Contacts of the strand formed by residues 646 - 651 (chain A) in PDB entry 3U1K
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 THR 646 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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609A THR* 3.2 35.4 - - + -
610A VAL 3.7 2.2 - - - +
611A GLN* 3.2 19.4 + - - +
641A GLN* 3.6 4.2 - - - +
642A VAL* 2.6 48.2 + - + -
643A ASP* 2.8 32.1 + - - +
644A GLU 3.7 1.0 - - - -
645A GLU* 1.3 78.1 - - - +
647A PHE* 1.3 58.8 + - - +
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Residues in contact with PHE 647 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608A GLU 3.9 0.3 - - - +
609A THR* 3.5 1.6 - - - -
610A VAL* 2.7 45.5 + - + +
612A VAL* 3.8 23.3 - - + -
617A ARG* 4.5 7.4 - - + -
620A PHE* 3.7 31.6 - + + -
621A VAL* 3.7 27.6 - - + -
628A LEU* 4.1 11.7 - - + -
639A ILE* 4.0 21.3 - - + -
640A SER 3.7 3.1 - - - -
641A GLN* 3.5 50.7 - - + -
642A VAL* 4.4 1.6 - - - -
644A GLU 4.7 3.6 - - - -
645A GLU 4.2 6.3 - - - -
646A THR* 1.3 79.6 - - - +
648A SER* 1.3 61.0 + - - +
649A VAL* 3.9 0.4 + - - -
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Residues in contact with SER 648 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A GLU* 5.3 2.1 - - - +
607A VAL* 3.4 23.0 - - - +
608A GLU 3.6 4.7 + - - -
609A THR* 4.6 6.6 + - - +
638A THR 3.7 1.2 - - - +
639A ILE* 3.3 5.0 - - - +
640A SER* 2.9 39.4 + - - -
642A VAL* 3.7 20.7 - - - +
647A PHE* 1.3 72.3 - - - +
649A VAL* 1.3 61.9 + - - +
650A PHE 4.2 0.2 - - - -
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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
----------------------------------------------------------
607A VAL* 3.2 9.0 - - - +
608A GLU* 2.7 37.3 + - + +
610A VAL* 3.9 28.0 - - + -
631A LEU* 5.9 0.2 - - + -
637A VAL* 4.1 20.6 - - + -
638A THR 3.6 4.3 - - - +
639A ILE* 3.5 23.6 - - + -
647A PHE 4.4 0.9 - - - +
648A SER* 1.3 77.4 + - - +
650A PHE* 1.3 70.6 + - - +
657A MET* 3.6 26.5 - - + +
660A ALA* 4.7 5.2 - - + -
664A ILE* 4.6 7.0 - - + -
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Residues in contact with PHE 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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399A PHE 4.0 3.8 - - - -
400A ASP* 3.5 20.2 - - - -
401A SER* 3.5 41.1 - - - -
402A LEU 5.3 0.4 - - - -
403A GLU* 4.7 5.2 - - - +
468A PHE* 3.5 35.9 - + - -
605A PRO* 3.5 25.6 - - + -
606A VAL 3.7 1.8 - - - -
607A VAL* 4.2 11.0 - - + -
636A GLY 5.2 0.7 - - - -
637A VAL* 3.3 7.3 - - - +
638A THR* 2.8 50.7 + - - +
648A SER* 4.2 0.8 + - - -
649A VAL* 1.3 72.7 - - - +
651A ALA* 1.3 60.7 + - - +
652A PRO* 3.9 24.0 - - + -
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Residues in contact with ALA 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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605A PRO* 3.0 6.9 - - - +
606A VAL* 2.8 34.5 + - + +
637A VAL* 4.0 6.7 - - + -
649A VAL 3.9 0.2 + - - -
650A PHE* 1.3 77.9 - - - +
652A PRO* 1.3 65.7 - - + +
653A THR 3.2 4.2 + - - +
657A MET* 3.4 54.3 - - + +
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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