
265A PHE* 4.5 7.6 - - + -
385A PHE* 4.5 9.4 - - + -
391A ALA* 3.0 29.9 + - + +
392A GLU 4.0 0.9 - - - +
394A GLU* 1.3 83.8 - - - +
396A GLU* 1.3 57.1 + - - +
399A LEU* 3.2 16.3 - - - +
402A THR* 3.2 41.7 + - + +
406A LEU* 4.4 11.9 - - + -
427A LEU* 5.6 8.1 - - + -
428A PHE* 4.5 8.5 - - + -
458A PHE* 3.5 37.0 - - + -
462A LEU* 3.8 28.0 - - + -
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Residues in contact with GLU 396 (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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392A GLU* 2.8 43.2 + - - +
393A ALA* 4.3 3.2 - - - +
395A LEU* 1.3 71.4 - - - +
397A GLN* 1.3 65.6 + - - +
398A ASN* 3.3 3.8 + - - -
399A LEU* 3.9 19.3 - - + +
453A PHE 5.6 1.1 - - - +
457A GLY* 4.4 9.1 - - - -
458A PHE* 3.2 40.0 + - + +
459A ARG* 4.0 1.6 + - - +
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Residues in contact with GLN 397 (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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393A ALA 3.0 18.3 + - - +
394A GLU* 3.0 28.1 + - - +
396A GLU* 1.3 76.2 - - - +
398A ASN* 1.3 65.7 + - + +
401A ARG* 4.0 19.4 + - - -
428A PHE* 5.6 3.1 - - - +
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Residues in contact with ASN 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 4.1 2.2 + - - -
396A GLU 3.3 0.2 - - - -
397A GLN* 1.3 89.0 + - + +
399A LEU* 1.3 59.2 + - - +
400A SER* 3.6 10.4 + - - -
401A ARG* 3.1 46.0 + - + +
402A THR* 2.5 39.6 + - - +
433A GLU* 5.0 5.5 + - - -
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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