Contacts of the strand formed by residues 646 - 651 (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 PHE 646 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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469C TRP* 3.6 2.0 - - - -
630C GLU* 4.0 13.0 - - + -
633C LEU* 3.6 39.7 - - + -
634C VAL* 4.3 3.6 - - + -
638C LEU* 3.6 39.0 - - + -
639C LYS 3.7 2.9 - - - -
640C HIS* 3.3 50.1 - + + -
641C GLY 2.8 34.2 + - - +
645C ASP* 1.3 78.1 - - - +
647C ALA* 1.3 59.9 + - - +
648C TYR* 4.6 3.8 - + - -
658C VAL* 4.1 15.0 - - + -
659C GLY 3.0 13.5 - - - +
660C CYS* 4.5 4.5 - - - -
665C ILE* 4.6 8.3 - - + -
669C VAL* 5.0 1.3 - - + -
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Residues in contact with ALA 647 (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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230C ASN* 3.7 19.3 - - + +
640C HIS* 3.1 9.2 - - + -
641C GLY 4.0 12.6 - - - +
642C TRP* 4.2 28.5 - - + -
646C PHE* 1.3 79.4 - - - +
648C TYR* 1.3 65.6 + - - +
649C MET* 3.5 1.6 + - - +
658C VAL* 3.6 1.4 - - - -
659C GLY* 2.7 38.7 + - - -
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Residues in contact with TYR 648 (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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223C LEU* 3.3 38.4 - - + -
227C GLN* 3.6 34.7 - - + +
230C ASN* 2.8 30.0 + - - +
626C ILE* 2.6 43.7 + - + +
629C THR* 3.8 8.4 - - + +
630C GLU* 3.5 22.7 + - + -
633C LEU* 5.1 1.1 - - + -
640C HIS* 2.6 26.9 + + + -
646C PHE* 4.6 6.7 - + - -
647C ALA* 1.3 70.8 - - - +
649C MET* 1.3 59.6 + - - +
650C ALA 5.8 1.1 - - - -
656C ILE* 4.4 10.7 - - + +
657C GLN 4.6 1.8 - - - -
658C VAL* 3.8 28.7 - - + +
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Residues in contact with MET 649 (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* 3.9 10.4 + - - +
231C GLY 3.6 22.2 - - - +
232C PHE* 3.4 30.1 - - + +
233C PRO* 3.8 22.4 - - - -
437C LEU* 5.8 0.3 - - - +
457C ALA* 4.1 13.2 - - + +
471C GLN* 4.1 16.8 - - + -
642C TRP* 4.0 13.9 - - + -
647C ALA 3.6 7.4 - - - +
648C TYR* 1.3 77.0 - - - +
650C ALA* 1.3 64.3 + - - +
657C GLN* 3.2 26.1 + - + +
658C VAL 3.3 10.3 - - - +
659C GLY* 3.2 33.9 - - - +
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Residues in contact with ALA 650 (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* 3.5 14.2 + - - +
232C PHE* 3.5 23.6 - - + -
437C LEU* 5.6 4.9 - - + +
648C TYR* 5.8 0.9 - - - -
649C MET* 1.3 85.2 - - - +
651C TRP* 1.3 61.2 + - - +
652C VAL* 4.2 2.5 - - + -
656C ILE* 3.2 7.3 - - - +
657C GLN* 2.9 33.6 + - + +
700C TRP* 4.4 14.8 - - + -
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Residues in contact with TRP 651 (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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220C ALA* 6.4 0.9 - - + -
224C LEU* 3.3 41.5 - - + -
227C GLN* 3.7 17.4 + - - +
420C VAL* 4.7 8.0 - - + +
422C PRO* 4.8 4.5 - - + -
428C GLY 4.9 6.3 - - - -
429C ARG* 5.7 2.0 - - - -
430C ALA* 3.4 35.6 - - + +
619C ALA* 5.0 2.9 - - - -
622C CYS* 4.1 8.9 - - + +
623C LYS* 4.3 29.2 - - + -
625C TRP* 6.1 0.7 - + - -
626C ILE* 4.0 17.2 - - + +
650C ALA* 1.3 77.2 - - - +
652C VAL* 1.3 58.9 + - - +
653C HIS* 2.8 32.8 + - - -
655C GLU 3.2 18.6 - - - -
656C ILE* 3.5 16.8 - - + -
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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