Contacts of the strand formed by residues 557 - 563 (chain B) in PDB entry 3E4Z
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552B LYS* 3.5 17.7 - - - +
553B ASP* 3.8 2.4 + - - -
554B THR* 3.0 29.4 + - - +
555B ALA 3.6 1.2 - - - -
556B MET* 1.3 82.3 - - - +
558B LYS* 1.3 61.8 + - - +
559B LEU 4.1 0.2 - - - -
724B HIS* 3.9 5.4 - - - -
725B ILE* 3.1 18.4 - - - -
742B MET* 3.9 12.4 - - - +
746B GLU* 2.6 30.7 + - - -
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Residues in contact with LYS 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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550B LEU* 3.4 26.0 - - + -
552B LYS 3.5 2.0 - - - -
553B ASP* 3.7 22.0 - - - +
557B SER* 1.3 74.7 - - - +
559B LEU* 1.3 57.9 + - - +
560B TRP* 4.0 5.6 + - - +
724B HIS* 3.4 29.6 + - + +
725B ILE 2.8 8.3 + - - +
726B GLU* 3.2 47.0 + - + +
727B ALA* 2.9 27.9 + - - +
742B MET* 5.4 0.2 - - - -
763B LEU* 6.0 1.2 - - - +
914B GLN* 4.6 6.4 - - - +
916B TYR* 3.7 12.6 + - - -
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Residues in contact with LEU 559 (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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550B LEU* 3.5 5.1 - - - +
551B ILE* 2.9 56.4 + - + +
552B LYS* 2.9 24.0 + - + -
557B SER 4.1 0.6 - - - -
558B LYS* 1.3 72.3 - - - +
560B TRP* 1.3 79.4 + - - +
727B ALA* 3.8 14.1 - - + -
729B LEU* 3.6 26.7 - - + -
738B ALA* 3.8 14.4 - - + +
739B LEU* 4.1 10.3 - - + -
742B MET* 3.7 33.4 - - + -
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Residues in contact with TRP 560 (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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548B PRO* 4.1 7.4 - - + -
549B ALA 3.4 7.9 - - - -
550B LEU* 3.6 52.0 - - + -
558B LYS* 4.2 9.3 - - - +
559B LEU* 1.3 81.5 - - - +
561B PHE* 1.3 60.4 + - - +
726B GLU* 2.9 32.0 + - + +
727B ALA 2.8 22.4 + - - +
728B LEU* 3.5 9.0 - - + -
729B LEU 2.9 25.6 + - - -
911B ILE* 3.7 28.0 - - + -
916B TYR* 3.3 39.7 - + + -
918B PHE* 3.8 25.6 - + - -
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Residues in contact with PHE 561 (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 GLU* 4.0 5.2 - - - -
544B ALA* 6.0 5.2 - - - -
545B THR* 4.1 4.9 + - - -
548B PRO* 3.3 3.7 - - - +
549B ALA* 2.8 39.0 + - + +
551B ILE* 3.5 33.4 - - + -
559B LEU* 5.0 0.4 - - + -
560B TRP* 1.3 76.2 - - - +
562B LYS* 1.3 68.3 + - - +
563B GLN* 3.6 25.8 - - + -
728B LEU* 4.8 0.2 - - - -
729B LEU 3.4 10.5 - - - +
733B ILE* 3.3 30.1 - - + -
734B THR* 3.6 11.0 - - - -
735B LYS* 3.3 37.0 - - + -
738B ALA* 3.5 18.6 - - + -
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Residues in contact with LYS 562 (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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545B THR* 3.5 22.2 - - - +
546B PRO 2.8 28.8 + - - +
547B TYR 4.0 5.6 - - - +
548B PRO* 3.9 14.8 - - + +
561B PHE* 1.3 83.5 - - - +
563B GLN* 1.3 73.3 + - - +
565B ASP* 2.9 29.6 + - - +
566B LYS* 3.8 5.3 - - - +
728B LEU* 4.9 0.8 - - - +
729B LEU 3.1 7.4 + - - +
730B HIS* 3.3 30.5 + - + +
731B GLY 3.2 22.9 + - - +
903B GLU* 2.9 22.1 + - - -
907B TYR* 4.0 10.1 - - + -
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Residues in contact with GLN 563 (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 LEU* 3.4 23.6 + - - +
539B PRO 3.0 23.4 + - - -
540B LEU* 3.6 15.8 - - + +
541B GLU* 2.9 37.8 + - - +
544B ALA* 4.1 10.7 - - + +
545B THR* 4.6 3.7 + - - +
561B PHE* 3.6 14.4 - - + -
562B LYS* 1.3 85.4 - - - +
564B ASP* 1.3 77.3 + - - +
565B ASP* 3.2 6.1 + - - +
731B GLY 3.5 7.2 - - - +
732B ASN* 5.4 2.1 + - - -
733B ILE 3.3 25.7 + - - +
734B THR* 4.7 2.6 - - - +
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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