Contacts of the helix formed by residues 659 - 666 (chain B) in PDB entry 3U11
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 GLY 659 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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623B ILE* 3.9 7.4 - - - -
631B LYS 3.7 9.4 - - - +
632B MET* 3.8 6.5 - - - +
658B PHE* 1.3 76.5 - - - +
660B GLU* 1.3 62.2 + - - +
663B LEU* 3.9 9.0 - - - +
669B ARG* 3.2 30.3 + - - -
846B CMP 3.0 26.9 + - - -
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Residues in contact with GLU 660 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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632B MET* 3.8 28.0 - - + -
657B TYR* 3.7 14.6 - - + -
658B PHE* 3.2 5.4 + - - -
659B GLY* 1.3 74.1 + - - +
661B ILE* 1.3 77.3 + - + +
663B LEU* 3.1 7.9 - - - +
664B LEU* 2.9 28.5 + - + +
689B PHE* 4.7 1.1 - - + -
703B PHE* 4.1 26.9 - - + +
706B VAL* 4.7 0.3 - - - +
707B ALA* 4.0 9.1 + - + -
710B ARG* 2.9 36.5 + - - -
846B CMP 2.6 25.8 + - - -
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Residues in contact with ILE 661 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659B GLY 3.4 1.4 - - - -
660B GLU* 1.3 84.2 - - - +
662B CYS* 1.3 62.4 + - - +
664B LEU* 3.0 6.6 + - + +
665B THR* 2.7 50.9 + - + +
670B THR* 4.0 9.6 - - + +
707B ALA* 3.3 30.1 - - + +
710B ARG* 4.4 2.0 - - + -
711B LEU* 3.9 31.6 - - + -
720B ILE* 3.9 15.7 - - + -
846B CMP 3.4 38.5 + - + +
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Residues in contact with CYS 662 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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629B GLY* 3.6 28.9 - - - -
661B ILE* 1.3 73.3 - - - +
663B LEU* 1.3 66.6 + - - +
665B THR* 3.3 9.2 - - - -
666B ARG* 2.6 36.9 + - - -
667B GLY 3.7 10.8 - - - +
668B ARG 3.5 26.5 - - - +
669B ARG* 3.4 28.7 - - - +
846B CMP 2.8 15.4 + - - +
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Residues in contact with LEU 663 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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629B GLY 4.2 4.7 - - - +
630B LYS* 4.0 5.8 - - - -
631B LYS 3.6 25.8 - - - +
632B MET* 3.4 34.5 - - + +
659B GLY 3.9 9.2 - - - +
660B GLU 3.1 15.0 - - - +
662B CYS* 1.3 94.5 - - - +
664B LEU* 1.3 56.9 + - - +
666B ARG* 4.3 9.2 + - - +
684B LEU 4.4 2.2 - - - +
686B VAL* 4.4 20.0 - - + +
689B PHE* 3.5 51.1 - - + -
690B ASN* 5.2 2.8 - - - +
700B ARG* 5.9 0.3 + - - -
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Residues in contact with LEU 664 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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660B GLU* 2.9 18.3 + - + +
661B ILE* 3.0 7.2 + - - +
663B LEU* 1.3 72.4 - - - +
665B THR* 1.3 67.6 + - + +
666B ARG* 3.5 14.1 + - - -
689B PHE* 4.4 11.7 - - + -
700B ARG* 3.7 64.1 + - + +
703B PHE* 3.5 31.2 - - + +
704B GLU* 3.7 22.7 - - + +
707B ALA* 4.1 13.5 - - + -
720B ILE* 5.0 5.8 - - + -
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Residues in contact with THR 665 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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661B ILE* 2.7 41.2 + - + +
662B CYS* 3.3 7.8 - - - -
664B LEU* 1.3 75.0 - - + +
666B ARG* 1.3 72.1 + - - +
667B GLY* 3.0 20.8 + - - -
668B ARG 4.6 2.4 + - - -
670B THR* 5.8 1.0 - - - +
718B ASN* 4.1 22.9 - - - +
719B SER* 6.1 0.4 - - - +
720B ILE* 3.8 25.1 - - + -
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Residues in contact with ARG 666 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628B ILE* 6.0 1.0 - - - +
662B CYS 2.6 17.7 + - - -
663B LEU 4.6 8.9 + - - +
664B LEU 3.5 14.7 + - - -
665B THR* 1.3 80.5 + - - +
667B GLY* 1.3 60.6 + - - +
686B VAL* 6.5 0.9 - - + -
700B ARG* 4.9 13.1 - - - +
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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