Contacts of the helix formed by residues 418 - 429 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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417A ARG* 3.3 42.7 + - - +
418A ASP* 4.9 0.2 - - - +
481B TRP* 5.4 0.2 - - - -
483B SER 4.4 0.3 - - - +
484B ALA* 5.5 0.2 - - - -
486B VAL* 3.4 35.1 - - + +
487B ARG 4.8 1.9 + - - -
481C TRP* 3.8 2.8 - - - -
258D ASP* 3.3 7.8 + - - +
416D THR* 3.2 8.5 + - - +
417D ARG* 1.3 77.9 - - - +
419D GLY* 1.3 61.9 + - - +
420D GLU* 3.3 12.8 + - - +
421D ALA* 2.9 30.8 + - + +
422D ALA* 3.5 20.1 + - - +
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Residues in contact with GLY 419 (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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417A ARG 3.0 13.3 + - - -
419A GLY* 4.1 1.3 - - - +
481B TRP* 3.4 43.8 + - - -
481C TRP* 4.3 11.7 - - - -
417D ARG 3.8 1.4 + - - -
418D ASP* 1.3 69.7 - - - +
420D GLU* 1.3 66.2 + - - +
422D ALA* 3.5 3.1 + - - +
423D ARG 3.1 18.2 + - - -
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Residues in contact with GLU 420 (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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481B TRP* 3.6 38.7 - - + +
483B SER 3.2 29.6 - - - +
484B ALA* 3.5 15.4 - - + +
487B ARG* 2.7 46.1 + - - +
418D ASP* 3.3 8.9 + - - +
419D GLY* 1.3 76.2 - - - +
421D ALA* 1.3 59.9 + - - +
423D ARG* 3.3 3.3 + - - +
424D TYR* 2.9 29.8 + - - +
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Residues in contact with ALA 421 (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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486B VAL* 4.6 6.7 - - + -
487B ARG* 4.2 13.7 - - + +
256D MET* 4.9 1.1 - - + -
396D MET* 3.4 23.0 - - - +
414D ILE* 4.7 2.2 - - + -
416D THR* 4.5 14.8 - - + +
418D ASP* 2.9 24.2 + - + +
419D GLY 3.3 0.2 - - - -
420D GLU* 1.3 82.2 + - - +
422D ALA* 1.3 58.1 + - - +
424D TYR 3.6 0.2 + - - -
425D PHE* 2.9 31.4 + - - +
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Residues in contact with ALA 422 (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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479C GLN* 4.9 3.8 - - - +
481C TRP* 3.7 31.0 - - + -
414D ILE* 4.7 4.5 - - - -
416D THR* 4.6 2.8 - - + +
418D ASP 3.5 3.8 + - - +
419D GLY 3.5 8.0 + - - +
420D GLU 3.2 0.2 - - - -
421D ALA* 1.3 77.7 - - - +
423D ARG* 1.3 60.3 + - - +
425D PHE* 3.6 4.5 - - - +
426D SER* 2.8 31.3 + - - -
436D ILE* 3.7 26.8 - - + +
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Residues in contact with ARG 423 (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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124B ARG* 4.8 0.6 - - - +
125B ASN* 3.6 18.4 + - - +
129B GLY* 4.3 24.8 + - - -
131B ASP* 2.8 51.2 + - - +
479B GLN* 4.7 10.1 - - - +
481B TRP* 4.1 21.3 - - + +
58C ASN* 6.4 0.2 - - - -
419D GLY 3.1 17.2 + - - +
420D GLU 3.8 3.1 - - - +
422D ALA* 1.3 72.2 - - - +
424D TYR* 1.3 71.0 + - - +
426D SER* 3.4 8.4 + - - +
427D ASP* 2.8 67.0 + - + +
428D ASN* 5.4 1.6 + - - -
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Residues in contact with TYR 424 (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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487B ARG* 3.0 57.9 + - - +
397D GLN* 3.2 20.6 + - - -
400D MET* 3.4 31.6 - - + -
420D GLU* 2.9 20.1 + - - +
421D ALA 3.9 0.4 - - - +
423D ARG* 1.3 78.9 - - - +
425D PHE* 1.3 64.0 + - - +
427D ASP* 4.8 0.9 - - - -
428D ASN* 3.0 54.9 + - + +
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Residues in contact with PHE 425 (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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254D ILE* 3.7 24.7 - - + -
396D MET* 3.8 6.3 - - + -
400D MET* 3.7 23.3 - - + -
403D ILE* 4.4 0.4 - - + -
412D THR* 3.4 41.5 - - + -
413D CYS 3.9 9.2 - - - -
414D ILE* 3.2 39.7 - - + -
421D ALA 2.9 20.4 + - - +
422D ALA 3.6 3.1 - - - +
424D TYR* 1.3 78.3 - - - +
426D SER* 1.3 57.7 + - - +
429D ILE* 3.1 54.0 + - + +
434D VAL* 3.7 16.4 - - + -
435D GLY 4.0 0.7 - - - -
436D ILE* 4.4 1.8 - - + -
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Residues in contact with SER 426 (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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133C TRP* 4.7 7.4 - - - -
135C GLU* 5.1 3.5 + - - +
137C GLN* 4.2 0.3 + - - -
475C LYS* 2.8 32.6 + - - +
477C VAL* 4.1 23.4 - - - +
422D ALA 2.8 22.6 + - - -
423D ARG* 3.4 12.3 + - - +
425D PHE* 1.3 71.1 - - - +
427D ASP* 1.3 60.6 + - - +
429D ILE* 4.4 0.3 - - - +
434D VAL* 3.9 25.6 - - - -
436D ILE* 4.2 4.3 - - - -
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Residues in contact with ASP 427 (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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124B ARG* 2.7 45.5 + - - +
57C ARG* 3.0 18.9 + - - -
58C ASN* 4.3 3.3 - - - +
135C GLU* 3.8 6.0 - - - +
137C GLN* 3.1 12.9 + - - +
475C LYS* 2.9 14.9 + - - -
423D ARG* 2.8 52.6 + - + +
426D SER* 1.3 80.5 + - - +
428D ASN* 1.3 69.9 + - - +
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Residues in contact with ASN 428 (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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57C ARG* 3.4 22.3 - - - +
58C ASN* 4.7 10.7 + - - +
400D MET* 5.4 3.8 - - - -
404D ASP* 4.3 5.1 - - - +
423D ARG* 5.4 1.4 + - - -
424D TYR* 3.0 58.0 + - + +
427D ASP* 1.3 84.9 + - - +
429D ILE* 1.3 63.0 + - - +
430D GLN* 2.8 25.2 + - - +
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Residues in contact with ILE 429 (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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475C LYS* 2.8 27.5 + - - +
400D MET* 3.9 20.6 - - + +
403D ILE* 3.9 24.5 - - + -
404D ASP* 3.6 15.7 - - - +
412D THR* 4.2 9.4 - - + -
425D PHE* 3.1 47.1 + - + +
427D ASP 3.7 0.2 - - - -
428D ASN* 1.3 77.5 - - - +
430D GLN* 1.3 61.1 + - - +
431D VAL* 3.1 22.3 + - + +
434D VAL* 3.8 30.3 - - + -
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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