Contacts of the strand formed by residues 560 - 565 (chain A) in PDB entry 2LTO
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 ASP 560 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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556A TRP* 5.2 5.9 - - + -
557A LYS* 4.6 13.4 - - - +
558A PRO 4.9 1.9 - - - +
559A GLY* 1.3 80.1 - - - +
561A GLU* 1.3 78.9 + - - +
562A CYS* 3.2 16.9 - - - -
576A GLU* 4.3 1.3 - - - +
577A VAL* 3.0 36.3 + - + +
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Residues in contact with GLU 561 (chain A).
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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560A ASP* 1.3 86.4 - - - +
562A CYS* 1.4 63.1 + - - +
575A ALA 3.8 6.1 - - - -
576A GLU* 4.0 21.4 + - + +
592A ILE* 4.2 20.4 - - + -
608A ILE* 3.5 28.4 + - + +
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Residues in contact with CYS 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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556A TRP* 3.2 44.2 - - + -
560A ASP* 3.2 20.4 - - - +
561A GLU* 1.4 78.3 - - - +
563A PHE* 1.3 58.3 + - - +
564A ALA 4.2 0.2 - - - -
574A ARG* 3.6 4.5 - - - -
575A ALA* 2.9 31.3 + - - +
577A VAL* 3.6 14.4 - - + -
589A VAL* 6.0 0.2 - - + -
605A ILE* 4.1 12.1 - - + -
606A LYS 4.0 3.1 - - - +
607A PRO* 5.4 0.9 - - - -
608A ILE* 3.3 19.2 - - - +
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Residues in contact with PHE 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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562A CYS* 1.3 70.6 - - - +
564A ALA* 1.3 59.0 + - - +
572A PHE* 3.7 17.9 - - + -
573A TYR* 3.2 31.9 - - - -
574A ARG* 3.4 26.2 - - + -
605A ILE* 3.1 3.4 - - - +
606A LYS* 2.8 63.7 + - + +
607A PRO 4.7 1.8 - - - -
608A ILE* 3.5 44.4 - - + +
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Residues in contact with ALA 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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562A CYS 4.2 0.4 - - - -
563A PHE* 1.3 72.1 - - - +
565A LEU* 1.3 62.2 + - - +
566A TYR 3.5 2.1 + - - -
572A PHE* 3.9 3.1 - - - -
573A TYR* 2.9 27.1 + - - +
575A ALA* 4.5 4.0 - - + +
589A VAL* 3.7 29.8 - - + -
591A PHE* 3.7 20.7 - - + -
600A VAL* 4.2 4.7 - - + -
604A ASN 3.8 4.3 - - - -
605A ILE* 3.9 16.4 - - + -
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Residues in contact with LEU 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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564A ALA* 1.3 68.7 - - - +
566A TYR* 1.3 60.1 + - - +
570A ASN* 3.4 57.0 - - - +
571A LYS* 3.4 11.0 - - - +
572A PHE* 3.8 28.0 - - + +
591A PHE* 5.3 0.2 - - - -
600A VAL* 3.4 22.2 - - - +
604A ASN* 2.8 54.1 + - + +
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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