Contacts of the helix formed by residues 399 - 416 (chain I) in PDB entry 1MKD
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 ASN 399 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398B ASP* 5.9 2.7 - - - +
399B ASN* 5.8 7.9 - - + -
398I ASP* 1.3 102.4 + - - +
400I TYR* 1.3 62.4 + - - +
401I SER* 2.6 46.7 + - - +
402I ASP* 3.2 24.5 + - - +
403I ARG* 3.1 27.9 + - - +
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Residues in contact with TYR 400 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286I GLU* 5.1 7.6 - - - -
359I LYS* 3.7 30.1 - - + +
360I MET* 3.8 31.1 - - + +
363I ASP* 2.9 24.2 + - - -
399I ASN* 1.3 69.9 - - - +
401I SER* 1.3 59.7 + - - +
402I ASP 2.9 4.3 - - - -
403I ARG* 2.7 25.2 + - + +
404I ILE* 2.7 65.7 + - + +
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Residues in contact with SER 401 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399I ASN* 2.6 22.6 + - - +
400I TYR* 1.3 83.1 - - - +
402I ASP* 1.3 60.7 + - - +
404I ILE* 3.5 15.1 - - - +
405I GLN* 3.2 32.0 + - - +
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Residues in contact with ASP 402 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383I MET* 3.2 26.9 - - + +
388I LYS* 5.0 3.1 + - - -
396I LEU 5.1 0.2 - - - +
397I LEU* 4.1 17.7 - - + +
398I ASP* 3.5 17.2 - - - +
399I ASN* 3.2 27.6 - - - +
400I TYR 2.9 1.0 - - - -
401I SER* 1.3 83.4 + - - +
403I ARG* 1.3 66.4 + - - +
405I GLN* 3.4 4.9 + - - +
406I VAL* 3.2 27.8 + - - +
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Residues in contact with ARG 403 (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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281I VAL* 3.7 22.9 - - - -
282I PHE* 3.7 12.4 - - + -
283I THR* 5.3 5.1 - - - +
286I GLU* 2.8 36.9 + - - +
397I LEU* 3.4 38.1 + - + -
398I ASP 2.8 29.1 + - - -
399I ASN 3.1 14.3 + - - +
400I TYR* 2.7 29.3 + - + +
402I ASP* 1.3 72.0 - - - +
404I ILE* 1.3 59.2 + - - +
405I GLN 3.1 1.8 - - - -
406I VAL* 3.1 4.3 + - - +
407I LEU* 3.0 31.8 + - + +
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Residues in contact with ILE 404 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360I MET* 3.9 36.6 - - + +
363I ASP* 4.1 14.6 - - + +
364I ILE* 4.2 13.0 - - + -
400I TYR* 2.7 61.5 + - + +
401I SER* 3.5 17.9 - - - +
403I ARG* 1.3 72.7 - - - +
405I GLN* 1.3 60.6 + - - +
407I LEU* 4.4 9.4 - - + -
408I GLN* 2.9 35.1 + - - +
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Residues in contact with GLN 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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376I LEU* 5.2 2.0 - - + -
379I ASP* 3.7 44.2 + - + +
380I LEU* 5.5 0.9 - - - +
383I MET* 3.1 27.2 - - + +
401I SER* 3.2 21.1 + - - +
402I ASP* 3.4 6.6 + - - +
403I ARG 3.1 0.4 - - - -
404I ILE* 1.3 81.5 - - + +
406I VAL* 1.3 59.1 + - + +
408I GLN* 3.4 15.6 + - - +
409I ASN* 2.9 46.0 + - - +
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Residues in contact with VAL 406 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278I LEU* 4.6 6.7 - - + -
282I PHE* 3.8 22.4 - - + -
380I LEU* 5.4 2.5 - - + -
383I MET* 3.7 20.9 - - - -
395I LEU* 5.7 0.9 - - + -
397I LEU* 3.6 19.3 - - + -
402I ASP 3.2 15.9 - - - +
403I ARG 3.1 6.8 + - - +
405I GLN* 1.3 75.4 - - - +
407I LEU* 1.3 60.0 + - - +
409I ASN* 3.4 5.0 + - - +
410I MET* 2.8 28.0 + - + +
481I TRP* 3.8 24.7 - - + -
484I LEU* 4.3 13.7 - - + -
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Residues in contact with LEU 407 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273I LEU* 4.1 12.3 - - + -
282I PHE* 3.6 32.5 - - + -
286I GLU* 4.1 35.7 - - + +
290I ALA* 4.1 17.7 - - + -
360I MET* 5.0 4.7 - - + -
364I ILE* 4.0 23.3 - - + -
403I ARG 3.0 20.1 + - - +
404I ILE* 3.8 15.0 - - + +
406I VAL* 1.3 72.7 - - - +
408I GLN* 1.3 66.4 + - - +
410I MET* 3.3 8.6 + - - +
411I VAL* 3.0 28.9 + - - +
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Residues in contact with GLN 408 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363I ASP* 3.1 37.5 - - - +
364I ILE* 4.0 15.3 - - + +
367I ALA* 3.7 21.3 - - + +
368I THR* 6.1 0.3 - - - +
376I LEU* 4.1 17.7 - - + +
404I ILE* 2.9 29.7 + - + +
405I GLN* 3.5 18.3 - - - +
