Contacts of the helix formed by residues 627 - 638 (chain B) in PDB entry 5AIM
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 627 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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624B PRO 4.8 2.6 + - - -
625B THR 3.3 4.1 - - - -
626B VAL* 1.3 83.8 - - - +
628B GLU* 1.3 66.3 + - - -
629B ASP* 3.3 2.7 - - - -
630B ALA 3.3 4.0 + - - -
631B ILE* 3.3 25.2 + - - +
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Residues in contact with GLU 628 (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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611B ARG* 2.8 33.2 + - - -
627B GLY* 1.3 71.6 - - - -
629B ASP* 1.3 64.5 + - - +
631B ILE* 3.2 8.6 + - - +
632B GLN* 2.6 63.9 + - + +
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Residues in contact with ASP 629 (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 3.3 1.0 - - - -
628B GLU* 1.3 77.9 - - - +
630B ALA* 1.3 57.8 + - - +
632B GLN* 3.3 5.4 + - - +
633B ARG* 2.8 69.8 + - - +
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Residues in contact with ALA 630 (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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567B GLY 5.4 1.8 - - - +
569B VAL* 4.1 5.2 - - + +
626B VAL* 3.7 33.0 + - + +
627B GLY 3.3 9.0 + - - +
628B GLU 3.3 0.4 - - - -
629B ASP* 1.3 76.2 + - - +
631B ILE* 1.3 66.2 + - - +
633B ARG* 3.6 26.4 + - - +
634B TYR* 2.9 24.8 + - - +
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Residues in contact with ILE 631 (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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569B VAL* 4.1 11.4 - - + -
611B ARG* 4.0 21.5 - - - +
620B ILE* 4.3 13.9 - - + -
622B PHE* 3.7 42.0 - - + -
626B VAL* 3.7 15.3 - - + -
627B GLY 3.3 16.4 + - - +
628B GLU* 3.2 22.8 + - - +
630B ALA* 1.3 75.7 - - - +
632B GLN* 1.3 60.3 + - - +
634B TYR* 3.2 4.7 + - - +
635B ILE* 2.9 48.7 + - + +
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Residues in contact with GLN 632 (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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611B ARG* 3.9 9.3 - - - +
628B GLU* 2.6 53.1 + - + +
629B ASP* 3.8 4.9 - - - +
631B ILE* 1.3 73.7 - - - +
633B ARG* 1.3 60.8 + - + +
635B ILE* 3.2 22.7 + - - +
636B LEU* 2.9 37.4 + - + +
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Residues in contact with ARG 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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629B ASP* 2.8 43.1 + - - +
630B ALA* 3.6 27.9 + - - +
632B GLN* 1.3 74.6 - - + +
634B TYR* 1.3 59.0 + - - +
636B LEU* 3.3 9.2 + - + +
637B LYS* 2.9 31.7 + - - +
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Residues in contact with TYR 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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566B ILE 5.9 2.2 - - - -
569B VAL* 3.4 40.2 - - + -
570B ALA* 3.5 11.2 - - - +
571B TYR* 3.1 46.8 + + - -
573B ARG* 3.5 18.9 + - - -
620B ILE* 3.7 10.5 - - + -
630B ALA 2.9 14.4 + - - +
631B ILE 3.4 7.0 - - - +
633B ARG* 1.3 76.7 - - - +
635B ILE* 1.3 65.6 + - - +
637B LYS* 3.2 27.4 + - - +
638B GLU* 3.0 39.7 + - + +
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Residues in contact with ILE 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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571B TYR* 3.7 20.7 + - - +
611B ARG* 5.5 3.8 - - - +
613B GLU* 3.7 32.1 - - + +
615B VAL* 5.9 1.8 - - + -
620B ILE* 3.7 21.8 - - + -
631B ILE* 2.9 34.2 + - + +
632B GLN* 3.2 29.6 + - - +
634B TYR* 1.3 75.2 - - - +
636B LEU* 1.3 66.3 + - + +
638B GLU* 3.3 3.3 + - - +
639B LYS* 3.2 23.0 + - + +
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Residues in contact with LEU 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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632B GLN* 2.9 23.6 + - + +
633B ARG* 3.8 8.7 - - + +
635B ILE* 1.3 79.6 - - + +
637B LYS* 1.3 62.5 + - - +
638B GLU 3.2 0.7 + - - -
639B LYS* 3.2 48.3 + - + +
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Residues in contact with LYS 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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575A GLN* 4.8 20.9 - - - +
637A LYS* 6.1 0.2 - - - -
638A GLU* 5.5 11.4 + - - +
633B ARG 2.9 17.1 + - - +
634B TYR* 3.6 26.5 - - - +
636B LEU* 1.3 76.5 - - - +
638B GLU* 1.3 89.4 + - - +
639B LYS* 3.4 2.3 + - - +
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Residues in contact with GLU 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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637A LYS* 3.3 29.4 + - - +
638A GLU* 5.5 1.2 - - - +
571B TYR* 3.8 18.8 - - + -
573B ARG* 2.9 25.6 + - - +
575B GLN* 5.5 1.1 + - - -
618B ARG* 3.2 21.3 + - - +
634B TYR* 3.0 44.7 + - + +
635B ILE 3.6 2.2 - - - +
636B LEU 3.2 0.2 - - - -
637B LYS* 1.3 102.7 + - - +
639B LYS* 1.3 66.3 + - - +
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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