Contacts of the helix formed by residues 400 - 418 (chain A) 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 GLY 400 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397A HIS* 2.7 20.6 + - - +
398A PRO 3.1 2.2 + - - -
399A ASP* 1.3 78.2 - - - +
401A PRO* 1.3 78.0 - - - +
402A ALA* 3.4 2.2 - - - -
403A ALA* 2.9 7.2 + - - +
404A GLY 2.9 16.6 + - - -
59H TYR* 3.8 15.0 - - - -
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Residues in contact with PRO 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A LEU* 3.6 24.5 - - + -
179A ASP* 5.2 4.9 - - + +
180A LEU* 3.5 24.6 - - + +
394A THR 3.8 13.6 - - - +
395A LEU* 4.7 12.6 - - + +
400A GLY* 1.3 81.5 - - - -
402A ALA* 1.3 57.0 + - - +
404A GLY* 2.5 24.6 + - - -
405A ALA 2.8 11.1 + - - -
59H TYR* 3.7 29.2 - - + -
61H TRP* 5.1 7.9 - - + -
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Residues in contact with ALA 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ASP* 4.6 20.7 - - + +
180A LEU* 4.1 1.5 - - - +
183A ASN* 3.5 31.9 - - - +
399A ASP 5.9 0.4 - - - +
400A GLY 3.3 1.0 + - - -
401A PRO* 1.3 78.7 - - - +
403A ALA* 1.3 62.8 + - - +
405A ALA* 3.3 5.6 + - - +
406A ARG* 3.2 27.7 + - - +
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Residues in contact with ALA 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A HIS* 3.5 9.0 - - + +
399A ASP* 3.2 37.2 + - + +
400A GLY 2.9 11.0 + - - +
402A ALA* 1.3 77.5 - - - +
404A GLY* 1.3 58.1 + - - +
406A ARG* 3.5 22.1 + - - +
407A ALA* 3.0 28.4 + - - +
430A GLU* 3.6 10.9 - - + +
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Residues in contact with GLY 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A PRO* 6.4 0.2 - - - -
393A GLY 4.9 1.5 - - - +
394A THR* 3.7 15.4 - - - -
397A HIS* 3.6 26.2 - - - -
400A GLY 2.9 6.7 + - - -
401A PRO 2.5 14.9 + - - -
403A ALA* 1.3 72.9 - - - +
405A ALA* 1.3 57.7 + - - -
407A ALA* 3.4 2.2 - - - +
408A VAL* 3.1 29.6 + - - +
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Residues in contact with ALA 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A TYR* 3.7 15.8 - - - +
180A LEU* 4.1 21.1 - - + +
183A ASN* 2.8 28.9 - - + +
185A ALA* 4.4 5.8 - - + +
394A THR* 3.9 1.4 - - - +
401A PRO 2.8 8.7 + - - +
402A ALA 3.6 8.1 - - - +
404A GLY* 1.3 73.4 - - - +
406A ARG* 1.3 63.9 + - - +
407A ALA 3.2 0.3 + - - -
408A VAL* 3.3 3.8 + - - +
409A ARG* 3.1 26.5 + - - +
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Residues in contact with ARG 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A ASN* 2.7 50.6 + - + +
402A ALA* 3.2 18.8 + - - +
403A ALA* 3.7 26.0 - - - +
405A ALA* 1.3 75.6 - - - +
407A ALA* 1.3 51.2 + - - +
409A ARG* 3.5 6.0 + - - +
410A GLN* 2.7 44.2 + - + +
430A GLU* 3.0 32.4 + - + +
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Residues in contact with ALA 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A PRO* 4.4 7.9 - - + -
397A HIS* 4.2 6.1 - - + -
403A ALA 3.0 18.4 + - - +
404A GLY* 3.4 10.1 - - - +
405A ALA 3.1 0.2 - - - -
406A ARG* 1.3 73.3 - - - +
408A VAL* 1.3 58.5 + - - +
410A GLN* 2.8 33.5 + - - +
411A ALA* 2.9 13.5 + - - +
430A GLU* 3.7 23.1 - - - +
431A LEU* 4.1 6.6 - - - +
434A ALA* 4.4 7.9 - - + -
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Residues in contact with VAL 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A TYR* 3.7 45.3 - - + +
372A PRO* 3.8 25.5 - - + +
375A ILE* 4.8 7.6 - - + -
388A LEU* 6.0 1.1 - - + -
390A LEU* 3.9 21.8 - - + -
393A GLY 4.2 3.4 - - - +
394A THR* 3.9 9.4 - - - +
404A GLY 3.1 15.1 + - - +
405A ALA 3.9 0.4 - - - +
407A ALA* 1.3 74.3 - - - +
409A ARG* 1.3 57.4 + - - +
411A ALA* 3.3 3.2 + - - +
412A ILE* 3.0 37.4 + - + +
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Residues in contact with ARG 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A ARG* 3.4 49.8 - - - +
158A TYR* 3.8 15.0 - - + -