406I VAL 3.2 0.2 - - - -
407I LEU* 1.3 77.2 - - - +
409I ASN* 1.3 64.2 + - - +
410I MET 3.2 0.3 + - - -
411I VAL* 3.3 2.1 + - - +
412I HIS* 2.9 23.2 + - - +
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Residues in contact with ASN 409 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376I LEU* 3.3 47.4 + - - +
377I LEU 4.3 0.9 + - - -
380I LEU* 3.7 42.3 - - + +
405I GLN* 2.9 31.4 + - - +
406I VAL 3.9 3.4 - - - +
408I GLN* 1.3 79.6 - - - +
410I MET* 1.3 53.4 + - - +
412I HIS* 3.4 7.0 - - - +
413I CYS* 2.8 39.7 + - - -
477I LEU* 4.3 10.6 - - + +
481I TRP* 4.4 5.4 - - + -
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Residues in contact with MET 410 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269I THR* 4.2 11.2 - - + +
272I LEU* 3.7 28.9 - - + +
273I LEU* 3.5 44.4 - - + -
278I LEU* 3.4 33.2 - - + -
282I PHE* 4.3 7.6 - - + -
290I ALA* 5.4 1.3 - - - -
406I VAL* 2.8 20.2 + - + +
407I LEU* 3.4 13.2 - - + +
408I GLN 3.1 0.2 - - - -
409I ASN* 1.3 74.6 - - - +
411I VAL* 1.3 61.1 + - - +
413I CYS* 3.0 7.9 + - - +
414I ALA* 2.9 26.7 + - - +
481I TRP* 3.8 18.6 - - + -
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Residues in contact with VAL 411 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265I VAL* 4.4 8.7 - - + -
269I THR* 3.9 17.9 - - + +
290I ALA* 4.0 15.7 - - + +
293I ALA 5.2 0.4 - - - -
294I SER* 3.7 31.9 - - - +
297I HIS* 5.2 2.5 - - + -
364I ILE* 3.5 31.2 - - + -
368I THR* 4.3 16.4 - - + -
407I LEU 3.0 13.6 + - - +
408I GLN 4.0 0.9 - - - +
410I MET* 1.3 77.0 - - + +
412I HIS* 1.3 52.7 + - - +
414I ALA* 3.5 0.9 - - - +
415I ASP* 2.8 32.6 + - + +
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Residues in contact with HIS 412 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367I ALA 3.9 16.6 + - - +
368I THR* 4.5 13.8 + - + +
370I MET* 3.9 17.0 - - - -
373I HIS* 2.8 36.3 + - + +
376I LEU* 4.1 20.2 - - + -
377I LEU 6.2 0.2 - - - -
408I GLN 2.9 17.5 + - - +
409I ASN* 3.4 9.0 - - - +
410I MET 3.1 0.2 - - - -
411I VAL* 1.3 74.9 - - - +
413I CYS* 1.3 63.4 + - - +
415I ASP* 3.3 9.1 + - - +
416I LEU* 3.0 43.6 + - + +
477I LEU* 3.5 28.5 - - + -
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Residues in contact with CYS 413 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272I LEU* 4.1 5.4 - - + -
409I ASN* 2.8 20.5 + - - -
410I MET* 3.0 8.7 + - - +
412I HIS* 1.3 72.8 - - - +
414I ALA* 1.3 65.5 + - - +
416I LEU 3.0 5.2 + - - -
417I SER 3.0 18.2 + - - -
477I LEU* 3.8 32.5 - - - -
478I TRP* 3.3 31.9 - - + -
481I TRP* 3.8 35.4 - - - -
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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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264I ASP* 5.4 0.9 - - - +
265I VAL* 3.8 24.7 - - + +
268I SER* 3.9 13.9 - - - -
269I THR* 3.4 28.9 - - - +
272I LEU* 4.1 5.1 - - + +
410I MET 2.9 11.6 + - - +
411I VAL 3.5 7.0 - - - +
413I CYS* 1.3 77.6 - - - +
415I ASP* 1.3 61.2 + - - +
417I SER* 2.8 27.6 + - - -
418I ASN* 5.5 0.7 + - - -
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Residues in contact with ASP 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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256I TYR* 4.3 6.9 + - - -
261I HIS* 2.9 17.0 + - - -
265I VAL* 3.9 8.9 - - + +
297I HIS* 2.8 16.8 + - + +
368I THR* 4.1 20.2 - - + +
411I VAL 2.8 21.5 + - - +
412I HIS* 3.6 11.5 + - - +
413I CYS 3.2 0.2 - - - -
414I ALA* 1.3 73.5 - - - +
416I LEU* 1.3 68.2 + - + +
417I SER 3.4 1.7 + - - -
418I ASN* 5.2 2.4 + - - +
2017I ZN 2.1 36.3 - - - -
3009I ZAR 6.0 1.6 - - - -
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Residues in contact with LEU 416 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370I MET* 4.0 14.6 - - - -
412I HIS* 3.0 48.3 + - + +
413I CYS 3.0 5.1 + - - +
415I ASP* 1.3 88.7 - - + +
417I SER* 1.3 57.0 + - - +
418I ASN* 3.5 2.9 - - - +
419I PRO* 4.0 4.8 - - - +
469I PHE* 3.7 26.5 - - + -
473I ILE* 3.9 20.6 - - + -
474I VAL* 3.7 20.0 - - + +
477I LEU* 3.8 16.4 - - + -
478I TRP* 3.2 14.6 + - - -
3009I ZAR 4.9 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
------------------------------------------------------------
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