Contacts of the strand formed by residues 472 - 479 (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 THR 472 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118I LEU* 3.9 20.4 - - + -
136I PHE* 3.5 37.8 - - + +
137I GLN 3.2 13.0 - - - +
139I MET* 3.6 7.0 - - - -
165I CYS* 4.0 11.2 - - + +
242I ARG* 2.8 26.5 + - - -
468I VAL* 2.7 22.7 + - + +
469I ARG* 2.8 20.1 + - - +
470I PHE 3.3 0.2 - - - -
471I TYR* 1.3 81.4 - - - +
473I LYS* 1.3 58.8 + - - +
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Residues in contact with LYS 473 (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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57I ARG* 6.2 0.4 - - - +
135I GLU 3.4 1.2 - - - +
136I PHE* 4.3 2.7 - - - -
137I GLN* 2.8 38.9 + - - +
138I PRO 3.5 18.2 - - - +
139I MET* 3.8 29.2 + - + +
218I LYS* 5.8 4.6 - - - +
242I ARG* 3.8 17.7 - - - +
472I THR* 1.3 75.6 - - - +
474I ARG* 1.3 64.1 + - - +
475I LYS 3.5 0.5 + - - -
430L GLN* 3.4 22.4 + - - -
452L TRP* 3.4 55.1 - - + +
453L LYS* 5.8 4.8 - - - +
461L HIS* 5.4 2.0 - - - +
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Residues in contact with ARG 474 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121I GLU* 5.0 7.9 + - - -
134I SER* 3.8 23.2 + - - -
135I GLU 3.6 4.9 - - - -
136I PHE* 3.8 28.5 - - + -
469I ARG* 3.5 15.7 - - - +
473I LYS* 1.3 70.6 - - - +
475I LYS* 1.3 63.2 + - - +
476I THR* 4.1 11.2 + - - +
432L GLY* 4.2 2.8 - - - +
447L HIS* 4.8 5.1 + - - -
448L SER* 3.9 32.2 + - - +
450L GLY 4.7 0.3 - - - +
452L TRP* 3.1 17.3 + - - -
461L HIS* 3.4 33.8 + - + +
465L PRO* 4.0 17.4 - - - +
466L ASP* 2.7 44.6 + - - +
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Residues in contact with LYS 475 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133I TRP 4.1 0.2 - - - +
134I SER* 3.3 4.9 - - - -
135I GLU* 2.8 44.1 + - + +
137I GLN* 3.1 30.3 + - + +
473I LYS 3.5 0.2 + - - -
474I ARG* 1.3 72.3 - - - +
476I THR* 1.3 70.4 + - - +
477I VAL* 4.2 8.9 + - + -
426L SER 2.9 29.2 + - - +
427L ASP 3.3 9.3 + - - -
428L ASN 4.3 0.2 - - - -
429L ILE* 2.8 24.3 + - - +
431L VAL 3.3 20.2 - - - +
432L GLY 3.2 12.8 - - - +
434L VAL* 4.0 14.1 - - + -
452L TRP* 3.8 13.2 - - + -
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Residues in contact with THR 476 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132I SER* 3.7 20.2 - - - +
133I TRP 3.7 4.9 - - - +
134I SER* 4.4 3.2 - - - +
474I ARG* 4.1 13.0 + - - +
475I LYS* 1.3 74.7 + - - +
477I VAL* 1.3 64.0 + - - +
478I THR* 4.0 3.9 + - - +
432L GLY 3.1 8.3 + - - -
433L MET* 3.6 8.6 - - - +
434L VAL 3.0 25.2 + - - +
441L PRO 5.1 1.0 - - - +
443L PRO* 4.0 32.5 - - + -
447L HIS* 4.2 16.1 + - + +
448L SER 3.6 16.1 + - - -
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Residues in contact with VAL 477 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132I SER* 2.9 19.8 + - - -
133I TRP* 3.0 67.8 + - + +
135I GLU* 5.2 4.7 - - + +
475I LYS* 4.4 18.4 - - + +
476I THR* 1.3 73.9 - - - +
478I THR* 1.3 70.1 + - - +
426L SER* 4.0 30.7 - - - +
434L VAL* 3.2 10.5 - - + +
436L ILE* 4.3 11.2 - - + -
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Residues in contact with THR 478 (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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126I VAL* 4.5 8.7 - - + -
130I ILE* 3.6 26.7 - - + -
131I ASP 3.5 4.5 - - - +
132I SER* 3.7 9.1 + - - -
476I THR* 4.8 5.2 + - - +
477I VAL* 1.3 76.5 + - - +
479I GLN* 1.3 57.5 + - - +
434L VAL 2.8 12.0 + - - -
435L GLY* 3.3 2.1 - - - -
436L ILE 2.8 32.2 + - - +
438L ILE* 4.0 16.7 - - + +
441L PRO* 4.2 26.2 + - + +
442L VAL 4.9 4.8 + - - +
443L PRO* 5.3 1.2 - - - +
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Residues in contact with GLN 479 (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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129I GLY 4.2 1.0 - - - +
130I ILE* 3.4 8.4 - - - +
131I ASP* 2.7 44.5 + - + +
133I TRP* 3.8 35.7 - - + -
477I VAL 4.2 0.4 - - - -
478I THR* 1.3 73.4 - - - +
480I ARG* 1.3 61.2 + - - +
481I TRP* 3.3 41.1 + - + +
479J GLN* 4.9 14.7 + - - +
481J TRP* 6.3 0.4 - - - -
423K ARG* 5.2 8.3 - - - +
422L ALA* 4.8 5.1 - - - +
436L ILE* 3.8 23.0 - - + +
438L ILE* 4.8 0.2 - - - -
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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