Contacts of the strand formed by residues 550 - 558 (chain B) in PDB entry 4YMJ
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 550 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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546B GLU* 3.5 4.4 - - - -
547B GLY* 3.0 27.9 + - - +
548B ALA 3.6 1.2 - - - -
549B PHE* 1.3 81.7 - - - +
551B LYS* 1.3 62.7 + - - -
552B VAL* 5.3 2.5 - - - +
572B LYS* 5.2 6.0 - - - +
573B ALA 3.2 14.4 - - - -
574B LEU* 4.4 3.6 - - - +
575B LYS* 4.1 8.5 - - - -
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Residues in contact with LYS 551 (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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543B GLU* 3.2 24.1 + - + +
545B GLY 3.5 4.5 - - - +
546B GLU* 3.8 38.8 - - + +
550B GLY* 1.3 73.0 - - - -
552B VAL* 1.3 62.5 + - - +
553B PHE* 3.5 36.6 - - + -
571B VAL 3.7 0.7 - - - +
572B LYS* 3.4 3.3 - - - +
573B ALA* 2.9 34.8 + - + +
575B LYS* 5.3 1.2 - - - +
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Residues in contact with VAL 552 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543B GLU* 3.5 4.0 - - - +
544B LEU* 2.7 49.0 + - + -
545B GLY 2.8 14.4 + - - +
550B GLY 5.3 2.2 - - - +
551B LYS* 1.3 77.5 - - - +
553B PHE* 1.3 60.2 + - - +
570B ALA* 4.5 4.0 - - + -
571B VAL 3.2 10.3 - - - +
572B LYS* 4.1 20.4 - - + -
700B MET* 5.5 1.6 - - + -
901B 4EJ 3.6 62.1 - - + -
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Residues in contact with PHE 553 (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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540B LEU* 3.9 44.9 - - + -
542B ARG* 3.3 7.0 - - - +
543B GLU* 3.7 33.9 - - + -
544B LEU* 3.9 6.4 - - - +
551B LYS* 3.5 44.4 - - + -
552B VAL* 1.3 75.7 - - - +
554B LEU* 1.3 67.3 + - - +
570B ALA* 3.3 6.1 - - - +
571B VAL* 2.6 47.6 + - + +
573B ALA* 4.5 12.3 - - + -
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Residues in contact with LEU 554 (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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541B LYS* 2.9 32.0 + - + -
542B ARG* 2.6 54.3 + - + +
544B LEU* 3.6 17.8 - - + +
553B PHE* 1.3 77.0 - - - +
555B ALA* 1.3 67.9 + - - +
568B LEU* 4.3 16.8 - - + -
569B VAL 3.5 10.8 - - - +
619B TYR* 3.4 48.7 - - + -
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Residues in contact with ALA 555 (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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538B ILE* 3.9 21.1 - - + -
539B VAL 3.3 15.9 - - - +
540B LEU* 3.9 8.7 - - + -
541B LYS* 4.0 5.4 - - - +
554B LEU* 1.3 77.9 - - - +
556B GLU* 1.3 63.8 + - - +
568B LEU* 3.3 10.0 - - - +
569B VAL* 2.8 45.5 + - + +
571B VAL* 4.0 5.8 - - + -
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Residues in contact with GLU 556 (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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537B ASP 3.5 0.7 - - - +
538B ILE* 3.4 3.3 - - - -
539B VAL* 2.7 49.6 + - + +
541B LYS* 3.2 36.2 + - + +
555B ALA* 1.3 75.2 - - - +
557B CYS* 1.3 61.7 + - - +
558B TYR* 4.0 10.3 + - + -
566B LYS* 2.9 49.2 + - + +
567B MET 3.4 5.8 - - - +
568B LEU* 3.6 23.7 - - + +
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Residues in contact with CYS 557 (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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533B ILE* 3.8 21.1 - - - -
537B ASP 3.2 4.5 - - - -
538B ILE* 3.5 26.0 - - + -
556B GLU* 1.3 75.1 - - - +
558B TYR* 1.3 74.9 + - - +
560B LEU* 3.8 24.4 + - + +
561B SER 5.3 0.3 + - - -
566B LYS* 3.3 3.2 - - - -
567B MET* 2.8 36.8 + - + +
569B VAL* 3.9 20.2 - - + -
616B VAL* 5.1 0.2 - - - -
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Residues in contact with TYR 558 (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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533B ILE* 5.4 0.5 - - - +
536B ARG 5.5 0.9 - - - -
537B ASP* 2.8 47.1 + - - +
539B VAL* 3.6 28.7 - - + +
556B GLU* 4.0 8.2 + - + -
557B CYS* 1.3 82.6 - - - +
559B ASN* 1.3 76.0 + - - +
560B LEU 3.1 4.5 + - - -
565B ASP* 3.6 21.8 - - + -
566B LYS* 3.5 36.1 + - + +
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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