Contacts of the helix formed by residues 655 - 666 (chain B) in PDB entry 3FA2
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 GLU 655 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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654B PRO* 1.3 83.2 - - + +
656B GLY* 1.3 70.2 + - - +
658B ARG* 3.1 11.4 + - - +
659B ARG* 2.9 39.4 + - - +
769B SER* 5.5 4.0 - - - +
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Residues in contact with GLY 656 (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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624B ILE* 4.8 3.1 - - - -
654B PRO 3.4 0.2 + - - -
655B GLU* 1.3 80.4 - - - +
657B PRO* 1.3 69.2 - - - +
659B ARG 3.2 0.3 + - - -
660B SER* 3.0 23.1 + - - -
768B MET 3.3 21.3 + - - -
769B SER* 3.6 21.6 + - - +
770B PHE* 3.5 6.6 - - - +
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Residues in contact with PRO 657 (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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614B VAL* 4.6 6.5 - - + -
624B ILE* 4.1 21.7 - - + -
628B CYS 4.1 5.9 - - - +
630B ILE* 3.5 36.8 - - + +
652B GLU* 3.8 4.1 - - - +
653B ILE* 3.4 30.7 - - + +
654B PRO 3.4 14.8 - - - +
655B GLU 3.5 0.2 - - - -
656B GLY* 1.3 88.8 - - - +
658B ARG* 1.3 56.8 + - - +
660B SER* 3.6 4.1 + - - -
661B ARG* 3.0 27.9 + - - +
768B MET 4.4 5.2 - - - +
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Residues in contact with ARG 658 (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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649B GLU* 6.1 3.0 - - - +
652B GLU* 3.3 31.6 + - + +
653B ILE 4.0 3.3 + - - +
654B PRO* 4.9 4.0 - - + -
655B GLU* 3.1 20.5 + - - +
657B PRO* 1.3 76.3 - - - +
659B ARG* 1.3 62.2 + - + +
661B ARG* 3.0 17.2 + - - +
662B LEU* 2.8 61.1 + - + +
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Residues in contact with ARG 659 (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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655B GLU* 2.9 32.9 + - - +
656B GLY 3.5 2.9 - - - +
658B ARG* 1.3 77.9 - - + +
660B SER* 1.3 58.2 + - - +
662B LEU* 3.4 8.3 + - - +
663B ASN* 2.9 29.1 + - - +
723B HIS* 5.4 6.1 + - - -
769B SER 3.6 14.0 + - - -
770B PHE* 3.1 36.6 + - + -
771B GLU* 4.3 20.6 + - - +
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Residues in contact with SER 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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624B ILE* 2.4 28.0 + - - -
627B GLY* 3.5 2.1 - - - -
656B GLY 3.0 16.2 + - - -
657B PRO 3.6 5.4 - - - -
659B ARG* 1.3 77.7 - - - +
661B ARG* 1.3 57.4 + - - +
663B ASN* 3.1 1.9 + - - +
664B ARG* 2.9 22.5 + - - +
770B PHE* 3.6 24.1 - - - -
778B GOL 2.0 43.8 + - - -
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Residues in contact with ARG 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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627B GLY* 3.6 24.2 - - - +
628B CYS 4.2 4.3 - - - +
629B TRP* 3.1 43.5 - - - -
649B GLU* 4.2 12.3 - - - +
652B GLU* 2.7 36.3 + - - +
657B PRO 3.0 16.7 + - - +
658B ARG* 3.0 25.1 + - - +
660B SER* 1.3 75.4 - - - +
662B LEU* 1.3 74.6 + - - +
664B ARG* 3.3 3.8 + - - +
665B GLU* 3.0 67.3 + - + +
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Residues in contact with LEU 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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658B ARG* 2.8 54.5 + - + +
659B ARG* 3.8 7.6 - - - +
661B ARG* 1.3 96.3 - - - +
663B ASN* 1.3 55.5 + - - +
665B GLU* 3.5 21.1 + - - +
666B GLN* 3.0 54.8 + - - +
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Residues in contact with ASN 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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659B ARG 2.9 13.9 + - - +
660B SER 3.1 9.4 + - - +
662B LEU* 1.3 74.5 - - - +
664B ARG* 1.3 63.4 - - - +
666B GLN* 3.3 2.5 + - - -
667B LEU 3.3 3.5 + - - -
668B LEU* 3.2 56.6 + - - +
669B PRO 2.8 24.2 + - - -
723B HIS* 3.1 20.3 - - - -
770B PHE* 3.7 20.4 - - + -
778B GOL 2.8 21.6 + - - -
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Residues in contact with ARG 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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602B SER 5.5 2.4 + - - -
605B THR* 6.4 0.2 - - - +
626B ASN* 3.0 45.4 + - - +
627B GLY* 3.7 13.7 + - - -
660B SER 2.9 9.3 + - - +
661B ARG 3.5 8.3 - - - +
663B ASN* 1.3 76.8 - - - +
665B GLU* 1.3 63.4 + - + +
667B LEU* 3.1 22.8 + - - +
668B LEU 5.4 0.4 - - - -
778B GOL 3.3 31.8 + - - +
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Residues in contact with GLU 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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629B TRP* 4.8 5.9 - - - -
661B ARG* 3.0 57.6 + - + +
662B LEU* 3.7 16.8 - - + +
664B ARG* 1.3 77.7 - - + +
666B GLN* 1.3 63.1 + - + +
667B LEU* 3.3 9.5 + - - +
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Residues in contact with GLN 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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662B LEU* 3.0 45.1 + - - +
663B ASN* 3.3 0.4 + - - -
664B ARG 3.2 0.6 - - - -
665B GLU* 1.3 79.6 - - + +
667B LEU* 1.3 71.0 + - - +
668B LEU* 3.2 38.3 + - + +
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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