Contacts of the helix formed by residues 654 - 665 (chain A) in PDB entry 3U44
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 ASP 654 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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652A GLY 3.6 3.4 + - - +
653A ALA* 1.3 74.1 - - - +
655A GLU* 1.3 61.4 + - - +
656A ASN* 3.2 11.6 + - + +
657A GLU* 3.2 38.1 + - + +
658A LEU* 2.7 36.3 + - - +
773B LYS* 3.9 29.0 - - - +
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Residues in contact with GLU 655 (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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647A ARG* 3.1 38.0 + - - +
653A ALA 5.4 0.9 - - - -
654A ASP* 1.3 79.2 - - - +
656A ASN* 1.3 58.5 + - - +
658A LEU* 4.4 4.3 - - + -
659A SER* 2.8 30.8 + - - -
771B GLU 3.5 3.5 - - - +
772B VAL* 3.3 32.3 - - + +
773B LYS* 3.1 32.2 + - - +
775B LEU* 3.9 14.3 - - + +
803B PHE* 4.3 4.3 - - + -
806B PHE* 3.5 22.8 - - + -
1108B VAL* 3.8 5.4 - - + -
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Residues in contact with ASN 656 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654A ASP* 3.9 15.6 + - + +
655A GLU* 1.3 77.9 - - - +
657A GLU* 1.3 58.1 + - + +
659A SER* 3.1 6.9 + - - -
660A LEU* 2.9 36.6 + - + +
773B LYS* 4.0 10.3 + - - +
774B GLN 3.3 21.4 + - - -
775B LEU* 3.3 5.5 - - - +
776B GLU* 2.9 41.3 + - - +
779B VAL* 3.2 14.4 - - + +
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Residues in contact with GLU 657 (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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652A GLY 5.0 0.6 - - - +
653A ALA* 3.3 9.1 - - + -
654A ASP* 3.2 39.1 + - + +
655A GLU 3.2 0.4 - - - -
656A ASN* 1.3 78.0 - - + +
658A LEU* 1.3 66.7 + - - +
660A LEU* 3.2 6.9 - - + +
661A ILE* 3.1 27.6 + - - +
686A GLU* 5.2 6.1 - - - +
687A LEU* 3.2 48.6 + - + +
690A LYS* 3.6 18.4 - - - +
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Residues in contact with LEU 658 (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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643A ALA* 4.9 5.6 - - + +
646A LEU* 3.9 26.0 - - + -
647A ARG* 4.1 33.0 - - + +
653A ALA* 3.8 20.4 - - + -
654A ASP 2.7 28.1 + - - +
655A GLU* 3.8 11.0 - - + +
657A GLU* 1.3 72.6 - - - +
659A SER* 1.3 58.2 + - - +
661A ILE* 2.9 21.4 + - + +
662A ARG 3.3 2.8 + - - -
670A TYR* 2.6 34.1 + - + +
803B PHE* 5.7 0.2 - - + -
806B PHE* 4.5 5.6 - - + -
811B LEU* 3.7 21.2 - - + +
1129B VAL* 5.5 4.0 - - + -
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Residues in contact with SER 659 (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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655A GLU 2.8 20.5 + - - -
656A ASN* 3.1 11.6 + - - -
658A LEU* 1.3 78.9 - - - +
660A LEU* 1.3 61.1 + - - +
661A ILE 3.3 0.3 + - - -
662A ARG* 3.3 8.9 + - - +
663A LEU* 3.2 22.1 + - - +
775B LEU* 4.4 2.0 - - - +
779B VAL* 3.3 17.8 - - - +
783B LEU* 3.5 29.7 - - - +
806B PHE* 3.9 9.9 - - - -
811B LEU* 3.4 12.0 - - - +
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Residues in contact with LEU 660 (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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656A ASN* 2.9 23.9 + - + +
657A GLU* 3.2 11.4 - - + +
659A SER* 1.3 76.4 + - - +
661A ILE* 1.3 62.8 + - - +
663A LEU* 3.4 33.7 - - + +
664A GLU* 4.0 4.0 + - - +
677A TYR* 3.9 24.2 - - + +
685A ASP* 5.6 0.9 - - - +
687A LEU* 3.7 22.0 - - + -
779B VAL* 5.3 10.5 - - + -
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Residues in contact with ILE 661 (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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646A LEU* 4.2 14.4 - - + -
657A GLU 3.1 16.3 + - - +
658A LEU* 2.9 13.9 + - + +
660A LEU* 1.3 74.2 - - - +
662A ARG* 1.3 66.7 + - - +
663A LEU 3.1 0.9 + - - -
664A GLU* 3.1 13.5 + - - +
670A TYR* 3.6 24.2 - - + +
673A ALA* 3.4 32.1 - - - +
674A MET* 3.6 16.2 - - + -
677A TYR* 4.3 9.2 - - + -
687A LEU* 4.4 8.7 - - + -
691A LEU* 3.8 37.9 - - + -
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Residues in contact with ARG 662 (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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639A ASP* 4.4 2.4 + - - -
658A LEU 3.3 4.2 + - - +
659A SER* 3.3 10.4 + - - +
661A ILE* 1.3 78.5 - - - +
663A LEU* 1.3 64.2 + - - +
665A ASN 2.8 37.6 + - - +
666A LYS* 2.9 34.7 + - + +
667A LYS 4.4 0.4 + - - -
668A ALA 2.6 27.3 + - - -
669A PRO 4.3 1.6 + - - -
670A TYR* 3.7 46.5 - - + +
673A ALA* 4.5 2.0 - - - +
783B LEU* 4.3 8.7 - - + -
810B GLY 4.3 12.8 - - - +
811B LEU* 2.9 37.9 + - + +
812B HIS* 3.1 22.1 + - + +
813B LEU* 4.6 0.2 - - - +
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Residues in contact with LEU 663 (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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659A SER 3.2 19.5 - - - +
660A LEU* 3.4 28.7 - - + +
662A ARG* 1.3 78.3 - - - +
664A GLU* 1.3 66.8 + - - +
665A ASN* 3.1 2.9 + - - -
666A LYS* 4.3 21.9 + - - +
778B SER 5.9 0.2 - - - +
779B VAL* 5.1 9.4 - - + -
782B GLN* 4.5 29.2 - - + +
783B LEU* 3.9 37.5 - - + +
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Residues in contact with GLU 664 (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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660A LEU 4.5 3.3 - - - +
661A ILE 3.1 10.7 + - - +
663A LEU* 1.3 79.9 - - - +
665A ASN* 1.3 61.5 + - - +
673A ALA 3.9 9.2 - - - +
676A ASP* 4.1 20.2 - - + +
677A TYR* 3.8 44.3 - - + -
680A ALA* 5.3 5.5 - - - +
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Residues in contact with ASN 665 (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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661A ILE 4.2 1.0 + - - -
662A ARG* 2.8 31.4 + - - +
664A GLU* 1.3 81.1 - - - +
666A LYS* 1.3 62.6 + - - +
667A LYS* 3.2 5.7 + - - +
668A ALA* 3.0 39.1 + - + +
672A GLU* 4.7 3.4 - - - -
673A ALA* 3.7 16.3 - - - +
676A ASP* 3.3 24.1 + - - +
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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