Contacts of the strand formed by residues 471 - 478 (chain B) in PDB entry 4IYM
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 471 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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458A ASP 5.6 0.2 - - - +
117B GLN* 3.8 23.6 - - + +
135B ARG* 3.9 29.3 + - + +
136B GLN 3.2 11.2 - - - +
138B VAL* 3.8 3.4 - - - -
164B CYS* 3.6 18.6 - - + -
241B ARG* 2.8 22.9 + - - -
467B ILE* 2.7 25.4 + - + +
468B LYS* 3.1 12.5 + - - +
469B PHE 3.3 0.8 - - - -
470B TRP* 1.3 84.3 - - - +
472B ARG* 1.3 60.2 + - - +
473B THR* 5.5 0.7 + - - -
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Residues in contact with ARG 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A ASN* 4.7 12.3 + - - +
451A TRP* 3.3 70.2 - - + +
452A LYS* 4.7 8.7 - - - +
134B ILE 3.5 0.3 - - - +
135B ARG* 3.5 3.3 - - - -
136B GLN* 2.8 32.8 + - - +
137B PRO 3.2 24.0 + - - +
138B VAL* 4.0 24.5 + - + +
139B GLY* 5.5 0.8 - - - -
241B ARG* 4.0 16.4 - - - +
471B THR* 1.3 76.5 - - - +
473B THR* 1.3 63.4 + - - +
474B LYS 3.8 0.2 + - - -
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Residues in contact with THR 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A GLY* 3.9 5.0 - - - +
447A SER* 4.5 12.3 - - - +
449A GLY 4.7 1.4 - - - +
451A TRP* 3.0 19.4 + - - +
460A ASN* 4.1 20.9 + - - +
465A ASP* 4.6 4.2 + - - -
133B SER* 3.8 26.2 - - - +
134B ILE 3.6 5.4 - - - +
135B ARG* 4.5 8.2 - - + +
468B LYS* 3.8 23.8 + - - +
471B THR* 5.5 0.9 + - - -
472B ARG* 1.3 73.4 - - - +
474B LYS* 1.3 61.8 + - - +
475B THR* 4.0 9.8 + - - +
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Residues in contact with LYS 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425A ALA 2.8 29.2 + - - +
426A SER 3.1 9.9 + - - -
427A ARG 4.2 0.2 - - - -
428A ILE* 2.7 32.6 + - - -
430A ILE 3.3 14.8 - - - +
431A GLY 3.2 10.3 - - - +
433A VAL* 4.2 11.2 - - + -
451A TRP* 3.7 13.5 - - + -
132B TYR 4.0 0.2 - - - +
133B SER* 2.9 4.3 - - - -
134B ILE* 2.7 46.1 + - + +
136B GLN* 2.8 27.9 + - - +
472B ARG 3.8 0.6 + - - -
473B THR* 1.3 74.1 - - - +
475B THR* 1.3 62.3 + - - +
476B ILE* 4.3 15.7 + - + -
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Residues in contact with THR 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431A GLY 2.8 10.5 + - - +
432A MSE 3.4 4.7 - - - +
433A VAL 2.8 25.8 + - - +
440A PRO 5.0 1.4 - - - +
442A PRO* 3.8 33.7 - - + -
446A HIS* 4.6 7.6 - - + +
447A SER* 3.9 14.4 + - - -
460A ASN* 5.5 0.5 + - - -
131B MSE 4.1 20.0 - - + -
132B TYR 3.4 12.1 - - - +
133B SER* 3.8 10.1 - - - +
473B THR* 4.0 8.0 - - - +
474B LYS* 1.3 76.2 + - - +
476B ILE* 1.3 64.9 + - - +
477B THR* 4.1 1.7 + - - +
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Residues in contact with ILE 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425A ALA* 3.8 19.7 - - + -
433A VAL* 3.3 23.3 - - + +
435A VAL* 4.0 23.3 - - + -
130B ASP 3.8 0.5 - - - +
131B MSE 3.3 5.7 - - - +
132B TYR* 2.7 79.6 + - + +
134B ILE* 3.6 25.4 - - + -
474B LYS* 4.3 10.5 - - + -
475B THR* 1.3 75.4 - - - +
477B THR* 1.3 68.0 + - - +
478B SER* 4.3 0.9 - - - -
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Residues in contact with THR 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433A VAL 2.7 11.8 + - - -
434A GLY* 3.4 2.9 - - - -
435A VAL 2.8 31.2 + - - -
437A VAL* 3.7 28.3 - - + +
440A PRO* 4.1 19.7 + - + +
441A VAL 4.8 0.6 + - - +
442A PRO* 4.9 0.5 - - - +
129B ILE* 3.5 25.1 - - + -
130B ASP 3.5 2.9 - - - +
131B MSE 3.4 30.3 - - + +
475B THR* 4.1 3.3 + - - +
476B ILE* 1.3 74.1 + - - +
478B SER* 1.3 57.5 + - - +
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Residues in contact with SER 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435A VAL* 3.6 20.9 - - - +
437A VAL* 4.4 2.0 - - - -
128B GLY 3.7 1.2 - - - +
129B ILE* 3.3 6.3 - - - -
130B ASP* 2.9 47.1 + - - +
132B TYR* 4.2 22.1 + - - -
476B ILE* 4.3 3.1 - - - -
477B THR* 1.3 77.2 - - - +
479B ARG* 1.3 62.8 + - - +
480B TRP* 3.9 18.9 + - - -
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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