Contacts of the strand formed by residues 528 - 535 (chain B) in PDB entry 1Q57
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 GLY 528 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298B LYS* 3.9 0.6 - - - -
517B ARG* 4.1 7.4 - - - -
518B ILE* 2.8 37.8 + - - +
527B THR* 1.3 79.8 + - - +
529B ILE* 1.3 69.8 + - - +
530B ALA* 3.2 5.2 + - - +
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Residues in contact with ILE 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298B LYS* 3.3 12.5 - - - -
515B LEU* 3.2 36.1 - - + -
516B VAL 3.6 3.6 - - - +
517B ARG* 3.1 38.4 - - + +
528B GLY* 1.3 71.6 - - - +
530B ALA* 1.3 63.1 + - - +
531B GLY 4.0 9.0 - - - +
532B TYR* 4.1 23.1 - - + +
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Residues in contact with ALA 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292B CYS* 3.7 5.1 - - - -
293B THR 4.0 1.0 - - - +
294B GLY* 3.1 29.1 - - - -
295B ILE* 4.1 19.5 - - + +
298B LYS* 4.4 9.9 - - + +
516B VAL 2.8 14.1 + - - +
518B ILE* 4.2 16.4 - - + -
528B GLY 3.6 8.5 - - - +
529B ILE* 1.3 75.7 - - - +
531B GLY* 1.3 59.7 + - - +
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Residues in contact with GLY 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292B CYS* 3.7 13.2 - - - -
293B THR 5.4 0.7 - - - -
515B LEU* 4.7 0.2 - - - +
516B VAL* 3.0 26.4 + - - +
529B ILE* 3.8 5.3 - - - +
530B ALA* 1.3 81.1 - - - +
532B TYR* 1.3 77.4 + - - -
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Residues in contact with TYR 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292B CYS* 4.0 7.8 - - - +
513B LEU* 3.6 37.7 - - + -
514B VAL 3.3 9.6 - - - +
515B LEU* 3.4 32.0 - - + +
529B ILE* 4.1 20.0 - - + +
531B GLY* 1.3 87.1 - - - -
533B MET* 1.3 68.0 + - - +
544B PRO* 4.0 2.6 - - - +
545B SER* 3.2 27.5 + - - +
547B TYR* 3.4 58.2 - + + -
548B SER* 5.0 5.8 + - - -
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Residues in contact with MET 533 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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290B SER 5.2 0.2 - - - +
291B GLY* 3.4 26.5 - - - +
292B CYS* 4.1 4.9 - - + -
321B PHE* 2.9 45.3 - - + -
502B LEU* 4.2 11.0 - - + -
513B LEU* 3.2 6.4 - - - +
514B VAL* 2.8 37.5 + - + +
516B VAL* 4.2 17.7 - - + -
532B TYR* 1.3 78.4 - - - +
534B GLU* 1.3 62.0 + - - +
542B LEU* 3.8 35.9 - - + +
543B GLU 3.0 16.2 - - - +
545B SER* 4.0 5.4 - - - +
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Residues in contact with GLU 534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510B MET* 5.5 4.9 - - - +
512B ASN* 3.4 28.9 + - - +
513B LEU* 4.9 8.4 - - + +
533B MET* 1.3 75.4 - - - +
535B TYR* 1.3 72.3 + - - +
536B ASN* 3.4 1.3 + - - -
541B TRP 3.5 0.2 - - - +
542B LEU* 4.0 3.8 - - - -
543B GLU* 2.8 43.7 + - + +
544B PRO 5.4 0.2 - - - +
545B SER* 4.3 17.4 + - - -
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Residues in contact with TYR 535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316B MET* 2.9 40.1 - - + +
317B VAL* 5.6 2.9 - - + -
320B THR* 4.4 2.7 - - + -
361B ARG* 3.8 27.7 + - - -
504B ARG* 4.2 15.5 - - - +
512B ASN* 2.9 45.0 + - - +
514B VAL* 5.4 1.3 - - + -
534B GLU* 1.3 79.4 - - - +
536B ASN* 1.3 61.2 + - - +
537B LYS* 3.4 46.6 + - + -
540B GLY* 3.3 29.4 + - - -
541B TRP 3.7 6.7 - - - -
542B LEU* 3.8 17.0 - - + +
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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