Contacts of the helix formed by residues 398 - 409 (chain A) in PDB entry 5IY8
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 ASN 398 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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392A GLU* 4.3 8.7 + - - +
393A ILE 3.9 15.6 + - - -
395A THR* 3.0 30.3 + - - +
397A PHE* 1.3 76.4 - - - +
399A ILE* 1.3 59.0 + - - +
400A ASP 3.1 2.7 - - - -
401A ARG* 2.7 61.3 + - - +
402A LEU* 2.8 29.1 + - + +
87F THR* 5.0 18.4 + - - +
89F PRO* 6.1 2.0 - - - +
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Residues in contact with ILE 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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394A VAL* 4.2 14.6 - - + -
395A THR 3.3 13.2 + - - +
396A PRO* 4.4 17.0 - - + +
397A PHE* 3.2 2.4 - - - +
398A ASN* 1.3 83.8 + - - +
400A ASP* 1.3 62.7 + - + +
402A LEU* 4.1 5.3 - - - +
403A GLN* 2.9 30.1 + - + +
440A LEU* 4.0 39.4 - - + +
441A GLN* 4.6 4.7 - - - +
442A THR* 5.3 1.3 - - - +
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Residues in contact with ASP 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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397A PHE 4.5 4.2 + - - +
398A ASN 3.1 0.8 - - - -
399A ILE* 1.3 83.1 - - + +
401A ARG* 1.3 64.7 + - - +
403A GLN* 3.5 9.8 + - - +
404A GLU* 3.2 22.9 + - - +
407A ARG* 5.4 1.0 + - - -
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Residues in contact with ARG 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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392A GLU* 3.6 27.3 + - - -
398A ASN* 2.7 41.7 + - - +
400A ASP* 1.3 73.3 + - - +
402A LEU* 1.3 80.4 + - - +
404A GLU* 3.2 19.2 + - + +
405A LEU* 3.3 28.1 + - + +
448A ARG* 5.4 0.6 - - - +
87F THR* 5.1 13.9 + - - +
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Residues in contact with LEU 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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392A GLU* 3.9 29.2 - - + +
394A VAL* 3.8 26.9 - - + -
398A ASN* 2.8 44.8 + - - +
399A ILE* 4.1 3.8 - - - +
401A ARG* 1.3 94.5 - - - +
403A GLN* 1.3 64.6 + - - +
405A LEU* 3.1 19.0 + - + +
406A VAL* 3.1 26.5 + - - +
440A LEU* 4.1 10.3 - - + -
446A VAL* 4.6 16.5 - - + +
448A ARG* 5.2 1.1 - - + -
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Residues in contact with GLN 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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399A ILE* 2.9 22.0 + - + +
400A ASP* 3.5 11.9 - - - +
402A LEU* 1.3 78.4 - - - +
404A GLU* 1.3 62.2 + - - +
406A VAL* 3.6 9.5 + - - +
407A ARG* 3.1 36.9 + - - +
436A SER 5.9 0.6 + - - -
438A LEU 3.5 20.9 + - - +
439A HIS* 4.2 4.6 + - - +
440A LEU* 3.5 36.1 + - + +
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Residues in contact with GLU 404 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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400A ASP* 3.2 12.4 + - - +
401A ARG* 3.2 14.4 + - + +
403A GLN* 1.3 78.4 - - - +
405A LEU* 1.3 54.7 + - + +
407A ARG* 3.2 34.6 + - - +
408A ARG* 2.8 67.0 + - + +
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Residues in contact with LEU 405 (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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401A ARG* 3.3 24.6 + - + +
402A LEU* 3.1 28.3 + - + +
404A GLU* 1.3 79.4 - - + +
406A VAL* 1.3 65.2 + - + +
408A ARG* 3.4 22.1 + - - +
409A GLY 3.5 3.5 + - - -
414A PRO* 3.5 22.7 - - + +
415A GLY 4.2 3.4 - - - +
416A ALA* 3.4 27.3 + - + -
446A VAL* 5.4 1.3 - - + -
448A ARG* 4.0 33.2 - - + -
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Residues in contact with VAL 406 (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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402A LEU 3.1 16.1 + - - +
403A GLN* 3.9 15.7 - - - +
405A LEU* 1.3 75.0 - - - +
407A ARG* 1.3 62.3 + - - +
409A GLY* 3.3 13.5 + - - -
416A ALA* 4.4 0.9 - - - -
419A ILE* 4.0 24.2 - - + -
429A LEU* 3.9 28.8 - - + +
435A PRO* 4.6 21.2 - - - +
438A LEU* 4.8 11.4 - - + +
440A LEU* 4.3 12.1 - - + -
446A VAL* 4.2 19.5 - - + -
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Residues in contact with ARG 407 (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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400A ASP 5.4 0.8 + - - -
403A GLN* 3.1 33.8 + - - +
404A GLU* 3.3 51.9 + - - +
406A VAL* 1.3 76.6 - - - +
408A ARG* 1.3 64.2 + - - +
409A GLY* 3.3 1.2 + - - -
435A PRO* 5.4 6.8 - - - +
436A SER* 5.7 11.9 - - - +
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Residues in contact with ARG 408 (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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404A GLU* 2.8 49.3 + - + +
405A LEU* 3.5 16.8 - - - +
406A VAL 3.3 0.2 - - - -
407A ARG* 1.3 72.8 - - - +
409A GLY* 1.3 64.3 + - - +
411A SER* 4.4 3.8 + - - -
412A GLN* 3.0 50.3 + - - +
414A PRO* 3.4 50.0 - - - +
415A GLY* 3.9 7.9 - - - -
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Residues in contact with GLY 409 (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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405A LEU 3.5 3.4 + - - -
406A VAL 3.3 13.3 + - - -
407A ARG 3.2 4.9 - - - -
408A ARG* 1.3 83.7 - - - +
410A ASN* 1.3 65.2 + - - -
411A SER* 3.2 2.0 - - - -
412A GLN 3.7 1.7 - - - +
415A GLY* 3.3 18.9 - - - -
416A ALA 4.2 9.6 - - - -
429A LEU* 5.3 8.1 - - - -
435A PRO* 5.8 5.8 - - - -
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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