Contacts of the strand formed by residues 557 - 565 (chain A) in PDB entry 4Y05
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 SER 557 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258A ARG* 3.1 22.5 + - - +
341A LYS* 3.3 24.3 - - - +
530A LEU* 3.5 17.0 - - - +
551A SER 3.5 18.8 + - - -
553A ILE 2.7 27.7 + - - -
554A GLY* 3.7 9.1 + - - -
555A GLU 3.5 2.4 - - - -
556A ASN* 1.3 76.2 + - - +
558A ARG* 1.3 64.8 + - - +
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Residues in contact with ARG 558 (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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256A GLU* 3.4 42.0 + - - +
257A HIS 3.1 26.5 + - - +
258A ARG* 3.3 21.0 - - + +
331A PRO 5.9 0.2 + - - -
332A LEU* 3.8 21.7 - - + +
335A THR* 3.5 27.8 + - + +
341A LYS 3.0 8.3 + - - +
342A ALA* 3.3 6.6 - - - +
343A THR* 3.1 21.7 + - - -
530A LEU* 4.4 3.4 - - - -
551A SER 5.0 2.1 - - - +
556A ASN* 4.8 5.9 - - - +
557A SER* 1.3 81.9 - - - +
559A THR* 1.3 61.6 + - - +
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Residues in contact with THR 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A HIS 4.9 1.2 - - - +
258A ARG 2.9 9.8 + - - +
259A ILE* 3.5 31.4 - - + -
260A CYS* 2.9 25.3 + - - +
332A LEU* 4.2 5.3 - - - +
343A THR* 2.7 28.5 + - - -
345A PHE* 3.5 17.5 - - - -
527A ILE* 3.9 21.7 - - + +
530A LEU* 3.7 11.0 - - + -
552A PHE* 5.7 1.3 - - - -
558A ARG* 1.3 73.8 - - - +
560A CYS* 1.3 68.0 + - - +
561A MET* 6.4 0.4 - - + -
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Residues in contact with CYS 560 (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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260A CYS* 3.3 23.3 - - + +
262A CYS* 4.3 0.4 - - - -
328A THR* 3.4 45.8 - - - +
332A LEU* 4.0 16.8 - - + -
343A THR 2.9 7.2 + - - +
344A CYS* 3.3 9.9 - - - -
345A PHE* 3.0 28.3 + - - -
559A THR* 1.3 77.6 + - - +
561A MET* 1.3 71.3 + - - +
562A ILE* 4.3 3.6 - - - -
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Residues in contact with MET 561 (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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260A CYS 2.8 12.1 + - - +
261A VAL* 3.5 12.9 - - + -
262A CYS* 2.8 33.4 + - - +
345A PHE* 3.4 18.4 - - + +
347A TYR* 4.0 19.5 - - + -
523A LEU* 4.0 19.3 - - + -
527A ILE* 3.7 27.1 - - + -
559A THR* 6.4 0.4 - - + -
560A CYS* 1.3 75.4 - - - +
562A ILE* 1.3 68.5 + - - +
563A ALA* 4.4 1.6 - - + +
581A TYR* 3.9 29.6 - - + -
582A ALA* 5.3 6.3 - - - -
585A VAL* 4.2 14.1 - - + -
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Residues in contact with ILE 562 (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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262A CYS* 3.7 10.1 - - + -
264A ARG* 4.0 28.3 - - + +
315A PHE* 5.3 0.4 - - + -
324A VAL* 4.1 10.1 - - + -
328A THR* 3.9 29.6 - - + +
344A CYS* 4.0 16.2 - - - -
345A PHE 2.8 11.7 + - - +
346A ALA* 3.4 4.9 - - - -
347A TYR 3.0 24.5 + - - +
357A THR* 4.1 12.6 - - + -
358A MET* 4.9 3.4 - - - -
373A ILE* 3.6 30.7 - - + -
560A CYS* 4.3 1.8 - - - -
561A MET* 1.3 75.4 - - - +
563A ALA* 1.3 60.9 + - - +
564A THR* 3.5 12.1 + - + +
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Residues in contact with ALA 563 (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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262A CYS 2.8 18.4 + - - +
263A VAL* 3.1 12.7 - - + +
264A ARG 2.8 29.3 + - - +
347A TYR* 3.2 13.2 - - + +
561A MET* 3.9 3.9 - - + +
562A ILE* 1.3 69.7 - - - +
564A THR* 1.3 57.7 + - - +
565A ILE* 3.9 1.7 + - + +
578A THR* 3.9 20.4 - - + -
582A ALA* 3.9 22.9 - - + -
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Residues in contact with THR 564 (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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264A ARG* 3.4 12.6 - - + -
346A ALA* 4.9 1.6 - - + -
347A TYR 2.8 8.7 + - - -
348A GLY* 3.6 11.6 - - - -
349A GLN 4.3 1.0 + - - -
352A SER* 2.7 43.8 + - - +
353A GLY* 3.9 20.4 - - - +
354A LYS* 3.3 22.4 - - + +
357A THR* 4.0 11.2 - - - +
562A ILE* 4.1 19.1 - - + +
563A ALA* 1.3 74.8 - - - +
565A ILE* 1.3 65.5 + - - +
578A THR* 3.9 2.6 + - - +
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Residues in contact with ILE 565 (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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263A VAL* 5.3 1.3 - - + -
264A ARG 2.9 18.5 + - - +
265A LYS* 3.8 10.6 - - + -
266A ARG* 3.3 28.4 + - - +
281A ILE* 3.9 19.7 - - + -
289A LEU* 3.5 32.5 - - + -
349A GLN* 5.9 0.7 - - - -
352A SER* 3.9 7.4 + - - +
563A ALA 4.4 5.6 - - - +
564A THR* 1.3 80.1 - - - +
566A SER* 1.3 59.7 + - - +
567A PRO 3.9 0.2 - - - -
575A THR* 4.0 33.2 - - + +
578A THR* 3.9 22.2 - - + -
579A LEU* 4.3 12.1 - - + -
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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
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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