Contacts of the helix formed by residues 418 - 429 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258I ASP* 3.1 13.4 + - - +
416I THR* 3.0 10.5 + - - +
417I ARG* 1.3 79.2 - - - +
419I GLY* 1.3 63.3 + - - +
420I GLU* 3.4 12.5 + - - +
421I ALA* 3.2 23.3 + - + -
422I ALA* 3.5 19.9 + - - +
417J ARG* 2.8 54.9 + - - +
418J ASP* 5.1 0.2 - - - +
481K TRP* 5.8 0.2 - - - -
486K VAL* 3.7 20.6 - - + +
481L TRP* 3.7 2.7 - - - -
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Residues in contact with GLY 419 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417I ARG 3.7 1.6 + - - -
418I ASP* 1.3 70.3 - - - +
420I GLU* 1.3 65.5 + - - +
421I ALA 3.3 0.2 - - - -
422I ALA* 3.4 3.3 + - - +
423I ARG 3.2 17.2 + - - -
417J ARG 3.0 12.9 + - - -
419J GLY* 4.2 1.1 - - - +
481K TRP* 3.5 44.3 + - - -
481L TRP* 4.3 11.2 - - - -
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Residues in contact with GLU 420 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418I ASP* 3.4 13.8 + - - +
419I GLY* 1.3 74.5 - - - +
421I ALA* 1.3 63.8 + - - +
423I ARG* 3.4 3.1 + - - +
424I TYR* 3.1 23.6 + - - +
417J ARG* 4.8 0.4 - - - +
481K TRP* 3.2 43.9 - - + +
482K PRO 5.0 0.7 - - - +
483K SER 4.0 6.1 - - - +
484K ALA* 3.7 30.1 + - - +
486K VAL 4.2 0.7 - - - +
487K ARG* 3.5 42.8 + - - +
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Residues in contact with ALA 421 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256I MET* 5.0 1.1 - - + -
396I MET* 3.6 22.6 - - + +
414I ILE* 4.6 2.9 - - + -
416I THR* 4.2 19.1 - - + +
418I ASP* 3.2 19.3 + - + +
419I GLY 3.3 0.4 - - - -
420I GLU* 1.3 85.6 - - - +
422I ALA* 1.3 58.4 + - - +
424I TYR* 3.3 1.6 + - - +
425I PHE* 2.9 31.8 + - - +
486K VAL* 3.8 15.9 - - + +
487K ARG* 4.9 0.2 - - - -
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Residues in contact with ALA 422 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414I ILE* 4.8 0.9 - - - -
416I THR* 4.4 7.6 - - + +
418I ASP 3.5 4.1 + - - +
419I GLY 3.4 8.3 + - - +
420I GLU 3.2 0.6 - - - -
421I ALA* 1.3 81.0 - - - +
423I ARG* 1.3 57.3 + - - +
425I PHE* 3.7 4.4 - - - +
426I SER* 3.0 30.8 + - - -
436I ILE* 3.9 23.8 - - + +
479L GLN* 5.1 3.4 - - - +
481L TRP* 3.6 32.1 - - + -
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Residues in contact with ARG 423 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419I GLY 3.2 10.6 + - - +
420I GLU 4.0 4.9 - - - +
422I ALA* 1.3 73.8 - - - +
424I TYR* 1.3 73.1 + - - +
425I PHE 3.1 1.6 - - - -
426I SER* 3.8 8.7 - - - +
427I ASP* 2.7 66.3 + - + +
428I ASN* 5.4 1.0 + - - -
124K ARG* 4.7 0.6 - - - +
125K ASN* 3.6 21.8 + - - +
129K GLY* 3.7 28.4 + - - -
131K ASP* 2.9 52.5 + - - +
479K GLN* 5.1 7.9 - - - +
481K TRP* 4.2 20.2 - - + +
58L ASN* 5.7 1.8 + - - -
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Residues in contact with TYR 424 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396I MET* 4.2 2.2 - - + -
397I GLN* 2.9 25.4 + - - -
400I MET* 3.4 33.4 - - + -
420I GLU* 3.1 20.4 + - - +
421I ALA* 3.7 4.3 - - - +
423I ARG* 1.3 79.9 - - - +
425I PHE* 1.3 64.7 + - - +
427I ASP* 4.7 1.3 - - - -
428I ASN* 3.0 60.0 + - + +
487K ARG* 3.3 43.1 - - + +
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Residues in contact with PHE 425 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254I ILE* 3.5 25.8 - - + -
396I MET* 3.9 2.2 - - + -
400I MET* 3.7 24.0 - - + -
403I ILE* 4.2 1.3 - - + -
412I THR* 3.4 42.2 - - + -
413I CYS 3.5 24.0 - - - -
414I ILE* 3.3 30.1 - - + -
421I ALA 2.9 18.5 + - - +
422I ALA 3.7 2.9 - - - +
424I TYR* 1.3 76.9 - - - +
426I SER* 1.3 59.1 + - - +
429I ILE* 3.0 55.2 + - + +
434I VAL* 3.8 15.9 - - + -
436I ILE* 4.5 0.9 - - + -
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Residues in contact with SER 426 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422I ALA 3.0 16.3 + - - -
423I ARG* 3.4 14.2 + - - +
425I PHE* 1.3 76.0 - - - +
427I ASP* 1.3 55.0 + - - +
429I ILE* 4.5 0.4 - - - +
434I VAL* 3.9 26.0 - - - -
436I ILE* 4.3 8.1 - - - -
133L TRP* 4.6 8.5 - - - -
135L GLU* 4.9 2.9 + - - +
137L GLN* 4.2 0.7 + - - -
475L LYS* 2.7 37.9 + - - +
477L VAL* 4.1 19.7 - - - +
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Residues in contact with ASP 427 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423I ARG* 2.7 59.0 + - + +
424I TYR* 4.7 0.2 - - - -
426I SER* 1.3 75.5 + - - +
428I ASN* 1.3 69.0 + - - +
124K ARG* 2.9 35.3 + - - +
57L ARG* 3.2 24.5 + - - -
58L ASN* 3.9 4.7 - - - +
135L GLU* 4.0 5.7 - - - +
137L GLN* 3.1 18.4 + - - +
475L LYS* 3.0 15.8 + - - -
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Residues in contact with ASN 428 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400I MET* 5.3 4.9 - - - -
404I ASP* 4.3 5.4 - - - +
423I ARG* 5.4 1.0 + - - -
424I TYR* 3.0 60.8 + - + +
427I ASP* 1.3 84.8 - - - +
429I ILE* 1.3 65.9 + - - +
430I GLN* 3.2 19.1 + - - +
57L ARG* 3.4 21.4 - - - +
58L ASN* 4.0 19.2 + - - +
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Residues in contact with ILE 429 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400I MET* 3.6 23.7 - - + -
403I ILE* 3.7 20.6 - - + -
404I ASP* 3.7 13.9 - - - +
412I THR* 4.1 7.0 - - + -
425I PHE* 3.0 52.9 + - + +
427I ASP 3.5 0.4 - - - -
428I ASN* 1.3 78.0 - - - +
430I GLN* 1.3 60.1 + - - +
431I VAL* 3.2 22.2 + - + +
434I VAL* 3.7 29.6 - - + -
452I TRP* 3.8 2.9 - - - -
475L LYS* 2.8 26.7 + - - +
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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
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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