Contacts of the helix formed by residues 375 - 383 (chain I) in PDB entry 3KDO
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 ILE 375 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370I LEU* 4.2 22.0 - - + -
371I HIS 3.1 19.3 - - - +
372I PRO* 3.9 11.9 - - + +
374I ASN* 1.3 82.8 - - - +
376I GLN* 1.3 67.6 + - - +
377I PRO 3.4 1.1 - - - -
378I VAL* 3.2 9.3 + - - +
379I ILE* 2.9 30.9 + - + +
388I LEU* 4.5 18.4 - - + -
390I LEU* 4.3 8.1 - - + -
408I VAL* 4.7 7.9 - - + +
411I ALA* 4.1 22.0 - - + -
412I ILE* 4.1 20.9 - - + -
415I ILE* 3.7 14.6 - - + -
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Residues in contact with GLN 376 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372I PRO 5.1 0.6 + - - -
373I GLY 5.5 2.2 - - - +
375I ILE* 1.3 82.1 - - - +
377I PRO* 1.3 98.6 - - + +
379I ILE* 3.2 2.3 + - - +
380I GLU* 2.9 46.1 + - - +
415I ILE* 3.3 34.4 - - + +
421I LEU* 5.0 12.6 - - + -
440I HIS* 6.4 0.2 - - - +
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Residues in contact with PRO 377 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318I ALA* 6.0 2.0 - - - +
320I ALA* 4.9 9.2 - - + -
327I ARG* 5.2 0.9 + - - -
373I GLY 5.0 1.6 - - - +
374I ASN* 3.6 20.4 - - + +
375I ILE 3.5 2.7 - - - -
376I GLN* 1.3 113.3 - - + +
378I VAL* 1.3 60.8 + - - +
380I GLU* 3.4 7.5 + - + +
381I ALA* 3.1 24.9 + - - +
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Residues in contact with VAL 378 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317I THR* 3.5 13.5 - - - +
318I ALA* 5.4 2.9 - - - +
320I ALA* 3.3 31.9 - - + -
366I SER* 3.5 32.1 - - - +
370I LEU* 4.1 12.3 - - + -
374I ASN 3.8 8.1 - - - +
375I ILE* 3.2 10.0 + - + +
377I PRO* 1.3 77.1 - - - +
379I ILE* 1.3 58.7 + - + +
381I ALA* 3.3 3.6 + - - -
382I LEU* 2.9 41.8 + - + +
386I ILE* 4.2 8.5 - - + -
388I LEU* 4.5 4.3 - - + -
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Residues in contact with ILE 379 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156I PRO* 4.1 13.0 - - + -
375I ILE* 2.9 21.9 + - + +
376I GLN 3.8 2.5 - - - +
378I VAL* 1.3 76.9 - - + +
380I GLU* 1.3 58.2 + - - +
383I GLY* 3.0 42.0 + - - +
384I THR* 4.2 15.9 - - + -
386I ILE* 4.4 8.5 - - + -
388I LEU* 4.1 27.8 - - + -
412I ILE* 5.0 6.3 - - + -
415I ILE* 3.8 42.4 - - + -
416I MET* 5.8 2.2 - - - -
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Residues in contact with GLU 380 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327I ARG* 4.2 16.1 + - - +
376I GLN* 2.9 41.5 + - - +
377I PRO* 3.7 6.8 - - - +
378I VAL 3.2 0.2 - - - -
379I ILE* 1.3 77.8 - - - +
381I ALA* 1.3 61.8 + - - +
383I GLY* 4.5 2.0 + - - -
415I ILE* 5.8 0.4 - - - +
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Residues in contact with ALA 381 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318I ALA* 4.7 6.3 - - + -
327I ARG* 3.5 44.5 + - + +
331I LEU* 3.3 25.7 - - + +
377I PRO 3.1 17.0 + - - +
378I VAL 3.9 2.7 - - - +
380I GLU* 1.3 79.5 - - - +
382I LEU* 1.3 70.5 + - + +
383I GLY 3.6 0.2 - - - -
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Residues in contact with LEU 382 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315I VAL* 5.0 1.6 - - + -
316I GLY 4.5 0.4 - - - +
318I ALA* 4.5 6.1 - - + -
330I THR* 3.7 30.3 - - + -
331I LEU* 3.8 24.0 - - + +
334I VAL* 3.6 26.0 - - + -
338I ARG* 2.8 35.5 + - - -
366I SER* 3.4 26.0 - - - +
378I VAL* 2.9 23.7 + - + +
381I ALA* 1.3 87.8 - - + +
383I GLY* 1.3 59.4 + - - +
386I ILE* 3.7 14.9 - - + +
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Residues in contact with GLY 383 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338I ARG* 4.6 4.0 - - - -
379I ILE* 3.0 31.4 + - - +
380I GLU 4.5 1.2 + - - -
381I ALA 3.6 2.0 + - - -
382I LEU* 1.3 82.0 - - - +
384I THR* 1.3 63.5 + - - -
385I ASP 3.5 0.9 - - - -
386I ILE* 3.9 11.3 - - - +
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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
------------------------------------------------------------
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