184A GLY* 2.5 65.9 + - - +
186A ASP* 4.2 1.4 + - - -
222A GLU* 5.2 6.7 + - - +
224A LYS* 5.0 2.6 - - - +
405A ALA 3.1 13.7 + - - +
406A ARG* 3.9 6.3 - - - +
408A VAL* 1.3 76.1 - - - +
410A GLN* 1.3 57.3 + - - +
412A ILE* 3.8 14.7 - - - +
413A ASP* 3.1 42.3 + - - +
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Residues in contact with GLN 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A ARG* 2.7 27.4 + - + +
407A ALA* 2.8 10.4 + - - +
409A ARG* 1.3 75.3 - - - +
411A ALA* 1.3 57.1 + - - +
413A ASP* 3.1 11.2 + - - +
414A ALA* 2.8 25.5 + - - +
424A TYR* 3.6 14.7 - - + -
428A HIS* 3.4 27.6 - - + +
430A GLU* 2.6 37.6 + - - +
431A LEU* 2.6 40.7 + - + +
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Residues in contact with ALA 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A PRO* 3.7 30.1 - - + +
375A ILE* 4.2 13.0 - - + -
407A ALA 2.9 10.6 + - - +
408A VAL 3.6 7.0 - - - +
410A GLN* 1.3 75.5 - - - +
412A ILE* 1.3 50.2 + - - +
414A ALA* 2.5 31.4 + - - +
415A ILE* 2.7 25.4 + - + +
421A LEU* 6.0 3.4 - - + -
431A LEU* 4.4 12.6 - - + +
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Residues in contact with ILE 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ARG* 4.2 25.8 - - + +
156A PRO* 4.3 14.6 - - + +
158A TYR* 3.9 27.8 - - + -
375A ILE* 4.5 14.1 - - + +
379A ILE* 4.8 10.0 - - + +
388A LEU* 4.6 10.3 - - + -
408A VAL* 3.0 26.2 + - + +
409A ARG* 3.8 17.9 - - - +
411A ALA* 1.3 74.2 - - - +
413A ASP* 1.3 62.5 + - - +
415A ILE* 3.3 6.6 + - - +
416A MET* 2.9 48.6 + - + +
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Residues in contact with ASP 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A ARG* 5.4 3.3 - - - -
409A ARG* 3.1 24.8 + - - +
410A GLN* 3.1 12.1 + - - +
412A ILE* 1.3 81.5 - - - +
414A ALA* 1.3 58.7 + - - +
416A MET* 3.6 6.1 + - - +
417A GLN* 2.8 41.6 + - - +
424A TYR* 4.0 15.5 + - - +
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Residues in contact with ALA 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410A GLN 2.8 10.9 + - - +
411A ALA* 2.5 25.2 + - - +
413A ASP* 1.3 68.0 - - - +
415A ILE* 1.3 59.2 + - + +
416A MET 3.1 1.6 - - - -
417A GLN* 3.0 4.7 + - - +
418A GLY 2.9 24.4 + - - -
419A ILE 3.4 26.4 + - - +
421A LEU* 4.9 8.5 - - + +
424A TYR* 3.7 30.0 - - + -
431A LEU* 5.0 0.2 - - + -
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Residues in contact with ILE 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A PRO 5.9 0.2 - - - +
375A ILE* 3.9 11.9 - - + -
376A GLN* 3.1 57.4 - - + +
379A ILE* 3.8 44.0 - - + -
380A GLU* 5.7 0.9 - - + +
411A ALA* 2.7 21.0 + - + +
412A ILE 4.0 3.4 - - - +
414A ALA* 1.3 73.0 - - + +
416A MET* 1.3 60.6 + - + +
418A GLY* 3.8 10.2 + - - +
419A ILE 5.0 0.9 - - - -
421A LEU* 6.3 2.9 - - + -
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Residues in contact with MET 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ASP* 4.3 11.7 - - + -
155A ARG* 3.9 33.9 - - + +
156A PRO* 4.3 4.3 - - - -
379A ILE* 5.7 3.4 - - + -
384A THR* 4.0 25.8 - - + -
412A ILE* 2.9 37.4 + - + +
413A ASP* 3.8 9.0 - - - +
415A ILE* 1.3 80.0 - - + +
417A GLN* 1.3 63.5 + - + +
418A GLY 3.4 0.2 - - - -
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Residues in contact with GLN 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A ASP* 2.8 30.9 - - - +
414A ALA 3.0 4.4 + - - +
416A MET* 1.3 80.8 - - + +
418A GLY* 1.3 56.1 + - - +
419A ILE* 3.1 38.5 + - + +
424A TYR* 4.1 16.6 + - - -
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Residues in contact with GLY 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414A ALA 2.9 6.2 + - - -
415A ILE* 3.8 8.1 + - - -
416A MET 3.4 3.2 - - - -
417A GLN* 1.3 76.9 - - - +
419A ILE* 1.3 64.1 + - - +
420A PRO* 3.0 10.7 - - - +
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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