Contacts of the helix formed by residues 395 - 405 (chain A) in PDB entry 5IG6
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 ASP 395 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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372A PHE* 3.7 5.2 - - - +
374A LYS* 3.3 24.6 - - - +
375A PRO* 3.3 26.8 - - + +
376A VAL* 5.2 1.1 - - + +
394A MET* 1.3 79.7 - - - +
396A LEU* 1.4 64.5 + - - +
397A SER* 2.6 38.2 + - - -
398A THR* 2.7 26.8 + - - -
399A VAL* 3.1 22.9 + - - +
421A MET* 3.7 13.2 - - - -
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Residues in contact with LEU 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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357A LEU* 4.0 16.7 - - + +
360A LEU* 4.0 41.7 - - + +
361A LEU* 3.8 31.3 - - + +
369A ALA 4.8 0.2 - - - +
372A PHE* 2.8 36.4 + - + +
373A TYR* 4.3 5.6 - - + +
395A ASP* 1.4 72.0 - - - +
397A SER* 1.3 56.8 + - - +
399A VAL* 3.4 10.5 + - + +
400A LYS* 2.9 29.3 + - - +
418A VAL* 5.1 5.2 - - + -
421A MET* 3.8 21.8 - - + -
442A LEU* 4.3 8.1 - - + -
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Residues in contact with SER 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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361A LEU* 5.3 2.0 - - - +
373A TYR 3.1 18.7 + - - -
374A LYS* 3.8 18.9 - - - +
375A PRO* 3.6 14.6 - - - +
395A ASP* 2.6 23.0 + - - -
396A LEU* 1.3 72.8 - - - +
398A THR* 1.3 58.5 + - - +
400A LYS* 3.4 8.6 + - - +
401A ARG* 3.0 27.0 + - - +
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Residues in contact with THR 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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375A PRO* 4.4 5.0 - - - +
393A PRO 5.8 0.2 - - - +
394A MET* 3.6 26.9 - - + -
395A ASP* 2.7 29.8 + - - -
397A SER* 1.3 80.1 + - - +
399A VAL* 1.3 65.6 + - - +
401A ARG* 3.3 29.2 + - - +
402A LYS* 2.9 31.9 + - + +
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Residues in contact with VAL 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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357A LEU* 4.0 12.6 - - + -
394A MET* 3.8 18.6 - - + -
395A ASP 3.1 16.4 + - - +
396A LEU* 3.4 13.2 + - + +
398A THR* 1.3 73.9 - - - +
400A LYS* 1.3 56.8 + - - +
402A LYS 3.3 1.0 + - - -
403A MET* 2.9 26.9 + - - +
408A TYR* 3.4 26.4 - - - +
414A PHE* 3.6 33.2 - - + -
417A ASP* 4.3 6.3 - - + -
418A VAL* 4.3 15.5 - - + +
421A MET* 5.6 0.9 - - - -
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Residues in contact with LYS 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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357A LEU* 3.6 20.6 - - + +
358A LYS* 4.0 22.9 - - - +
361A LEU* 4.1 20.0 - - + -
396A LEU 2.9 17.2 + - - +
397A SER* 3.7 8.5 - - - +
399A VAL* 1.3 77.0 - - - +
401A ARG* 1.3 57.7 + - - +
403A MET* 3.2 2.1 + - + +
404A GLU* 2.5 65.7 + - + +
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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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397A SER 3.0 17.4 + - - +
398A THR* 3.7 25.2 + - - +
400A LYS* 1.3 75.3 - - - +
402A LYS* 1.3 82.0 + - - +
404A GLU* 3.3 11.6 + - - +
405A ASN* 2.9 64.9 + - - +
407A ASP* 4.4 8.3 + - - -
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Residues in contact with LYS 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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394A MET* 4.6 4.6 - - + +
398A THR* 2.9 33.1 + - + +
401A ARG* 1.3 99.3 - - - +
403A MET* 1.3 60.5 + - - +
405A ASN* 3.4 1.0 + - - -
406A ARG 3.2 2.9 + - - -
407A ASP* 2.9 46.6 + - + +
408A TYR* 3.5 29.7 + - + +
413A GLU* 5.0 1.4 + - - +
417A ASP* 2.8 34.5 + - - +
504A GOL 3.1 36.8 + - - -
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Residues in contact with MET 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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350A LEU* 4.0 28.3 - - + +
353A CYS* 3.8 19.7 - - + -
354A ASN* 3.4 35.4 - - - +
357A LEU* 4.3 6.5 - - + -
399A VAL 2.9 16.7 + - - +
400A LYS 3.2 5.1 + - - +
402A LYS* 1.3 76.6 - - - +
404A GLU* 1.3 64.1 + - + +
406A ARG* 3.0 18.6 + - - +
408A TYR* 3.8 14.5 - - + +
414A PHE* 3.6 33.4 - - + -
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Residues in contact with GLU 404 (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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358A LYS* 5.2 1.2 + - - -
400A LYS* 2.5 66.5 + - + +
401A ARG* 3.7 11.6 - - - +
403A MET* 1.3 74.2 - - + +
405A ASN* 1.3 65.6 + - - +
406A ARG* 3.3 7.8 + - - +
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Residues in contact with ASN 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* 2.9 46.8 + - - +
402A LYS* 4.0 4.7 - - - +
404A GLU* 1.3 82.8 - - - +
406A ARG* 1.3 67.1 + - - +
407A ASP* 3.2 10.7 + - + +
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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