Contacts of the helix formed by residues 629 - 637 (chain E) in PDB entry 1XMI
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 THR 629 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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613E ALA 5.9 0.7 - - - -
614E ASP 3.9 20.6 - - - +
615E LYS* 4.5 10.3 - - - +
616E ILE* 4.3 2.2 - - - +
626E PHE* 3.3 11.9 - - - -
628E GLY* 1.3 75.6 - - - -
630E PHE* 1.3 65.7 + - - +
631E SER* 3.8 9.5 + - - -
632E GLU* 3.1 38.5 + - - +
633E LEU 3.2 15.8 + - - -
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Residues in contact with PHE 630 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607E MET* 3.7 29.4 - - + -
610E LEU* 3.6 39.2 + - + +
611E LYS* 3.5 48.5 - - + +
613E ALA 5.6 2.4 + - - +
616E ILE* 4.5 8.6 - - + +
629E THR* 1.3 71.0 - - - +
631E SER* 1.3 64.8 + - - +
633E LEU* 3.2 21.2 + - + +
634E GLN* 2.9 65.1 + - + +
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Residues in contact with SER 631 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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629E THR* 3.3 8.6 + - - -
630E PHE* 1.3 87.0 - - - +
632E GLU* 1.3 62.6 + - - +
634E GLN* 3.2 8.2 + - - +
635E ASN* 3.1 31.8 + - - -
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Residues in contact with GLU 632 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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626E PHE* 3.8 12.4 - - + -
627E TYR 4.9 0.5 - - - +
628E GLY* 3.6 8.8 - - - -
629E THR* 3.1 43.4 + - - +
631E SER* 1.3 77.3 - - - +
633E LEU* 1.3 57.8 + - - +
635E ASN* 3.4 8.9 + - - +
636E LEU* 3.0 35.8 + - + +
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Residues in contact with LEU 633 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610E LEU* 4.5 9.4 - - + -
616E ILE* 3.6 20.0 - - + -
618E ILE* 4.5 3.6 - - + -
625E TYR* 5.3 2.2 - - + -
626E PHE* 3.5 46.9 - - + -
629E THR 3.2 4.4 + - - +
630E PHE* 3.2 21.6 + - + +
632E GLU* 1.3 75.7 - - - +
634E GLN* 1.3 61.5 + - + +
636E LEU* 3.7 2.8 - - + +
637E GLN* 2.8 46.8 + - + +
645E MET* 3.8 30.5 - - + -
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Residues in contact with GLN 634 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607E MET* 4.9 9.7 - - + +
611E LYS* 5.7 1.6 - - - +
630E PHE* 2.9 51.5 + - + +
631E SER* 3.2 12.2 + - - +
633E LEU* 1.3 75.4 - - + +
635E ASN* 1.3 67.9 + - - +
637E GLN 3.5 9.8 + - - +
638E PRO* 3.6 19.9 - - + +
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Residues in contact with ASN 635 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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631E SER* 3.1 22.9 + - - +
632E GLU* 3.4 12.5 - - - +
634E GLN* 1.3 79.3 - - - +
636E LEU* 1.3 61.1 + - + +
637E GLN 3.5 0.3 + - - -
638E PRO* 4.1 6.4 - - - +
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Residues in contact with LEU 636 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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626E PHE* 3.9 24.2 - - + -
632E GLU* 3.0 22.6 + - + +
633E LEU* 4.0 4.7 - - + +
635E ASN* 1.3 81.4 - - + +
637E GLN* 1.3 64.2 + - + +
638E PRO* 3.9 4.5 - - - +
639E ASP* 5.1 0.3 - - - +
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Residues in contact with GLN 637 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625E TYR* 2.4 38.2 + - - -
633E LEU* 2.8 30.8 + - + +
634E GLN* 3.6 7.6 - - - +
635E ASN 3.3 0.6 - - - -
636E LEU* 1.3 83.4 - - + +
638E PRO* 1.3 66.6 - - - +
639E ASP* 3.2 46.1 + - - +
640E PHE* 5.2 1.5 - - - +
641E SER* 5.0 2.8 - - - +
644E LEU* 3.5 23.4 - - - +
645E MET* 5.0 5.5 - - - +
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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