Contacts of the strand formed by residues 460 - 470 (chain A) in PDB entry 3MHS
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 ALA 460 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362A LEU* 3.4 16.3 - - + +
364A ARG* 2.8 33.4 + - - +
380A ILE 5.1 1.9 + - - +
382A PHE* 3.7 22.2 - - + -
416A ILE* 4.1 9.6 - - + -
417A VAL 4.1 3.6 - - - -
458A GLU 3.3 4.8 + - - -
459A GLN* 1.3 72.2 - - - +
461A TYR* 1.3 56.0 + - - +
463A LEU* 3.4 34.8 - - + -
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Residues in contact with TYR 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ASP* 2.8 31.3 + - - -
239A HIS* 4.2 4.3 - - + -
360A LEU 3.7 0.3 - - - +
361A GLN* 2.9 32.6 + - + -
362A LEU* 2.9 57.2 + - - +
364A ARG* 4.3 10.5 - - + +
365A PHE* 3.8 11.5 - + - -
417A VAL* 2.8 18.8 + - + +
418A SER* 4.5 5.6 - - - -
419A HIS 4.6 5.2 - - - +
428A TYR* 3.4 37.0 - + - -
459A GLN 3.5 1.0 + - - +
460A ALA* 1.3 73.3 - - - +
462A LEU* 1.3 76.0 + - + +
463A LEU* 5.4 0.4 - - - +
73D LEU* 3.8 22.7 - - + -
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Residues in contact with LEU 462 (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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151A ILE* 3.6 30.1 - - + -
238A ALA* 4.2 5.6 - - + -
239A HIS* 3.9 34.3 - - + +
242A TRP* 4.7 4.9 - - + -
359A VAL* 5.3 5.2 - - + -
360A LEU 3.3 3.8 - - - +
361A GLN* 3.9 28.5 - - + -
416A ILE* 3.3 5.8 - - - +
417A VAL* 2.9 39.1 + - + +
461A TYR* 1.3 95.1 + - + +
463A LEU* 1.3 67.9 + - - +
464A PHE* 4.0 16.4 - - + -
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Residues in contact with LEU 463 (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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316A LEU* 3.9 29.8 - - + -
358A LEU 3.6 1.4 - - - +
359A VAL* 3.4 6.8 - - - +
360A LEU* 2.9 42.1 + - + +
362A LEU* 5.1 6.5 - - + -
382A PHE* 3.9 28.3 - - + -
413A LEU* 4.2 1.8 - - + -
415A GLY 3.5 2.5 - - - -
416A ILE* 2.3 43.7 - - + -
460A ALA* 3.4 21.8 - - + -
461A TYR 5.4 1.1 - - - +
462A LEU* 1.3 75.2 - - - +
464A PHE* 1.3 62.0 + - - +
465A TYR* 3.9 17.7 - - + -
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Residues in contact with PHE 464 (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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151A ILE* 4.6 2.7 - - + -
154A CYS* 3.8 34.3 - - + -
158A ASN* 5.4 4.0 - - - +
242A TRP* 3.7 48.0 - + - -
279A PHE* 5.3 0.2 - + - -
357A VAL* 4.8 9.2 - - + -
358A LEU 3.7 2.2 - - - -
359A VAL* 3.7 25.8 - - + -
413A LEU* 3.6 4.2 - - - +
414A ILE* 2.9 35.9 + - + +
415A GLY* 2.8 33.6 + - - +
416A ILE 4.5 0.2 - - - -
417A VAL* 4.2 5.4 - - + -
462A LEU* 4.0 28.9 - - + -
463A LEU* 1.3 74.5 - - - +
465A TYR* 1.3 61.4 + - - +
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Residues in contact with TYR 465 (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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316A LEU* 3.8 4.0 - - + +
357A VAL* 3.2 7.7 - - - +
358A LEU* 2.8 46.2 + - + +
360A LEU* 4.1 10.5 - - + -
382A PHE* 3.9 4.9 - - - +
383A PRO* 2.8 45.1 + - - +
