Contacts of the helix formed by residues 400 - 418 (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 GLY 400 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59E TYR* 3.4 17.0 - - - -
394I THR 4.8 0.4 - - - -
397I HIS* 3.0 17.5 + - - +
398I PRO 3.2 1.2 + - - -
399I ASP* 1.3 80.2 - - - +
401I PRO* 1.3 66.3 - - - -
402I ALA 3.4 2.2 - - - -
403I ALA* 2.9 5.4 + - - +
404I GLY 2.7 30.8 + - - -
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Residues in contact with PRO 401 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59E TYR* 3.8 30.3 - - + -
61E TRP* 4.9 9.9 - - + -
176I LEU* 3.5 34.1 - - + -
179I ASP* 5.3 5.4 - - + +
180I LEU* 3.8 16.9 - - + +
394I THR 4.3 10.0 - - - +
395I LEU* 4.1 9.6 - - + +
400I GLY* 1.3 79.4 - - - +
402I ALA* 1.3 57.3 + - - +
404I GLY* 2.6 23.0 + - - +
405I ALA 2.9 12.1 + - - -
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Residues in contact with ALA 402 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179I ASP* 4.5 20.5 - - + +
180I LEU* 4.4 0.6 - - - +
183I ASN* 3.6 27.4 - - - +
400I GLY 3.4 0.4 - - - -
401I PRO* 1.3 80.3 - - - +
403I ALA* 1.3 60.8 + - - +
405I ALA* 3.6 3.4 + - - +
406I ARG* 3.3 36.2 + - - +
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Residues in contact with ALA 403 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397I HIS* 3.5 8.3 - - + +
399I ASP* 3.2 38.5 + - + +
400I GLY 2.9 12.0 + - - +
402I ALA* 1.3 79.0 - - - +
404I GLY* 1.3 61.9 + - - +
406I ARG* 3.3 21.5 + - - +
407I ALA* 3.0 18.5 + - - +
430I GLU* 3.5 15.9 - - + +
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Residues in contact with GLY 404 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393I GLY 5.4 0.9 - - - -
394I THR* 3.5 27.1 - - - -
397I HIS* 3.6 15.8 - - - -
400I GLY 2.7 7.1 + - - -
401I PRO 2.6 14.1 + - - -
403I ALA* 1.3 68.3 - - - +
405I ALA* 1.3 64.3 + - - -
407I ALA* 3.0 13.4 + - - +
408I VAL* 3.0 17.4 + - - +
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Residues in contact with ALA 405 (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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158I TYR* 3.5 25.0 - - + +
180I LEU* 3.9 28.3 - - + +
183I ASN* 3.7 18.8 - - + +
185I ALA* 5.0 0.4 - - + -
394I THR* 3.8 2.6 - - - +
401I PRO 2.9 12.8 + - - +
402I ALA 3.9 6.5 - - - +
404I GLY* 1.3 71.5 - - - +
406I ARG* 1.3 62.0 + - - +
408I VAL* 3.4 2.6 + - - +
409I ARG* 3.2 27.2 + - - +
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Residues in contact with ARG 406 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183I ASN* 2.6 50.7 + - + +
402I ALA* 3.3 23.6 + - - +
403I ALA* 3.6 26.2 - - - +
404I GLY 3.2 0.8 - - - -
405I ALA* 1.3 76.5 - - - +
407I ALA* 1.3 57.9 + - - +
409I ARG* 3.5 4.8 + - - +
410I GLN* 2.8 40.5 + - + +
430I GLU* 2.9 35.3 + - + +
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Residues in contact with ALA 407 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372I PRO* 4.4 6.1 - - + -
397I HIS* 4.1 10.1 - - + -
403I ALA 3.0 12.4 + - - +
404I GLY 3.0 8.8 + - - +
406I ARG* 1.3 74.1 - - - +
408I VAL* 1.3 66.8 + - - +
410I GLN* 3.0 5.7 + - - +
411I ALA* 2.8 22.3 + - - +
430I GLU* 3.6 31.5 - - - +
431I LEU* 3.8 12.0 - - - +
434I ALA* 4.2 7.4 - - + -
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Residues in contact with VAL 408 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158I TYR* 3.4 35.4 - - + +
372I PRO* 4.2 8.1 - - + -
375I ILE* 5.0 4.5 - - + -
388I LEU* 6.3 0.2 - - + -
390I LEU* 3.8 25.4 - - + -
393I GLY 4.2 7.4 - - - +
394I THR* 3.5 23.8 - - - +
404I GLY 3.0 13.9 + - - +
405I ALA 3.4 6.3 + - - +
407I ALA* 1.3 75.2 - - - +
409I ARG* 1.3 63.1 + - - +
411I ALA* 2.9 18.9 + - - +
412I ILE* 2.9 22.2 + - + +
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Residues in contact with ARG 409 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155I ARG* 3.5 46.2 - - - +
158I TYR* 3.9 12.8 - - + -
183I ASN 4.6 0.7 - - - +
184I GLY* 2.8 49.9 + - - +
