Contacts of the strand formed by residues 648 - 652 (chain A) in PDB entry 1SLL
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 648 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597A GLN* 4.2 6.3 + - - -
646A GLN* 4.9 0.4 - - - -
647A LEU* 1.3 76.8 - - - +
649A VAL* 1.3 62.5 + - - +
650A ILE* 4.2 5.9 - - - +
664A LEU* 3.2 5.0 - - - +
665A SER* 2.8 32.3 + - - +
714A SER* 3.5 28.0 + - - -
715A CYS* 3.5 11.1 - - - -
716A LEU* 2.9 35.3 + - - +
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Residues in contact with VAL 649 (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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543A ILE* 5.2 1.9 - - - +
597A GLN* 3.7 42.8 + - + +
598A ILE 4.2 4.5 - - - +
599A VAL* 3.7 22.0 - - + +
609A TYR* 3.8 25.1 - - + -
647A LEU* 4.0 10.8 - - + -
648A SER* 1.3 75.5 + - - +
650A ILE* 1.3 69.3 + - - +
662A ILE* 4.3 15.0 - - + -
663A ILE 3.1 15.9 - - - +
664A LEU* 4.2 13.5 - - + -
698A TRP* 4.5 0.2 - - + -
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Residues in contact with ILE 650 (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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543A ILE* 4.2 21.3 - - + -
545A LYS* 5.6 1.1 - - - +
597A GLN* 5.9 0.4 - - - +
598A ILE 5.3 0.7 - - - -
599A VAL* 3.5 9.9 - - - -
648A SER* 4.2 4.5 - - - +
649A VAL* 1.3 81.6 - - - +
651A ASN* 1.3 71.2 + - - +
652A TYR* 5.5 0.2 - - + -
662A ILE* 3.2 5.9 - - - +
663A ILE* 2.9 53.6 + - + +
716A LEU* 3.6 44.6 - - + +
717A ALA* 3.9 12.8 - - - +
718A GLU* 4.0 16.4 - - + +
724A VAL* 4.7 5.8 - - + -
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Residues in contact with ASN 651 (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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545A LYS* 2.8 32.5 + - - +
599A VAL* 3.4 5.5 - - - -
600A GLU* 2.8 45.8 + - - +
650A ILE* 1.3 88.2 - - - +
652A TYR* 1.3 63.2 + - - +
661A ALA 4.1 4.2 + - - -
662A ILE* 3.8 13.9 - - - +
718A GLU* 4.2 6.9 - - - +
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Residues in contact with TYR 652 (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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650A ILE* 5.5 0.9 - - + -
651A ASN* 1.3 77.4 - - - +
653A SER* 1.3 62.0 + - - +
654A GLN* 3.1 50.2 + - + +
655A PRO 5.2 0.2 - - - -
656A ILE* 4.1 13.5 - - + -
660A PRO* 5.9 0.2 - - - +
661A ALA* 3.2 27.8 + - + +
663A ILE* 3.8 28.7 - - + -
718A GLU* 3.6 31.5 + - + -
722A GLY* 2.6 37.1 + - - -
724A VAL* 4.0 6.5 - - + -
752A ILE* 3.4 30.3 - - + +
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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