Contacts of the strand formed by residues 471 - 478 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A GLN* 3.9 20.4 - - + +
135A ARG* 3.9 26.6 - - + -
136A GLN 3.3 11.0 - - - +
138A VAL* 3.8 2.9 - - - -
164A CYS* 3.6 22.4 - - + -
241A ARG* 2.9 20.9 + - - -
467A ILE* 2.6 26.1 + - + +
468A LYS* 3.0 15.8 + - - +
469A PHE 3.3 1.0 + - - -
470A TRP* 1.3 84.4 - - - +
472A ARG* 1.3 61.4 + - - +
473A THR* 5.5 0.5 + - - -
458B ASP 5.4 0.5 - - - +
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Residues in contact with ARG 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A ILE 3.5 1.6 - - - +
135A ARG* 3.6 2.4 - - - -
136A GLN* 2.8 34.2 + - - +
137A PRO 2.9 26.8 + - - +
138A VAL* 3.6 29.8 + - + +
139A GLY* 4.8 2.2 - - - +
241A ARG* 4.1 15.5 - - - +
471A THR* 1.3 74.5 - - - +
473A THR* 1.3 63.2 - - - +
474A LYS 3.7 0.2 + - - -
429B ASN* 4.7 10.7 - - - +
451B TRP* 3.3 65.2 - - + +
452B LYS* 5.2 7.3 - - - +
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Residues in contact with THR 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A SER* 4.2 11.2 - - - -
134A ILE 3.7 4.9 - - - -
135A ARG* 4.8 10.4 - - + +
468A LYS* 4.0 21.0 + - - -
471A THR* 4.3 1.1 + - - -
472A ARG* 1.3 72.5 - - - +
474A LYS* 1.3 64.3 + - - +
475A THR* 3.7 21.1 - - - +
431B GLY* 3.9 4.3 - - - +
447B SER* 3.9 7.4 + - - +
449B GLY 4.8 1.7 - - - +
451B TRP* 2.9 20.5 + - - +
460B ASN* 3.7 28.3 + - - +
465B ASP* 4.8 3.4 + - - -
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Residues in contact with LYS 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A TYR 4.1 0.2 - - - +
133A SER* 3.0 4.0 - - - -
134A ILE* 2.7 48.2 + - + +
136A GLN* 2.8 28.2 + - - +
472A ARG 3.7 0.4 + - - -
473A THR* 1.3 73.9 - - - +
475A THR* 1.3 63.3 + - - +
476A ILE* 4.2 15.8 + - + -
425B ALA 2.7 28.4 + - - +
426B SER 3.1 10.3 + - - -
428B ILE 2.7 24.2 + - - -
430B ILE 3.3 20.6 - - - +
431B GLY 3.2 10.1 - - - +
433B VAL* 4.1 14.1 - - + -
451B TRP* 3.8 14.1 - - + -
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Residues in contact with THR 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A MSE 4.2 16.6 - - + -
132A TYR 3.6 14.8 - - - +
133A SER* 3.9 5.3 - - - +
473A THR* 3.7 15.1 - - - +
474A LYS* 1.3 76.7 + - - +
476A ILE* 1.3 63.8 + - - +
477A THR* 4.2 1.5 + - - +
431B GLY 2.8 12.7 + - - -
432B MSE 3.4 6.0 - - - +
433B VAL 2.8 26.2 + - - +
440B PRO 4.9 2.1 - - - +
442B PRO* 3.7 33.2 - - + -
446B HIS* 4.6 7.9 - - + +
447B SER* 3.7 13.3 + - - -
460B ASN* 5.3 0.2 + - - -
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Residues in contact with ILE 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A ASP 3.9 0.3 - - - +
131A MSE 3.3 5.0 - - - +
132A TYR* 2.8 81.5 + - + +
134A ILE* 3.6 24.5 - - + -
474A LYS* 4.3 11.0 - - + -
475A THR* 1.3 76.8 - - - +
477A THR* 1.3 66.9 + - - +
478A SER* 4.2 1.3 - - - -
425B ALA* 3.7 21.3 - - + -
433B VAL* 3.2 22.0 - - + +
435B VAL* 4.1 22.7 - - + -
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Residues in contact with THR 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A ILE* 3.5 25.4 - - + -
130A ASP 3.4 2.7 - - - +
131A MSE 3.9 28.4 - - + +
475A THR* 4.2 2.3 + - - +
476A ILE* 1.3 72.4 + - - +
478A SER* 1.3 63.4 + - - +
433B VAL 3.0 6.1 + - - +
434B GLY* 3.4 3.5 - - - -
435B VAL* 2.9 25.8 + - - +
437B VAL* 3.9 20.1 - - + +
440B PRO* 4.1 28.3 + - + +
441B VAL 4.6 1.8 + - - +
442B PRO* 4.8 2.1 - - - +
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Residues in contact with SER 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A GLY 3.7 0.9 - - - +
129A ILE* 3.3 6.7 - - - -
130A ASP* 2.8 45.7 + - - +
132A TYR* 4.2 23.7 + - - -
476A ILE* 4.3 3.6 - - - -
477A THR* 1.3 78.7 - - - +
479A ARG* 1.3 62.9 + - - +
480A TRP* 4.1 15.6 + - - -
435B VAL* 3.6 22.4 - - - +
437B VAL* 4.6 0.4 - - - -
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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