386A LEU* 3.6 45.1 - - + -
411A TYR* 3.5 18.7 - - + -
412A GLU 3.4 5.4 - - - -
413A LEU* 3.5 40.6 - - + +
414A ILE* 4.9 0.4 - - - -
463A LEU* 3.9 23.6 - - + -
464A PHE* 1.3 76.5 - - - +
466A THR* 1.3 59.4 + - - +
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Residues in contact with THR 466 (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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159A PRO* 4.4 1.4 - - + +
160A TYR* 3.4 28.2 - - - -
356A SER 3.6 3.0 + - - -
357A VAL* 3.9 4.8 - - - +
411A TYR* 3.3 5.7 - - - -
412A GLU* 2.8 47.0 + - + +
414A ILE* 3.7 39.2 - - + +
464A PHE 4.4 0.2 + - - -
465A TYR* 1.3 71.3 - - - +
467A ILE* 1.3 66.7 + - - +
68E PRO* 3.9 27.4 - - + +
69E LEU* 5.0 0.4 - - + -
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Residues in contact with ILE 467 (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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160A TYR* 3.8 18.5 + - - +
356A SER* 2.9 25.9 + - - +
409A ILE* 3.7 29.2 - - + -
410A ILE 3.5 17.0 - - - +
411A TYR* 3.4 20.5 - - + -
466A THR* 1.3 77.3 + - - +
468A ARG* 1.3 57.9 + - - +
469A GLN 4.2 0.4 - - - +
470A VAL* 3.8 22.2 - - + -
49E MET* 4.3 11.2 - - - +
58E PHE* 3.7 15.0 - - + -
64E LEU* 4.0 20.4 - - + -
65E ILE 4.3 4.8 - - - +
67E ASP 5.2 0.3 + - - -
68E PRO* 4.2 14.6 - - - +
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Residues in contact with ARG 468 (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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385A TYR* 3.3 17.5 + - + -
410A ILE 2.9 17.2 + - - +
411A TYR 4.4 0.7 - - - -
412A GLU* 2.8 52.4 + - + +
466A THR* 3.3 6.5 + - + +
467A ILE* 1.3 75.4 - - - +
469A GLN* 1.3 57.2 + - + +
34B LEU* 3.6 38.1 - - + +
39B VAL* 4.2 8.7 - - - +
40B ASP* 5.2 1.0 + - - -
43B LYS* 4.2 20.0 - - - +
48E HIS* 3.2 24.7 + - + -
49E MET* 4.2 10.6 - - - +
66E GLU* 5.2 0.2 - - - +
67E ASP* 2.9 46.0 + - - +
68E PRO* 4.7 2.2 - - - -
69E LEU* 6.0 0.4 - - - +
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Residues in contact with GLN 469 (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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408A ASP 3.9 0.9 - - - +
409A ILE* 3.5 2.1 - - - -
410A ILE* 2.8 42.8 + - + +
467A ILE* 4.5 0.4 - - - +
468A ARG* 1.3 80.1 - - - +
470A VAL* 1.3 67.6 + - - +
471A ASN* 2.8 27.2 - - - +
27B ASN* 3.1 20.3 - - - +
30B LYS* 3.9 13.6 + - - +
31B ALA* 3.6 20.7 + - - +
34B LEU* 3.8 26.1 - - + +
48E HIS* 3.4 29.3 - - + +
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Residues in contact with VAL 470 (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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408A ASP 3.7 2.7 - - - -
409A ILE* 4.3 14.8 - - + -
467A ILE* 3.8 28.3 - - + -
469A GLN* 1.3 79.4 - - - +
471A ASN* 1.3 62.7 + - - +
27B ASN* 5.6 0.3 - - - +
48E HIS 3.0 13.1 + - - +
49E MET* 4.0 14.8 - - + -
50E ASN* 2.8 27.7 + - - +
53E SER* 3.6 27.4 - - - -
54E LEU* 4.1 15.3 - - + +
58E PHE* 4.0 19.7 - - + -
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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