Contacts of the helix formed by residues 394 - 404 (chain S) in PDB entry 1I84
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 394 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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388S CYS* 3.9 6.1 - - - -
393S ILE* 1.3 82.4 - - - +
395S VAL* 1.3 84.1 + - - +
396S THR* 2.6 20.0 + - - +
397S ASP* 2.4 34.5 + - + +
398S PHE* 2.9 22.9 + - - +
612S LEU* 4.5 2.6 - - + +
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Residues in contact with VAL 395 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381S ASN* 6.3 2.0 - - + -
384S ALA* 4.3 7.9 - - + +
385S GLN* 3.9 31.9 - - + +
388S CYS* 3.9 12.8 - - + +
394S ASN* 1.3 82.3 - - - +
396S THR* 1.3 71.2 + - + +
398S PHE* 2.5 29.9 + - - +
399S THR* 2.7 17.6 + - - +
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Residues in contact with THR 396 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394S ASN* 2.6 21.6 + - - +
395S VAL* 1.3 87.0 - - + +
397S ASP* 1.3 75.1 + - - +
399S THR* 3.2 9.2 + - - -
400S ARG* 2.9 23.5 + - - +
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Residues in contact with ASP 397 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394S ASN* 2.4 37.7 + - + +
395S VAL 2.7 3.2 + - - -
396S THR* 1.3 87.4 + - - +
398S PHE* 1.3 62.0 + - - +
400S ARG* 3.0 27.7 + - - +
401S SER* 2.5 30.9 + - - +
612S LEU* 3.4 22.2 - - + +
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Residues in contact with PHE 398 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362S LEU* 4.8 0.2 - - + -
365S ILE* 3.9 3.8 - - + -
367S PHE* 6.1 0.2 - + - -
384S ALA* 3.9 24.0 - - + -
387S VAL* 4.6 8.3 - - + -
388S CYS* 3.2 17.7 - - - -
391S MET* 4.3 9.9 - - + -
393S ILE* 3.4 15.0 - - + -
394S ASN 2.9 18.2 + - - +
395S VAL 2.5 7.4 + - - +
397S ASP* 1.3 75.9 - - - +
399S THR* 1.3 58.0 + - - +
401S SER* 3.1 7.0 + - - -
402S ILE* 2.5 58.7 + - + +
427S ILE* 3.3 35.0 - - + -
430S LEU* 4.1 10.8 - - + -
609S VAL* 3.3 28.0 - - + -
612S LEU* 3.9 6.8 - - - +
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Residues in contact with THR 399 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378S MET* 3.8 26.2 - - + -
381S ASN* 6.1 0.9 - - - +
384S ALA* 5.8 3.7 - - + +
395S VAL* 2.7 27.6 + - - +
396S THR* 3.2 9.7 + - - -
398S PHE* 1.3 77.4 - - + +
400S ARG* 1.3 53.4 + - - +
402S ILE* 2.9 8.3 + - + +
403S LEU* 2.6 64.6 + - + +
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Residues in contact with ARG 400 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396S THR* 2.9 16.0 + - - +
397S ASP* 3.5 37.0 + - - +
399S THR* 1.3 70.3 - - - +
401S SER* 1.3 63.6 + - - +
403S LEU* 2.6 12.1 + - - -
404S THR* 2.4 66.4 + - + +
406S ARG* 4.3 42.6 - - - +
415S GLN* 5.3 1.1 - - - +
608S ASN* 5.1 4.4 - - - +
612S LEU* 6.1 0.2 - - - +
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Residues in contact with SER 401 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397S ASP* 2.5 26.7 + - - -
398S PHE* 3.3 5.8 - - - -
400S ARG* 1.3 82.3 + - - +
402S ILE* 1.3 57.4 + - - +
403S LEU 3.5 0.2 + - - -
404S THR 3.9 2.0 - - - -
405S PRO* 4.0 5.9 - - - +
418S GLN* 4.0 3.1 - - - +
606S ASN* 2.5 28.1 + - - -
608S ASN* 3.4 38.8 + - - +
609S VAL* 3.9 14.1 - - - -
612S LEU* 4.2 8.5 - - - +
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Residues in contact with ILE 402 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367S PHE* 3.3 29.4 - - + -
378S MET* 5.5 0.4 - - - -
398S PHE* 2.5 53.2 + - + +
399S THR* 3.3 12.6 - - + +
401S SER* 1.3 74.5 - - - +
403S LEU* 1.3 64.9 + - + +
418S GLN* 2.9 17.7 + - - +
423S ALA* 4.1 13.0 - - - +
426S ALA* 5.3 5.3 - - + +
427S ILE* 3.5 28.9 - - + +
430S LEU* 4.5 4.9 - - + -
606S ASN* 4.3 4.5 - - + +
609S VAL* 3.7 26.2 - - + -
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Residues in contact with LEU 403 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367S PHE* 3.4 23.6 - - + -
376S ALA 3.5 24.5 - - - +
377S SER* 3.7 16.8 - - - +
378S MET* 4.0 5.8 - - + +
399S THR* 2.6 55.0 + - + +
400S ARG* 2.6 4.2 + - - +
402S ILE* 1.3 80.3 - - + +
404S THR* 1.3 66.2 + - + +
405S PRO* 3.3 3.8 - - - +
417S ALA* 3.7 3.2 - - - +
418S GLN* 2.9 35.3 + - - +
423S ALA* 5.2 6.0 - - + +
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Residues in contact with THR 404 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400S ARG* 2.4 61.8 + - + +
401S SER* 3.9 1.2 - - - -
403S LEU* 1.3 78.0 - - + +
405S PRO* 1.3 65.2 - - - +
406S ARG* 2.9 10.0 + - - -
415S GLN* 4.1 13.6 + - - -
416S LYS 3.2 8.3 - - - -
417S ALA* 4.0 13.5 - - + +
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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