Contacts of the strand formed by residues 655 - 660 (chain C) in PDB entry 1SL0
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 GLU 655 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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452C ARG* 5.1 1.9 + - - -
474C ILE 3.4 11.4 - - - +
475C ASP* 3.6 14.5 - - + +
625C TRP* 4.7 2.0 - - - -
651C TRP* 3.2 3.6 - - - -
652C VAL* 3.1 45.2 + - + +
653C HIS 3.3 2.4 + - - -
654C ASP* 1.3 86.0 - - - +
656C ILE* 1.3 73.7 + - - +
657C GLN* 2.5 28.8 + - - +
700C TRP* 3.5 15.4 + - - -
703C CYS 5.3 0.3 - - - +
704C HIS* 4.9 9.0 - - - +
21Q 2DT 4.0 23.9 + - - +
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Residues in contact with ILE 656 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227C GLN* 5.5 0.2 - - - +
472C ALA 3.5 1.4 - - - +
473C GLY* 3.4 0.5 - - - -
474C ILE* 2.8 50.2 + - + +
625C TRP* 4.0 25.6 - - + -
626C ILE* 3.7 17.9 - - + -
629C THR* 4.8 11.0 - - + +
648C TYR* 4.4 20.0 - - + +
650C ALA 3.2 12.6 - - - +
651C TRP* 3.5 23.1 - - + -
655C GLU* 1.3 85.6 - - - +
657C GLN* 1.3 68.7 + - - +
658C VAL* 3.8 21.1 - - + -
673C ALA* 5.2 1.1 - - + -
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Residues in contact with GLN 657 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232C PHE* 4.4 11.0 - - + -
471C GLN* 5.5 3.3 - - + +
472C ALA 3.8 2.5 - - - -
473C GLY* 3.3 23.8 + - - -
648C TYR* 5.4 0.2 - - - -
649C MET* 3.2 33.9 + - + +
650C ALA* 2.9 24.5 + - + +
652C VAL* 5.7 0.9 - - + -
655C GLU* 2.5 32.9 + - - +
656C ILE* 1.3 86.5 + - - +
658C VAL* 1.3 62.4 + - - +
700C TRP* 3.6 41.2 - - + +
703C CYS* 3.8 17.8 + - - +
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Residues in contact with VAL 658 (chain C).
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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472C ALA* 2.6 47.5 + - + +
474C ILE* 6.2 0.9 - - + -
629C THR* 5.8 0.4 - - + -
646C PHE* 4.1 15.9 - - + -
647C ALA 3.7 11.0 - - - +
648C TYR* 3.8 26.2 - - + -
649C MET* 3.3 5.4 - - - +
656C ILE* 4.3 20.0 - - + -
657C GLN* 1.3 74.3 - - - +
659C GLY* 1.3 72.6 + - - +
660C CYS* 4.0 4.9 - - - -
669C VAL* 3.9 30.7 - - + -
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Residues in contact with GLY 659 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457C ALA* 4.5 2.0 - - - -
469C TRP* 3.1 13.4 - - - -
470C VAL 3.8 3.8 - - - -
642C TRP* 5.0 0.9 - - - -
646C PHE* 3.0 8.0 - - - +
647C ALA* 2.7 43.8 + - - -
649C MET* 3.2 21.7 - - - +
658C VAL* 1.3 72.5 - - - +
660C CYS* 1.3 60.4 + - - -
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Residues in contact with CYS 660 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469C TRP* 3.1 7.6 - - - +
470C VAL* 2.7 38.2 + - - +
472C ALA* 3.9 16.6 - - - -
645C ASP 3.6 3.8 - - - -
646C PHE* 4.3 1.8 - - - +
658C VAL* 4.0 6.1 - - - -
659C GLY* 1.3 79.0 - - - -
661C ARG* 1.3 62.0 + - - +
662C THR 3.9 1.8 - - - +
665C ILE* 4.2 4.0 - - + -
666C ALA* 3.2 48.0 - - + +
669C VAL* 3.4 22.7 - - - -
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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