Contacts of the strand formed by residues 606 - 611 (chain D) 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 VAL 606 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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468D PHE* 4.4 2.7 - - - -
604D GLY 4.5 1.6 - - - +
605D PRO* 1.3 77.2 - - - +
607D VAL* 1.3 71.8 + - - +
608D GLU* 3.7 27.6 - - + +
649D VAL 3.6 1.4 - - - +
650D PHE* 3.5 1.6 - - - -
651D ALA* 2.8 35.1 + - + +
653D THR 4.1 15.3 - - - +
654D PRO* 4.1 15.3 - - + -
657D MET* 4.1 15.0 - - + +
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Residues in contact with VAL 607 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467D PRO* 5.0 5.4 - - + +
468D PHE* 3.5 17.7 - - + -
606D VAL* 1.3 77.9 - - - +
608D GLU* 1.3 69.2 + - - +
609D THR* 6.5 0.4 - - + -
648D SER* 3.6 22.7 - - - +
649D VAL 3.2 7.9 - - - +
650D PHE* 3.4 37.5 - - + -
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Residues in contact with GLU 608 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606D VAL* 3.7 19.2 - - - +
607D VAL* 1.3 78.7 - - - +
609D THR* 1.3 66.9 + - - +
610D VAL* 4.5 0.2 - - - +
648D SER* 4.9 0.4 - - - -
649D VAL* 3.1 30.1 + - - +
657D MET* 3.0 26.5 - - + +
661D ARG* 2.3 41.9 + - - +
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Residues in contact with THR 609 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608D GLU* 1.3 79.2 - - - +
610D VAL* 1.3 66.0 + - - +
611D GLN* 3.9 11.7 + - - -
642D VAL* 5.9 2.7 - - + -
646D THR* 3.9 20.4 - - + -
647D PHE 3.3 9.0 - - - +
648D SER* 4.5 9.0 - - - +
661D ARG* 4.3 6.9 + - - -
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Residues in contact with VAL 610 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608D GLU 4.5 0.7 - - - +
609D THR* 1.3 80.7 - - - +
611D GLN* 1.3 78.9 + - - +
612D VAL* 3.9 3.8 + - + -
620D PHE* 5.8 0.9 - - + -
645D GLU 3.7 0.7 - - - +
646D THR* 3.6 1.6 - - - -
647D PHE* 2.8 43.3 + - + +
649D VAL* 4.0 15.0 - - + -
657D MET* 4.9 0.2 - - + -
661D ARG* 3.5 30.3 - - - +
664D ILE* 3.7 41.5 - - + -
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Residues in contact with GLN 611 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609D THR* 3.9 14.1 + - - -
610D VAL* 1.3 81.9 - - - +
612D VAL* 1.3 62.1 + - - +
613D PRO* 4.2 4.4 - - + +
645D GLU* 3.4 15.3 - - + +
646D THR* 3.2 35.9 + - - +
664D ILE* 5.4 1.2 - - - +
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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