186I ASP* 4.3 1.0 + - - -
222I GLU* 5.5 5.5 + - - -
224I LYS* 5.2 2.8 - - - +
405I ALA 3.2 16.2 + - - +
406I ARG* 3.8 5.2 - - - +
408I VAL* 1.3 78.4 - - - +
410I GLN* 1.3 58.1 + - - +
412I ILE* 3.0 16.1 + - - +
413I ASP* 2.9 47.0 + - - +
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Residues in contact with GLN 410 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406I ARG* 2.8 32.9 + - - +
407I ALA 3.0 5.4 + - - +
409I ARG* 1.3 76.3 - - + +
411I ALA* 1.3 58.0 + - - +
413I ASP* 3.9 5.1 - - - +
414I ALA* 3.0 24.4 + - - +
424I TYR* 3.2 25.4 - - + +
428I HIS* 2.9 41.6 - - + +
430I GLU* 3.1 26.5 - - - +
431I LEU* 3.1 27.7 - - + +
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Residues in contact with ALA 411 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372I PRO* 3.6 36.8 - - + +
375I ILE* 4.1 7.2 - - + -
407I ALA 2.8 12.4 + - - +
408I VAL 2.9 9.8 + - - +
410I GLN* 1.3 75.4 - - - +
412I ILE* 1.3 58.6 + - - +
414I ALA* 3.5 2.3 + - - +
415I ILE* 2.9 36.1 + - - +
421I LEU* 3.7 15.7 - - + +
431I LEU* 4.2 4.4 - - + +
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Residues in contact with ILE 412 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155I ARG* 4.2 15.3 - - + +
156I PRO* 4.1 36.1 - - + +
158I TYR* 4.0 26.2 - - + -
375I ILE* 4.1 14.4 - - + -
379I ILE* 5.0 2.9 - - + -
388I LEU* 4.7 7.4 - - + -
408I VAL* 2.9 24.4 + - + +
409I ARG* 3.0 18.4 + - - +
411I ALA* 1.3 72.8 - - - +
413I ASP* 1.3 56.6 + - - +
415I ILE* 3.2 8.6 + - - +
416I MET* 2.7 53.1 + - + +
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Residues in contact with ASP 413 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155I ARG* 5.1 5.2 - - - -
409I ARG* 2.9 35.6 + - - +
410I GLN* 3.9 6.3 - - - +
412I ILE* 1.3 79.4 - - - +
414I ALA* 1.3 55.7 + - - +
416I MET* 3.0 10.0 + - - +
417I GLN* 2.7 49.0 + - - +
424I TYR* 4.0 15.1 + - - +
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Residues in contact with ALA 414 (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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410I GLN 3.0 19.2 + - - +
413I ASP* 1.3 76.8 - - - +
415I ILE* 1.3 51.2 + - - +
417I GLN* 3.2 5.0 + - - +
418I GLY 2.7 30.1 + - - -
419I ILE* 2.9 21.6 + - - +
421I LEU* 3.5 24.0 - - + -
424I TYR* 3.5 30.8 - - + -
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Residues in contact with ILE 415 (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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375I ILE* 3.7 17.9 - - + -
376I GLN* 3.3 52.5 - - + +
379I ILE* 3.8 33.7 - - + -
380I GLU 5.8 0.2 - - - +
411I ALA 2.9 24.3 + - - +
412I ILE* 3.5 4.5 - - - +
414I ALA* 1.3 74.2 - - - +
416I MET* 1.3 68.3 + - + +
418I GLY* 2.9 15.3 + - - -
419I ILE 4.8 1.8 - - - +
421I LEU* 4.3 12.6 - - + -
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Residues in contact with MET 416 (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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154I ASP* 4.4 11.2 - - + -
155I ARG* 3.9 38.6 - - + +
156I PRO* 4.1 5.4 - - - -
379I ILE* 5.8 3.4 - - - -
384I THR* 3.9 22.2 - - + -
412I ILE* 2.7 38.9 + - + +
413I ASP* 3.3 12.6 - - - +
415I ILE* 1.3 76.1 - - - +
417I GLN* 1.3 64.5 + - + +
418I GLY* 3.3 0.3 + - - -
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Residues in contact with GLN 417 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413I ASP* 2.7 31.6 + - - +
414I ALA 3.8 2.0 - - - +
416I MET* 1.3 75.5 - - + +
418I GLY* 1.3 64.5 + - - +
419I ILE* 3.8 20.4 - - + +
424I TYR* 3.8 25.8 + - - -
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Residues in contact with GLY 418 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414I ALA 2.7 5.7 + - - -
415I ILE* 2.9 16.2 + - - -
416I MET 3.1 1.1 - - - -
417I GLN* 1.3 81.1 - - - +
419I ILE* 1.3 59.0 + - - +
420I PRO* 4.0 6.1 - - - +
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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