Contacts of the helix formed by residues 632 - 642 (chain B) in PDB entry 2FJU
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 632 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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609B SER* 3.6 10.2 - - - -
610B ASN* 2.8 51.0 + - - +
630B THR* 2.9 14.1 + - + +
631B MET* 1.3 74.8 - - - +
633B LEU* 1.3 69.4 + - - +
634B PRO* 3.4 15.3 - - + +
635B MET 2.9 4.2 + - - -
636B GLN* 2.9 23.0 + - - +
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Residues in contact with LEU 633 (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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612B MET* 3.7 28.3 - - + -
632B ASP* 1.3 73.7 - - - +
634B PRO* 1.3 71.6 - - + +
636B GLN* 2.9 34.8 + - + +
637B GLN* 2.9 13.2 + - - +
702B GLU* 4.5 9.2 - - - +
704B PHE* 4.1 12.6 - - + -
748B ARG* 3.5 35.7 - - - +
763B ILE* 4.4 5.4 - - + -
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Residues in contact with PRO 634 (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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610B ASN* 3.3 42.0 - - + +
611B TYR 3.1 26.0 - - - +
612B MET* 3.6 13.2 - - - -
613B PRO* 3.8 16.8 - - + +
626B LEU* 3.7 7.6 - - + +
632B ASP* 3.4 9.4 - - + +
633B LEU* 1.3 94.9 - - + +
635B MET* 1.3 55.4 + - - +
637B GLN* 3.4 4.4 + - + +
638B ASN* 3.0 25.6 + - - +
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Residues in contact with MET 635 (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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107B MET* 5.3 0.2 - - + -
610B ASN* 3.4 14.4 - - - +
626B LEU* 3.8 19.5 - - + -
627B ASN 3.4 5.8 - - - +
628B PHE* 3.6 56.3 - - + +
630B THR 3.2 28.0 - - - +
631B MET* 3.8 17.0 - - + -
632B ASP* 2.9 6.3 + - - +
634B PRO* 1.3 76.3 - - - +
636B GLN* 1.3 65.2 + - - +
638B ASN* 4.0 6.3 - - - +
639B MET* 2.9 57.4 + - + +
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Residues in contact with GLN 636 (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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631B MET 2.9 23.1 + - - +
632B ASP* 2.9 20.4 + - - +
633B LEU* 2.9 24.6 + - - +
635B MET* 1.3 77.5 - - - +
637B GLN* 1.3 60.3 - - - +
639B MET* 3.8 2.5 + - - +
640B ALA* 3.3 23.2 + - - +
748B ARG* 4.9 5.0 + - - -
758B PHE* 4.0 17.3 - - - -
761B HIS* 3.9 20.1 + - - +
763B ILE* 3.9 7.1 - - + +
781B GLU* 3.3 45.3 - - - +
783B ASN* 5.3 0.7 - - - +
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Residues in contact with GLN 637 (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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612B MET* 4.1 9.9 - - - +
613B PRO* 3.7 18.0 - - - +
614B GLN* 2.9 34.1 + - - +
617B TRP* 3.7 18.8 - - + -
633B LEU 2.9 10.1 + - - +
634B PRO 3.7 6.3 - - - +
636B GLN* 1.3 77.0 - - - +
638B ASN* 1.3 65.9 + - - +
640B ALA* 3.2 2.9 + - - +
641B VAL* 2.9 35.0 + - + +
704B PHE* 3.6 34.0 - - + +
746B SER* 3.9 4.6 + - - -
763B ILE* 3.5 19.9 - - + +
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Residues in contact with ASN 638 (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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324B ASN* 2.9 27.0 + - - +
325B SER 5.0 1.8 + - - -
617B TRP* 3.6 15.1 - - + -
624B VAL 4.9 4.5 - - - +
626B LEU* 3.7 19.3 - - + +
628B PHE* 3.7 20.4 - - - -
634B PRO 3.0 17.8 + - - +
635B MET* 3.3 9.2 + - - +
637B GLN* 1.3 77.0 - - - +
639B MET* 1.3 65.2 + - - +
641B VAL* 3.4 7.6 - - - +
642B PHE* 3.1 50.7 + - - +
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Residues in contact with MET 639 (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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65B ARG* 5.8 1.8 - - - +
107B MET* 3.8 27.8 - - + -
324B ASN* 5.8 2.7 - - - +
351B SER* 3.9 15.5 - - - +
628B PHE* 4.4 8.3 - - - -
631B MET* 3.6 19.5 - - + +
635B MET* 2.9 41.4 + - + +
636B GLN 4.1 2.5 - - - +
638B ASN* 1.3 77.4 - - - +
640B ALA* 1.3 61.5 + - - +
642B PHE* 3.6 3.2 + - - -
643B GLU* 3.3 22.5 + - - +
647B GLN* 5.1 10.5 + - - +
782B SER* 3.5 20.6 - - - +
783B ASN* 3.8 18.2 - - + +
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Residues in contact with ALA 640 (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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636B GLN 3.3 16.2 + - - +
637B GLN 3.2 5.3 + - - +
639B MET* 1.3 82.0 - - - +
641B VAL* 1.3 59.9 + - - +
643B GLU* 3.5 9.2 + - - +
644B PHE* 3.5 20.7 - - - -
761B HIS* 5.1 1.1 - - - +
763B ILE* 3.5 39.4 - - + +
765B PRO* 5.5 0.2 - - - -
783B ASN* 3.7 19.9 - - - +
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Residues in contact with VAL 641 (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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617B TRP* 3.9 20.9 - - + -
637B GLN* 2.9 40.9 + - + +
638B ASN 3.4 7.0 - - - +
640B ALA* 1.3 73.2 - - - +
642B PHE* 1.3 74.8 + - + +
643B GLU 3.2 3.7 + - - -
644B PHE* 3.4 23.1 + - - +
651B LEU* 3.6 22.1 - - + +
746B SER* 4.5 19.1 - - - +
763B ILE* 4.7 3.6 - - + -
765B PRO* 5.1 8.3 - - + -
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Residues in contact with PHE 642 (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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322B PHE* 3.6 25.1 - - + -
323B ILE 3.7 6.3 - - - -
324B ASN* 3.3 60.1 - - + +
325B SER 5.1 0.2 - - - -
351B SER 5.6 0.7 - - - +
617B TRP* 3.8 17.7 - + - -
638B ASN* 3.1 45.0 + - - +
639B MET* 3.9 3.6 - - - +
641B VAL* 1.3 82.2 - - + +
643B GLU* 1.3 63.7 + - - +
644B PHE 3.1 5.9 - - - +
647B GLN* 3.2 25.0 - - - +
648B SER 4.6 0.2 + - - -
649B GLY* 3.6 18.8 + - - -
651B LEU* 3.7 24.0 - - + -
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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