Contacts of the helix formed by residues 375 - 383 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370F LEU* 4.2 15.5 - - + -
371F HIS 3.5 10.1 - - - +
372F PRO* 3.4 19.1 - - + +
374F ASN* 1.3 79.1 - - - +
376F GLN* 1.3 71.6 + - - +
377F PRO 3.3 0.7 - - - -
378F VAL* 2.7 18.6 + - - +
379F ILE* 3.0 14.8 + - + +
388F LEU* 4.3 26.2 - - + -
390F LEU* 4.2 15.0 - - + -
408F VAL* 4.6 8.3 - - + +
411F ALA* 3.9 24.9 - - + -
412F ILE* 4.3 17.5 - - + -
415F ILE* 3.8 16.2 - - + -
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Residues in contact with GLN 376 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372F PRO 4.7 0.4 + - - -
373F GLY 5.5 2.5 - - - +
374F ASN* 4.7 0.6 - - - +
375F ILE* 1.3 84.9 - - - +
377F PRO* 1.3 75.8 - - + +
379F ILE* 3.3 2.8 + - - +
380F GLU* 3.1 32.8 + - - +
415F ILE* 3.5 32.4 - - + +
421F LEU* 4.5 19.1 - - + +
440F HIS* 6.2 1.3 - - - +
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Residues in contact with PRO 377 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318F ALA* 5.4 1.6 - - - +
320F ALA* 4.9 9.0 - - + -
327F ARG* 4.9 3.3 + - - -
373F GLY 5.2 1.1 - - - +
374F ASN* 3.5 19.3 - - + +
375F ILE 3.4 4.0 - - - -
376F GLN* 1.3 105.8 - - + +
378F VAL* 1.3 58.9 + - - +
380F GLU* 3.7 8.6 - - + +
381F ALA* 3.4 22.2 + - - +
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Residues in contact with VAL 378 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317F THR 3.7 12.1 - - - +
318F ALA* 5.2 2.2 - - - -
320F ALA* 3.6 20.0 - - + -
366F SER* 3.6 25.6 - - - +
370F LEU* 4.1 13.2 - - + -
374F ASN 3.6 19.1 - - - +
375F ILE* 2.7 17.8 + - + +
377F PRO* 1.3 70.4 - - - +
379F ILE* 1.3 61.6 + - + +
381F ALA* 3.2 2.3 + - - -
382F LEU* 2.9 52.1 + - + +
386F ILE* 4.1 10.1 - - + -
388F LEU* 4.5 5.8 - - + -
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Residues in contact with ILE 379 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156F PRO* 3.9 23.1 - - + -
375F ILE* 3.0 11.6 + - + +
376F GLN 3.9 5.4 - - - +
378F VAL* 1.3 74.9 - - - +
380F GLU* 1.3 59.7 + - - +
383F GLY* 2.8 45.9 + - - +
384F THR* 4.1 16.6 - - + -
386F ILE* 4.5 9.9 - - + -
388F LEU* 4.2 19.1 - - + -
412F ILE* 5.1 5.4 - - + -
415F ILE* 3.6 44.4 - - + -
416F MET* 5.8 1.8 - - - -
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Residues in contact with GLU 380 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327F ARG* 4.7 6.8 + - - +
376F GLN* 3.1 32.5 + - - +
377F PRO* 3.7 9.0 - - + +
378F VAL 3.1 0.2 - - - -
379F ILE* 1.3 80.1 - - - +
381F ALA* 1.3 61.2 + - - +
383F GLY* 4.3 2.3 + - - -
415F ILE* 5.7 0.2 - - - +
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Residues in contact with ALA 381 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318F ALA* 4.8 1.3 - - + -
327F ARG* 3.2 48.7 - - + +
331F LEU* 3.4 29.7 - - + +
377F PRO 3.4 10.4 + - - +
378F VAL 3.2 2.0 + - - -
380F GLU* 1.3 79.6 - - - +
382F LEU* 1.3 74.1 + - + +
383F GLY 3.6 0.2 - - - -
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Residues in contact with LEU 382 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315F VAL* 5.0 1.8 - - + -
316F GLY 4.4 1.3 - - - +
318F ALA* 3.8 17.3 - - + -
327F ARG 5.1 0.2 - - - +
330F THR* 3.9 20.9 - - + -
331F LEU* 4.7 11.2 - - + +
334F VAL* 3.8 21.2 - - + +
338F ARG* 2.8 37.0 + - - +
366F SER* 4.2 15.5 - - - +
378F VAL* 2.9 35.2 + - + +
381F ALA* 1.3 98.1 - - + +
383F GLY* 1.3 60.7 + - - +
386F ILE* 3.8 16.8 - - + +
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Residues in contact with GLY 383 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338F ARG* 4.5 3.4 - - - -
379F ILE* 2.8 27.9 + - - +
380F GLU 4.3 2.1 + - - -
381F ALA 3.6 1.8 - - - -
382F LEU* 1.3 82.9 - - - +
384F THR* 1.3 64.6 + - - -
385F ASP 3.4 1.5 + - - -
386F ILE* 3.8 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