Contacts of the helix formed by residues 418 - 429 (chain K) in PDB entry 4ZZ7
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 ASP 418 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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484I ALA 3.8 3.8 - - - +
486I VAL* 3.4 19.2 - - + +
487I ARG 5.1 0.2 + - - -
481J TRP* 3.7 2.6 - - - -
258K ASP* 3.2 17.6 + - - +
416K THR* 3.0 10.7 + - - +
417K ARG* 1.3 78.2 - - - +
419K GLY* 1.3 64.0 + - - +
420K GLU* 3.3 12.8 + - - +
421K ALA* 3.1 27.2 + - + +
422K ALA* 3.3 22.2 + - - +
417L ARG* 2.8 46.0 + - - +
418L ASP* 5.2 0.2 - - - +
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Residues in contact with GLY 419 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481I TRP* 3.5 43.5 + - - -
481J TRP* 4.3 10.8 - - - -
417K ARG 3.6 1.4 + - - -
418K ASP* 1.3 71.4 - - - +
420K GLU* 1.3 62.1 + - - +
422K ALA* 3.2 5.5 + - - +
423K ARG 3.1 18.4 + - - -
417L ARG 3.1 12.9 + - - -
419L GLY* 4.5 1.3 - - - -
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Residues in contact with GLU 420 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481I TRP* 3.3 44.2 - - + +
482I PRO 4.8 0.7 - - - +
483I SER 3.3 26.2 - - - +
484I ALA* 3.5 17.7 - - - +
487I ARG* 2.8 41.2 + - - +
418K ASP* 3.3 10.3 + - - +
419K GLY* 1.3 72.8 - - - +
421K ALA* 1.3 64.0 + - - +
423K ARG* 3.3 2.4 + - - +
424K TYR* 3.0 24.8 + - - +
417L ARG* 4.7 0.4 - - - +
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Residues in contact with ALA 421 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486I VAL* 4.7 9.6 - - + -
487I ARG* 4.5 5.4 - - + -
256K MET* 4.9 1.1 - - + -
396K MET* 3.4 27.1 - - + +
414K ILE* 4.6 2.0 - - + -
416K THR* 4.0 14.4 - - + +
418K ASP* 3.1 28.7 + - + +
420K GLU* 1.3 80.4 + - - +
422K ALA* 1.3 63.8 + - - +
424K TYR* 3.5 0.3 + - - +
425K PHE* 3.1 25.8 + - - +
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Residues in contact with ALA 422 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479J GLN* 5.3 3.8 - - - +
481J TRP* 3.6 22.2 - - + -
414K ILE* 4.7 0.9 - - - -
416K THR* 4.3 6.5 - - + +
418K ASP 3.3 11.3 + - - +
419K GLY 3.2 10.2 + - - +
421K ALA* 1.3 80.7 - - - +
423K ARG* 1.3 56.8 + - - +
425K PHE* 3.7 2.4 - - - +
426K SER* 3.0 30.2 + - - -
436K ILE* 3.7 28.1 - - + +
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Residues in contact with ARG 423 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124I ARG* 4.9 1.6 - - - +
125I ASN* 3.6 20.8 + - - +
129I GLY* 3.7 28.0 + - - -
131I ASP* 3.0 45.6 + - - +
479I GLN* 5.2 6.5 - - - +
481I TRP* 3.9 30.7 - - + +
58J ASN* 6.1 1.4 - - - -
135J GLU* 5.6 0.2 + - - -
419K GLY 3.1 7.8 + - - +
420K GLU 3.3 3.1 + - - +
421K ALA 3.3 0.2 - - - -
422K ALA* 1.3 74.3 - - - +
424K TYR* 1.3 68.7 + - - +
426K SER* 3.4 8.2 + - - +
427K ASP* 2.9 65.9 + - + +
428K ASN* 5.7 0.4 + - - -
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Residues in contact with TYR 424 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487I ARG* 3.3 51.1 - - - +
396K MET* 4.5 0.7 - - + -
397K GLN* 2.9 31.3 + - - -
400K MET* 3.5 22.6 - - + +
420K GLU* 3.0 19.7 + - - +
421K ALA 4.0 2.9 - - - +
423K ARG* 1.3 79.8 - - - +
425K PHE* 1.3 61.1 + - - +
427K ASP* 4.9 0.9 - - - -
428K ASN* 3.0 57.0 + - + +
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Residues in contact with PHE 425 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254K ILE* 3.3 32.1 - - + -
396K MET* 3.9 6.5 - - + -
400K MET* 3.9 17.7 - - + -
403K ILE* 4.3 0.4 - - + -
412K THR* 3.4 33.0 - - + -
413K CYS 3.7 9.9 - - - -
414K ILE* 3.2 38.4 - - + -
421K ALA 3.1 17.8 + - - +
422K ALA 3.7 3.4 - - - +
424K TYR* 1.3 75.9 - - - +
426K SER* 1.3 65.7 + - - +
429K ILE* 3.0 48.2 + - + +
434K VAL* 3.6 26.0 - - + -
436K ILE* 4.4 1.1 - - + -
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Residues in contact with SER 426 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133J TRP* 4.8 6.1 - - - -
135J GLU* 5.2 5.1 + - - -
475J LYS* 2.6 39.2 + - - +
477J VAL* 4.0 30.0 - - - +
422K ALA 3.0 16.3 + - - -
423K ARG* 3.4 12.0 + - - +
425K PHE* 1.3 78.7 - - - +
427K ASP* 1.3 55.8 + - - +
429K ILE* 4.2 1.0 - - - +
434K VAL* 4.0 19.5 - - - -
436K ILE* 4.3 4.5 - - - -
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Residues in contact with ASP 427 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124I ARG* 2.6 41.0 + - - +
57J ARG* 2.8 28.1 + - - -
58J ASN* 4.1 4.0 + - - +
135J GLU* 4.0 5.6 - - - +
137J GLN* 3.2 16.0 + - - +
475J LYS* 2.9 15.1 + - - -
423K ARG* 2.9 49.5 + - + +
424K TYR* 4.4 1.6 - - - +
426K SER* 1.3 80.3 + - - +
428K ASN* 1.3 69.2 + - - +
430K GLN* 5.3 0.2 + - - -
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Residues in contact with ASN 428 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57J ARG* 3.3 23.0 - - - +
58J ASN* 4.3 12.7 - - - +
400K MET* 5.2 4.9 - - - -
404K ASP* 4.3 4.5 - - - +
423K ARG* 5.7 0.3 + - - -
424K TYR* 3.0 57.9 + - + +
427K ASP* 1.3 87.5 + - - +
429K ILE* 1.3 67.3 + - - +
430K GLN* 3.0 21.1 + - - +
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Residues in contact with ILE 429 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475J LYS* 2.8 28.7 + - - +
400K MET* 4.0 22.6 - - + +
403K ILE* 3.7 22.9 - - + -
404K ASP* 3.5 15.9 - - - +
412K THR* 4.0 11.4 - - + -
425K PHE* 3.0 45.8 + - + +
426K SER 4.2 0.2 - - - +
427K ASP 3.5 0.2 - - - -
428K ASN* 1.3 76.8 - - - +
430K GLN* 1.3 60.8 + - - +
431K VAL* 3.0 26.3 + - + +
434K VAL* 3.9 28.9 - - + -
452K TRP* 3.8 2.4 - - - -
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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