Contacts of the helix formed by residues 658 - 670 (chain D) in PDB entry 3UEO
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 658 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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621D ASP* 5.3 4.3 - - - -
657D ALA* 1.3 75.7 - - - +
659D ALA* 1.3 64.6 + - - -
661D LYS* 2.9 10.8 + - - +
662D GLU* 2.9 31.8 + - - +
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Residues in contact with ALA 659 (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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614D THR* 4.2 12.6 - - + +
617D VAL* 3.9 29.1 - - + +
618D THR* 3.7 20.9 - - - +
621D ASP* 4.8 5.5 + - - +
657D ALA 3.4 0.6 + - - -
658D GLY* 1.3 71.2 - - - -
660D GLU* 1.3 64.4 + - - +
662D GLU* 3.1 14.6 + - - +
663D SER* 2.9 25.6 + - - -
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Residues in contact with GLU 660 (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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614D THR* 4.4 6.6 - - + +
618D THR* 4.5 7.2 + - + +
631D ASN* 3.2 28.0 + - - +
633D LEU* 3.5 23.2 - - + +
634D PHE* 6.1 2.7 - - + -
656D CYS* 4.5 10.9 - - + +
657D ALA 3.5 8.6 + - - +
658D GLY 3.3 0.6 - - - -
659D ALA* 1.3 78.7 - - - +
661D LYS* 1.3 57.8 + - - +
663D SER* 3.3 2.6 + - - -
664D LEU* 2.9 43.9 + - + +
698D LYS* 3.0 37.1 + - - -
718D ILE* 4.1 6.9 - - - +
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Residues in contact with LYS 661 (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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653D PHE* 4.7 21.3 - - + -
656D CYS* 3.2 34.6 + - + +
657D ALA* 3.4 14.6 + - - +
658D GLY 2.9 11.0 + - - +
660D GLU* 1.3 78.5 - - - +
662D GLU* 1.3 57.4 + - + +
664D LEU* 4.1 4.8 - - - +
665D THR* 2.6 46.1 + - - +
677D GLU* 2.7 35.1 + - - -
704D LYS* 6.1 0.6 - - - +
4E SEP 5.4 5.7 + - - -
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Residues in contact with GLU 662 (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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658D GLY* 2.9 22.7 + - - +
659D ALA* 3.5 14.2 + - - +
661D LYS* 1.3 76.6 - - + +
663D SER* 1.3 57.5 + - - +
665D THR* 3.7 5.6 - - - -
666D PHE* 2.8 27.9 + - - +
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Residues in contact with SER 663 (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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598D LEU* 3.8 21.9 - - - +
614D THR* 2.7 28.6 + - - -
633D LEU* 4.1 11.9 - - - -
659D ALA 2.9 13.3 + - - -
660D GLU 3.5 8.1 - - - -
662D GLU* 1.3 74.3 - - - +
664D LEU* 1.3 60.3 + - - +
666D PHE* 3.0 9.2 + - - +
667D LEU* 2.9 33.3 + - - +
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Residues in contact with LEU 664 (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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633D LEU* 3.7 25.1 - - + -
653D PHE* 3.5 30.3 - - + -
656D CYS* 3.8 16.2 - - + -
660D GLU* 2.9 31.5 + - + +
661D LYS* 4.1 2.5 - - - +
663D SER* 1.3 72.7 - - - +
665D THR* 1.3 58.8 + - - +
667D LEU* 3.2 3.8 + - + +
668D ALA* 2.8 30.3 + - - +
718D ILE* 3.7 48.0 - - + -
721D LEU* 3.6 21.2 - - + +
722D LEU* 4.7 3.1 - - + -
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Residues in contact with THR 665 (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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653D PHE* 3.7 20.0 - - - -
661D LYS* 2.6 29.1 + - - +
662D GLU* 3.7 5.6 - - - -
664D LEU* 1.3 76.8 - - - +
666D PHE* 1.3 63.6 + - - +
668D ALA* 3.7 2.4 - - - +
669D ASN* 3.0 45.1 + - - +
675D VAL* 3.7 26.6 - - + +
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Residues in contact with PHE 666 (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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598D LEU* 3.6 20.2 - - + -
599D LEU* 3.7 28.0 - - + -
662D GLU 2.8 16.2 + - - +
663D SER* 3.0 12.1 + - - +
665D THR* 1.3 78.7 - - - +
667D LEU* 1.3 69.1 + - + +
669D ASN* 3.3 7.3 + - + +
670D LEU* 3.0 43.3 + - + +
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Residues in contact with LEU 667 (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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598D LEU* 3.8 25.4 - - + -
599D LEU* 4.0 9.2 - - + -
633D LEU* 3.9 13.5 - - + -
637D VAL* 4.4 7.6 - - + -
639D VAL* 3.7 29.8 - - + -
663D SER 2.9 21.1 + - - +
664D LEU* 3.2 8.0 + - + +
666D PHE* 1.3 75.4 - - + +
668D ALA* 1.3 63.4 + - - +
670D LEU* 3.2 10.5 + - + +
671D LEU* 3.0 31.3 + - + +
721D LEU* 4.3 10.5 - - + -
722D LEU* 3.8 28.5 - - + -
725D ALA* 5.2 3.8 - - + -
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Residues in contact with ALA 668 (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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646D LEU* 4.8 1.6 - - - -
651D ILE* 4.4 18.4 - - + -
653D PHE* 4.6 5.8 - - + -
664D LEU 2.8 17.4 + - - +
665D THR* 3.7 1.3 - - - +
667D LEU* 1.3 76.5 - - - +
669D ASN* 1.3 62.8 + - - +
671D LEU* 3.3 8.7 + - - +
673D ALA* 3.1 25.4 + - + +
675D VAL* 3.7 25.4 - - + -
721D LEU* 4.2 15.1 - - + +
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Residues in contact with ASN 669 (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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665D THR* 3.0 38.8 + - - +
666D PHE* 3.7 6.0 - - + +
668D ALA* 1.3 74.6 - - - +
670D LEU* 1.3 56.2 + - - +
672D GLY* 2.6 27.9 + - - -
673D ALA 3.6 17.9 - - - +
674D SER* 4.4 0.9 - - - -
675D VAL* 4.0 16.2 + - - +
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Residues in contact with LEU 670 (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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599D LEU* 4.2 16.6 - - + -
639D VAL* 3.8 33.4 - - + -
641D THR* 5.2 6.1 - - + -
643D MET 4.1 7.3 - - - +
644D THR* 4.3 6.2 - - - +
666D PHE* 3.0 37.4 + - + +
667D LEU* 3.2 12.8 - - + +
669D ASN* 1.3 76.6 - - - +
671D LEU* 1.3 61.5 + - + +
672D GLY* 3.1 4.7 + - - -
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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