Contacts of the strand formed by residues 581 - 588 (chain A) in PDB entry 2FBW
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 LYS 581 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A LEU* 3.6 12.4 - - - +
542A ARG* 2.7 31.2 + - - -
575A PHE* 3.0 54.6 + - + +
576A GLU* 3.9 14.1 + - - +
578A HIS* 3.1 21.4 + - + +
579A TRP* 2.8 28.9 + - + +
580A ARG* 1.3 74.6 - - - +
582A HIS* 1.3 53.7 + - - +
598A TYR* 3.6 37.6 - - + +
599A ARG 3.5 13.0 - - - +
601A VAL* 4.0 6.5 - - - +
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Residues in contact with HIS 582 (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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90A LEU* 3.0 30.4 + - + +
92A ASP* 2.9 26.2 + - - -
245A GLN* 3.4 23.2 - - + +
246A ASP* 2.5 34.7 + - - +
402A SER* 4.0 15.9 - - - -
581A LYS* 1.3 70.4 - - - +
583A THR* 1.3 59.8 + - - +
584A LEU 3.7 0.2 + - - -
598A TYR* 3.2 11.6 - - - -
599A ARG* 2.9 52.3 + - + +
600A PRO 3.8 17.9 - - - -
601A VAL* 3.9 7.0 - - + +
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Residues in contact with THR 583 (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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244A CYS 3.7 0.2 - - - +
245A GLN* 3.1 10.7 - - - +
246A ASP* 3.0 33.1 + - - +
247A LEU 5.8 0.2 - - - +
248A GLU* 2.7 38.0 + - - +
534A GLN 6.0 0.2 - - - +
538A GLY* 4.5 7.8 + - - -
542A ARG* 3.0 12.3 + - - +
579A TRP* 5.2 0.2 - - - -
582A HIS* 1.3 71.0 - - - +
584A LEU* 1.3 71.3 + - - +
585A SER* 4.7 3.6 - - - +
596A LEU* 4.1 19.5 - - + -
598A TYR* 3.5 23.4 - - + +
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Residues in contact with LEU 584 (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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243A PRO* 4.1 17.7 - - + -
244A CYS 3.3 11.4 - - - +
245A GLN* 3.7 26.9 - - + +
371A PRO* 4.5 7.4 - - + -
381A HIS* 3.5 34.8 - - + -
582A HIS 4.5 0.4 - - - +
583A THR* 1.3 75.0 - - - +
585A SER* 1.3 59.9 + - - +
586A TYR* 4.4 10.2 - - + +
595A THR 3.9 0.3 - - - +
596A LEU* 3.3 6.4 - - - +
597A LYS* 2.7 52.3 + - - +
598A TYR 4.4 5.4 - - - +
599A ARG* 3.8 24.0 - - + -
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Residues in contact with SER 585 (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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242A LEU 4.2 0.9 - - - +
243A PRO* 3.3 7.1 - - - +
244A CYS* 3.0 38.8 + - - +
245A GLN* 5.4 0.5 - - - -
246A ASP 5.8 0.2 + - - -
247A LEU* 4.3 4.7 + - - +
534A GLN* 2.7 47.3 + - - +
583A THR* 4.2 4.9 + - - -
584A LEU* 1.3 74.1 - - - +
586A TYR* 1.3 63.6 + - - +
594A VAL* 4.7 0.9 - - - -
595A THR 3.4 4.0 - - - -
596A LEU* 3.6 20.0 - - - -
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Residues in contact with TYR 586 (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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238A THR* 5.5 0.4 - - - -
241A GLY* 3.8 21.1 - - - -
242A LEU 4.2 4.7 - - - -
243A PRO* 3.7 45.7 - - + +
380A THR* 4.2 3.8 + - - -
381A HIS 4.0 5.7 + - - -
534A GLN* 4.4 1.3 - - - -
584A LEU* 4.4 7.6 - - + +
585A SER* 1.3 75.9 - - - +
587A VAL* 1.3 68.9 + - - +
594A VAL* 3.3 7.4 - - - +
595A THR* 2.8 51.2 + - + +
597A LYS* 2.7 49.9 + - + -
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Residues in contact with VAL 587 (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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238A THR* 3.7 27.0 + - + +
241A GLY* 5.7 2.3 - - - -
530A LEU* 4.0 24.0 - - + +
533A LEU* 4.7 4.3 - - + -
534A GLN* 3.3 36.6 - - + +
586A TYR* 1.3 83.6 - - - +
588A ASP* 1.3 73.7 + - - +
589A VAL* 3.4 10.2 + - + +
592A GLY* 4.0 17.5 - - - +
593A LYS 3.3 9.6 - - - +
594A VAL* 4.4 6.7 - - + -
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Residues in contact with ASP 588 (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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587A VAL* 1.3 68.1 - - - +
589A VAL* 1.3 56.7 + - - +
590A LYS* 3.3 10.0 + - - +
591A SER* 2.9 32.1 + - - +
592A GLY* 2.6 34.3 + - - -
593A LYS* 2.8 20.5 + - + +
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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