Contacts of the helix formed by residues 379 - 387 (chain D) in PDB entry 4K9P
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 THR 379 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355D PRO* 3.4 30.3 - - + -
359D PHE* 3.5 25.0 - - - -
374D ASN* 5.1 0.4 + - - -
376D SER* 3.1 27.1 + - - +
377D THR 3.2 0.8 - - - -
378D SER* 1.3 93.7 - - - +
380D THR* 1.3 65.5 + - - +
381D ALA 3.3 2.7 - - - -
382D GLN* 3.3 14.8 + - - +
383D MET* 3.0 19.1 + - - +
453D MET* 4.5 4.1 - - + +
602D TPP 5.0 0.2 - - - +
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Residues in contact with THR 380 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252D LEU* 4.3 11.9 - - + -
374D ASN* 2.9 31.4 + - - +
376D SER 3.6 4.1 + - - -
377D THR* 3.6 15.3 + - - -
378D SER 3.7 1.8 - - - -
379D THR* 1.3 76.5 - - - +
381D ALA* 1.3 63.1 + - - +
383D MET* 3.1 13.9 + - - +
384D TRP* 3.2 29.0 + - + +
395D TYR* 4.1 4.3 - - - +
397D PHE* 4.1 16.1 - - + -
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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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252D LEU* 5.0 11.0 - - + -
379D THR 3.3 0.6 - - - -
380D THR* 1.3 80.9 - - - +
382D GLN* 1.3 71.1 + - + +
383D MET 3.4 0.2 + - - -
384D TRP* 3.5 4.4 + - - +
385D GLN* 3.4 31.2 + - - +
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Residues in contact with GLN 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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355D PRO* 4.0 8.1 - - - +
356D GLU* 3.7 37.5 + - + +
359D PHE* 3.9 13.5 - - + -
378D SER 3.7 9.6 + - - +
379D THR* 3.3 38.5 + - - +
380D THR 4.1 0.2 + - - -
381D ALA* 1.3 84.2 + - + +
383D MET* 1.3 64.8 + - - +
385D GLN* 3.4 9.7 + - - +
386D ARG* 3.2 33.3 + - - +
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Residues in contact with MET 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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359D PHE* 3.6 26.9 - - + -
372D TYR* 3.8 20.9 - - + -
373D LEU 4.0 9.0 - - - +
374D ASN* 3.5 34.3 - - + +
379D THR 3.0 12.9 + - - +
380D THR* 3.1 11.2 + - - +
382D GLN* 1.3 79.5 - - - +
384D TRP* 1.3 63.6 + - + +
386D ARG 3.4 0.2 + - - -
387D LEU* 3.2 56.5 + - + +
389D MET* 5.2 1.0 - - + +
395D TYR* 4.2 11.7 - - + -
425D VAL* 3.9 24.0 - - + -
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Residues in contact with TRP 384 (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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233D VAL* 4.1 13.5 - - + -
237D ALA* 3.9 12.6 + - + +
239D ARG 3.7 12.8 - - - -
240D CYS* 3.5 41.1 - - + -
244D THR* 4.0 12.8 - - + +
245D ARG* 4.5 4.5 + - - -
249D PHE* 3.8 33.4 - + + -
251D GLY* 6.1 0.4 - - - -
252D LEU* 3.7 42.0 - - + +
380D THR* 3.2 25.8 + - + +
381D ALA 3.9 7.2 - - - +
382D GLN 3.4 0.2 - - - -
383D MET* 1.3 79.1 - - + +
385D GLN* 1.3 64.1 + - + +
386D ARG 3.6 0.2 + - - -
387D LEU 4.0 10.7 - - - +
389D MET* 4.3 9.2 - - + -
395D TYR* 3.4 44.8 + + - -
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Residues in contact with GLN 385 (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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245D ARG* 3.1 17.8 + - - +
343D PRO* 3.0 34.4 - - + +
381D ALA* 3.4 20.8 + - - +
382D GLN* 3.4 12.6 + - - +
383D MET 3.2 0.8 - - - -
384D TRP* 1.3 82.3 - - + +
386D ARG* 1.3 66.4 + - + +
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Residues in contact with ARG 386 (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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245D ARG* 4.2 6.2 + - - +
343D PRO* 3.8 24.8 + - + +
344D ALA* 2.6 33.1 + - - +
345D LYS* 4.6 1.0 - - - +
346D VAL* 4.1 8.3 - - - +
356D GLU* 3.6 47.4 + - - +
359D PHE* 3.8 14.3 - - + +
360D ASP* 2.8 49.0 + - - +
363D ASN* 3.3 27.0 + - - +
382D GLN* 3.2 22.6 + - - +
383D MET 4.6 0.2 - - - +
384D TRP 3.3 0.2 - - - -
385D GLN* 1.3 89.7 + - + +
387D LEU* 1.3 61.9 + - - +
388D ASN 3.9 0.4 + - - -
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Residues in contact with LEU 387 (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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244D THR* 3.0 16.8 + - - -
245D ARG* 4.0 3.7 + - - -
359D PHE* 3.5 35.7 - - + +
362D LEU* 4.3 6.1 - - + -
363D ASN* 3.8 11.4 - - + +
372D TYR* 3.8 34.1 - - + +
383D MET* 3.2 54.1 + - + +
384D TRP 4.0 7.4 - - - +
385D GLN 3.7 0.2 - - - -
386D ARG* 1.3 80.3 - - - +
388D ASN* 1.3 60.6 + - - +
389D MET* 3.5 22.2 + - + +
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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