Contacts of the strand formed by residues 745 - 750 (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 LEU 745 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A GLU 4.4 0.9 - - - +
279A ASN* 3.6 20.3 + - - +
280A ILE* 4.9 1.4 + - + -
281A PHE* 4.0 26.1 + - + +
292A PHE* 4.1 19.5 - - + -
293A ARG* 4.6 7.6 - - - +
295A PRO* 3.9 31.4 - - + -
309A ALA* 3.8 28.0 - - + -
727A LEU* 4.1 20.0 - - + +
728A TYR 3.3 15.7 - - - +
729A GLU* 4.0 9.4 - - + -
743A ASP* 3.6 1.2 - - - +
744A ILE* 1.3 81.2 - - + +
746A LYS* 1.3 61.3 + - - +
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Residues in contact with LYS 746 (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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181A ARG* 6.0 0.2 - - - +
276A TYR 4.0 19.2 + - - -
277A GLY 5.2 0.8 + - - -
278A GLU* 3.7 10.6 + - - +
279A ASN* 2.7 32.2 + - - +
726A LEU 3.3 2.1 - - - +
727A LEU* 3.2 6.4 - - - +
728A TYR* 2.8 52.7 + - + +
730A LYS* 4.1 22.4 - - + -
743A ASP* 3.3 30.4 + - - +
744A ILE 3.9 8.3 - - - +
745A LEU* 1.3 75.8 - - - +
747A PHE* 1.3 61.0 + - - +
748A GLU* 4.1 8.3 - - + +
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Residues in contact with PHE 747 (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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277A GLY* 3.5 1.7 - - - -
278A GLU* 2.8 62.7 + - + +
279A ASN 5.3 0.2 - - - -
280A ILE* 4.2 10.5 - - + -
297A LEU* 3.8 33.0 - - + -
334A GLY* 3.1 28.7 - - - -
337A TRP* 3.9 16.6 - + - -
719A LEU* 4.5 7.6 - - + -
725A GLY* 3.9 5.8 - - - -
726A LEU 3.2 23.6 - - - -
727A LEU* 4.0 13.2 - - + +
746A LYS* 1.3 71.8 - - - +
748A GLU* 1.3 65.3 + - - +
749A LYS* 3.6 29.2 - - + -
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Residues in contact with GLU 748 (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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181A ARG* 3.0 20.2 + - - -
184A TYR* 3.9 18.0 - - + +
276A TYR 4.6 3.3 - - - +
277A GLY* 4.0 14.4 - - - -
704A VAL* 4.7 1.9 - - - +
725A GLY* 3.4 2.4 - - - -
726A LEU* 2.6 43.2 + - + +
728A TYR* 2.9 39.7 + - + -
746A LYS* 4.3 6.2 - - + +
747A PHE* 1.3 80.4 - - - +
749A LYS* 1.3 63.3 + - - +
750A TYR* 2.5 42.1 + - + +
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Residues in contact with LYS 749 (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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184A TYR* 5.4 0.6 + - - -
185A LYS* 2.8 29.1 + - - +
333A GLY 3.6 11.3 + - - -
334A GLY 3.4 26.8 + - - -
335A ASN* 2.7 30.9 + - - +
719A LEU* 3.8 19.1 - - + -
723A GLN* 3.7 28.8 - - - +
724A VAL 3.4 7.4 - - - +
747A PHE* 3.6 17.3 - - + -
748A GLU* 1.3 77.2 - - - +
750A TYR* 1.3 64.2 + - - +
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Residues in contact with TYR 750 (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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184A TYR* 4.3 7.1 - - - -
185A LYS* 3.8 24.4 + - + -
678A ILE* 3.9 22.4 - - + -
702A TYR* 3.5 34.5 - + - -
704A VAL* 3.7 21.7 + - + +
723A GLN* 3.5 6.3 - - - -
724A VAL* 2.8 39.7 + - + +
726A LEU* 4.4 8.1 - - + -
748A GLU* 2.5 44.0 + - + -
749A LYS* 1.3 79.8 - - - +
751A SER* 1.3 62.5 + - - +
754A GLU* 3.4 8.1 - - - +
755A LEU* 3.5 24.2 - - + -
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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