Contacts of the helix formed by residues 375 - 383 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370D LEU* 4.1 18.8 - - + -
371D HIS 3.4 14.1 - - - +
372D PRO* 3.6 22.2 - - + +
373D GLY 3.8 0.2 - - - -
374D ASN* 1.3 80.8 - - - +
376D GLN* 1.3 67.7 + - - +
377D PRO* 3.2 2.5 - - - -
378D VAL* 2.9 9.2 + - - +
379D ILE* 2.9 25.5 + - + +
388D LEU* 4.3 28.9 - - + -
390D LEU* 4.4 7.0 - - + -
408D VAL* 4.7 8.3 - - + +
411D ALA* 4.1 17.0 - - + -
412D ILE* 4.1 20.0 - - + -
415D ILE* 3.8 14.6 - - + -
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Residues in contact with GLN 376 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372D PRO 5.0 0.4 + - - -
373D GLY 5.7 1.3 - - - +
374D ASN 4.8 0.2 - - - +
375D ILE* 1.3 82.1 - - - +
377D PRO* 1.3 80.9 - - + +
379D ILE* 3.4 1.9 + - - +
380D GLU* 3.0 52.7 + - - +
415D ILE* 3.3 35.0 - - + +
421D LEU* 4.7 15.9 - - + -
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Residues in contact with PRO 377 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318D ALA* 5.5 1.4 - - - +
320D ALA* 4.9 9.0 - - + -
327D ARG* 5.4 0.9 + - - -
373D GLY 5.0 2.0 - - - +
374D ASN* 3.5 22.7 - - + +
375D ILE 3.3 3.8 - - - -
376D GLN* 1.3 109.5 - - + +
378D VAL* 1.3 55.1 + - - +
380D GLU* 3.8 8.0 - - + +
381D ALA* 3.1 28.4 + - - +
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Residues in contact with VAL 378 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317D THR* 3.5 24.5 - - - +
318D ALA* 5.1 2.5 - - - +
320D ALA* 3.6 19.3 - - + -
366D SER* 3.7 19.1 - - - +
370D LEU* 4.1 13.5 - - + -
374D ASN 3.8 7.9 - - - +
375D ILE* 2.9 11.4 + - + +
377D PRO* 1.3 75.2 - - - +
379D ILE* 1.3 61.3 + - + +
381D ALA* 3.2 3.3 + - - -
382D LEU* 2.8 53.9 + - + +
386D ILE* 4.1 10.1 - - + -
388D LEU* 4.6 4.0 - - + -
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Residues in contact with ILE 379 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D PRO* 3.9 22.4 - - + -
375D ILE* 2.9 18.8 + - + +
376D GLN 4.0 2.7 - - - +
378D VAL* 1.3 75.3 - - + +
380D GLU* 1.3 58.8 + - - +
383D GLY* 2.8 42.0 + - - +
384D THR* 4.1 21.1 - - + -
386D ILE* 4.4 14.6 - - + -
388D LEU* 4.2 14.1 - - + -
412D ILE* 5.0 5.4 - - + -
415D ILE* 3.7 44.6 - - + -
416D MET* 5.7 1.3 - - - -
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Residues in contact with GLU 380 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327D ARG* 4.7 10.8 + - - +
376D GLN* 3.0 44.6 + - - +
377D PRO* 3.8 7.2 - - - +
378D VAL 3.2 0.2 - - - -
379D ILE* 1.3 78.6 - - - +
381D ALA* 1.3 62.1 + - - +
383D GLY* 4.4 1.7 + - - -
415D ILE* 5.7 0.2 - - - +
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Residues in contact with ALA 381 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318D ALA* 4.4 5.4 - - + -
327D ARG* 3.8 44.8 + - + +
331D LEU* 3.6 23.3 - - + +
377D PRO 3.1 19.0 + - - +
378D VAL 3.8 2.2 - - - +
380D GLU* 1.3 79.6 - - - +
382D LEU* 1.3 72.0 + - + +
383D GLY 3.8 0.3 + - - -
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Residues in contact with LEU 382 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315D VAL* 4.9 0.2 - - + -
316D GLY 4.4 1.3 - - - +
318D ALA* 4.2 13.2 - - + -
330D THR* 3.6 35.0 - - + -
331D LEU* 3.7 23.1 - - + +
334D VAL* 3.6 19.9 - - + +
338D ARG* 2.9 33.7 + - - -
366D SER* 3.3 26.5 - - - +
378D VAL* 2.8 32.9 + - + +
381D ALA* 1.3 76.9 - - + +
383D GLY* 1.3 58.6 + - - +
386D ILE* 3.8 15.1 - - + +
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Residues in contact with GLY 383 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338D ARG* 4.5 5.4 - - - -
379D ILE* 2.8 26.8 + - - +
380D GLU 4.4 1.5 + - - -
381D ALA 3.5 2.4 + - - -
382D LEU* 1.3 82.7 - - - +
384D THR* 1.3 65.0 + - - -
385D ASP 3.5 1.1 - - - -
386D ILE* 3.7 14.0 - - - +
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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