Contacts of the helix formed by residues 391 - 400 (chain A) in PDB entry 4Y2P
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 391 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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389A GLU 3.0 0.2 + - - -
390A PRO* 1.3 71.5 - - - +
392A VAL* 1.3 65.6 + - - +
394A GLU* 2.8 30.8 + - - +
395A ALA* 3.2 23.4 + - - +
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Residues in contact with VAL 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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386A TYR* 3.8 31.7 + - + +
389A GLU* 3.2 37.3 + - + +
390A PRO 4.6 1.3 - - - +
391A GLY* 1.3 79.4 - - - +
393A ALA* 1.3 68.2 + - - +
395A ALA* 3.2 11.1 + - - +
396A GLU* 3.2 9.4 + - - +
426A GLY 5.7 1.1 - - - +
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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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386A TYR* 3.8 21.2 + - + +
387A PHE* 3.7 39.9 - - + -
389A GLU 4.5 2.6 + - - -
392A VAL* 1.3 79.8 - - - +
394A GLU* 1.3 59.6 + - - +
396A GLU* 3.2 0.4 + - - -
397A LEU* 2.8 35.4 + - + +
463A LEU* 3.8 17.9 - - + -
467A ARG* 4.7 1.8 - - - +
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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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390A PRO* 4.6 1.2 - - - +
391A GLY* 2.8 37.7 + - - +
392A VAL 3.1 0.8 + - - -
393A ALA* 1.3 76.8 - - - +
395A ALA* 1.3 57.2 + - - +
398A GLU* 2.8 49.1 + - - +
459A PHE* 4.0 5.4 - - - -
460A ARG* 3.6 40.4 - - + +
463A LEU* 3.6 11.0 - - + +
467A ARG* 2.8 36.1 + - - -
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Residues in contact with ALA 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 GLY 3.2 15.6 + - - +
392A VAL* 3.2 5.4 + - - +
394A GLU* 1.3 81.0 - - - +
396A GLU* 1.3 63.9 + - - +
398A GLU* 4.0 3.2 - - - -
399A GLN* 3.2 22.9 + - - +
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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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386A TYR* 2.5 40.2 + - - +
392A VAL 3.2 6.1 + - - +
393A ALA 4.0 2.9 - - - +
395A ALA* 1.3 80.7 - - - +
397A LEU* 1.3 65.5 + - + +
399A GLN* 3.4 15.9 + - - +
400A ASN 4.6 0.9 + - - -
403A ARG* 5.8 2.1 + - - +
404A THR* 4.1 4.3 + - - -
426A GLY 5.3 0.4 - - - -
427A GLY* 3.6 6.1 - - - -
428A LEU* 2.7 25.3 + - - +
429A PHE* 2.8 45.6 + - + +
430A VAL* 3.9 4.5 + - - +
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Residues in contact with LEU 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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267A PHE* 4.2 8.1 - - + -
386A TYR* 6.1 0.2 - - + -
387A PHE* 4.4 7.2 - - + -
393A ALA* 2.8 33.2 + - + +
394A GLU 4.3 0.2 - - - +
396A GLU* 1.3 78.4 - - + +
398A GLU* 1.3 61.2 + - - +
399A GLN 3.5 0.5 + - - -
400A ASN 4.4 0.9 + - - -
401A LEU* 3.8 9.2 - - - +
404A THR* 2.7 32.8 + - + -
408A LEU* 4.7 5.2 - - + -
428A LEU* 4.4 13.0 - - + -
429A PHE* 3.7 29.6 - - + -
459A PHE* 3.7 38.2 - - + -
463A LEU* 4.0 19.3 - - + -
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Residues in contact with GLU 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 38.3 + - - +
395A ALA* 4.0 2.7 - - - +
397A LEU* 1.3 70.0 - - - +
399A GLN* 1.3 65.5 + - - +
400A ASN* 3.2 4.8 + - - -
401A LEU* 4.2 17.2 - - + +
457A SER 4.8 0.5 - - - +
458A GLY* 3.5 10.9 - - - -
459A PHE* 2.8 43.9 + - + +
460A ARG* 4.0 2.8 + - - +
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Residues in contact with GLN 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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395A ALA 3.2 17.7 + - - +
396A GLU* 3.7 9.9 - - - +
397A LEU 3.3 3.0 - - - -
398A GLU* 1.3 79.9 - - - +
400A ASN* 1.3 73.1 + - - +
403A ARG* 5.2 8.1 + - - +
434A GLU* 5.1 4.5 - - - +
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Residues in contact with ASN 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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396A GLU 4.6 1.2 + - - -
397A LEU 4.4 0.8 + - - -
399A GLN* 1.3 95.8 + - - +
401A LEU* 1.3 59.3 + - - +
402A SER* 3.5 9.4 + - - -
403A ARG* 3.1 39.6 + - + +
404A THR* 2.9 27.8 + - - -
434A GLU* 4.2 13.1 + - - -
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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