Contacts of the strand formed by residues 356 - 362 (chain A) in PDB entry 5M5X
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 PHE 356 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A PRO* 4.9 10.8 - - + +
85A CYS* 3.6 8.7 - - - +
86A TYR* 3.6 38.6 - + + -
94A LEU* 4.9 3.1 - - + -
317A SER 5.9 0.2 - - - -
320A VAL* 3.8 16.4 - - + -
321A LYS* 3.6 46.7 - - + +
324A LEU* 3.6 19.1 - - + -
352A ALA* 3.2 23.6 + - + +
353A ASP* 3.3 23.5 - - - +
354A SER 3.4 1.7 - - - +
355A PHE* 1.3 101.1 - + - +
357A MET* 1.3 62.9 + - - +
358A ASP* 3.6 3.3 + - - +
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Residues in contact with MET 357 (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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19A LEU 6.1 1.1 - - - -
81A LEU* 3.7 13.6 - - + +
84A PRO* 3.6 2.1 - - - +
85A CYS* 3.0 51.9 + - - +
86A TYR 3.9 3.6 - - - +
87A ASN* 3.2 31.4 - - - +
354A SER 5.4 1.1 - - - -
355A PHE 3.0 5.1 + - - +
356A PHE* 1.3 69.8 - - - +
358A ASP* 1.3 59.9 + - - +
359A VAL 4.9 5.2 - - - +
360A LEU* 3.6 42.0 - - + +
434A VAL* 3.7 15.3 - - + -
438A ILE* 5.1 1.6 - - + -
1193B GLY* 6.5 0.9 - - - -
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Residues in contact with ASP 358 (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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21A ALA* 5.4 14.2 - - + +
24A ILE* 5.8 1.2 - - - +
25A ARG* 3.0 29.1 + - - -
80A GLU* 4.4 1.2 - - - +
81A LEU* 3.3 38.4 + - - +
82A PRO 5.0 1.4 - - - +
84A PRO* 3.7 32.9 - - + +
321A LYS* 6.2 1.3 - - - +
353A ASP* 5.5 4.5 - - - +
356A PHE 3.6 5.3 + - - +
357A MET* 1.3 72.9 - - - +
359A VAL* 1.3 63.0 + - + +
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Residues in contact with VAL 359 (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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21A ALA* 6.1 1.8 - - - -
24A ILE* 3.3 38.8 - - + +
25A ARG* 3.7 15.7 - - - +
78A HIS* 3.5 25.1 - - + -
79A ILE 3.2 17.5 - - - +
80A GLU* 3.3 28.9 - - - +
357A MET* 4.9 7.9 - - - +
358A ASP* 1.3 92.1 + - + +
360A LEU* 1.3 72.5 + - - +
361A VAL* 4.3 1.6 - - - +
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Residues in contact with LEU 360 (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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78A HIS* 3.3 20.8 - - - +
79A ILE* 3.1 44.5 + - + +
81A LEU* 4.7 7.5 - - + +
357A MET* 3.6 27.0 - - + +
359A VAL* 1.3 83.1 - - - +
361A VAL* 1.3 65.6 + - - +
362A VAL* 5.6 0.2 - - + -
386A LEU* 4.3 13.9 - - + -
389A VAL* 4.3 11.7 - - + -
434A VAL* 3.9 17.9 - - + -
437A PHE* 3.8 29.2 - - + -
438A ILE* 5.1 3.4 - - + -
1191B ALA 4.4 8.7 - - - +
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Residues in contact with VAL 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 5.3 4.9 - - + -
24A ILE* 3.8 29.8 - - + -
27A LEU* 5.7 1.1 - - + -
76A GLN* 3.4 39.3 - - + +
77A GLY 3.6 10.3 - - - +
78A HIS* 5.1 0.2 - - + -
359A VAL 4.3 4.5 - - - +
360A LEU* 1.3 85.2 - - - +
362A VAL* 1.3 62.0 + - - +
363A PRO* 4.3 0.3 - - - +
437A PHE* 4.7 6.6 - - - -
1187B SER 5.5 0.2 - - - +
1190B SER* 3.8 28.7 - - - +
1191B ALA* 3.5 23.9 + - + +
1193B GLY* 6.4 0.7 - - - -
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Residues in contact with VAL 362 (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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32A ILE* 5.3 5.4 - - + -
49A LEU* 4.9 7.4 - - + +
54A LEU* 4.5 12.6 - - + -
76A GLN* 2.8 16.1 - - - +
77A GLY* 3.3 31.7 + - - -
78A HIS* 3.7 4.7 - - - +
79A ILE* 4.0 17.3 - - + -
360A LEU* 4.3 1.1 - - + -
361A VAL* 1.3 78.1 - - - +
363A PRO* 1.3 69.4 - - + +
368A ARG* 3.5 14.8 - - - +
386A LEU* 3.8 36.8 - - + -
437A PHE* 5.9 1.1 - - + -
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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
------------------------------------------------------------
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