Contacts of the helix formed by residues 625 - 636 (chain A) in PDB entry 1QXP
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 SER 625 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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624A MET* 1.3 71.0 - - - +
626A ALA* 1.3 69.7 + - - +
627A TYR* 4.1 19.7 + - - -
628A GLU* 3.0 22.8 + - - +
629A MET 3.6 2.8 + - - -
656A GLU 5.2 0.5 + - - -
657A LEU* 3.2 14.4 + - - +
658A ILE* 4.3 8.4 - - - +
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Residues in contact with ALA 626 (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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368A GLY* 3.1 23.9 - - - +
624A MET 3.2 5.7 + - - -
625A SER* 1.3 68.7 - - - +
627A TYR* 1.3 52.5 + - - +
628A GLU 2.5 2.1 + - - -
629A MET* 2.5 35.3 + - - +
630A ARG 4.2 1.0 + - - -
649A VAL* 3.7 23.3 - - + +
653A ALA* 4.3 5.8 - - + -
657A LEU* 2.6 26.1 + - + +
658A ILE* 4.0 0.6 - - - +
659A ILE* 4.2 12.5 - - + +
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Residues in contact with TYR 627 (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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368A GLY* 2.8 41.3 + - - -
369A SER* 3.5 12.1 - - - +
371A ALA* 3.1 33.9 + - - +
379A ALA 6.0 0.7 - - - +
380A THR* 4.2 24.2 - - + -
382A TRP* 3.9 21.4 - - + +
383A VAL* 4.0 23.4 - - + +
492A PRO* 5.4 0.4 - - + -
493A ASN* 2.2 39.4 + - - -
625A SER* 3.1 18.1 + - - -
626A ALA* 1.3 71.2 - - + +
628A GLU* 1.3 58.7 + - + +
630A ARG* 4.5 5.9 + - - +
657A LEU* 5.1 7.0 - - + -
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Residues in contact with GLU 628 (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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382A TRP* 4.7 3.6 - - - -
451A ARG* 5.0 7.7 + - - -
616A PHE* 3.4 30.6 - - + +
624A MET* 4.3 3.6 - - + -
625A SER* 3.6 17.5 - - - +
626A ALA 2.5 6.9 + - - -
627A TYR* 1.3 78.7 - - + +
629A MET* 1.4 67.9 - - - +
630A ARG 2.7 2.7 - - - +
631A MET* 2.5 44.8 + - - +
632A ALA* 3.0 11.1 + - - +
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Residues in contact with MET 629 (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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624A MET* 3.1 32.4 - - + +
625A SER 3.6 2.4 + - - -
626A ALA* 2.5 26.2 + - - +
628A GLU* 1.4 74.9 - - - +
630A ARG* 1.3 62.8 + - - +
631A MET 2.6 1.7 + - - -
632A ALA* 3.1 0.5 + - - +
633A ILE* 2.7 59.5 + - + +
648A ILE* 4.0 9.4 - - + -
649A VAL* 4.9 9.9 - - + -
652A PHE* 5.6 0.9 - - + -
659A ILE* 3.1 34.3 - - + -
664A PHE* 3.5 29.4 - - + +
667A CYS* 3.4 28.5 - - + -
668A LEU* 4.9 1.1 - - + -
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Residues in contact with ARG 630 (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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369A SER 4.6 7.8 + - - +
370A THR* 5.1 0.8 - - - +
382A TRP* 3.7 27.8 - - + -
383A VAL* 4.3 16.3 + - - +
448A HIS* 2.7 50.8 + - - +
450A LYS* 3.5 15.8 + - - +
514A ASP* 3.1 15.0 + - - -
515A ASP* 5.0 2.0 - - - +
626A ALA 4.2 1.2 + - - -
627A TYR 4.6 6.3 - - - +
628A GLU 2.7 1.6 - - - -
629A MET* 1.3 82.0 - - - +
631A MET* 1.4 61.4 + - - +
633A ILE* 3.3 10.4 + - - +
634A GLU* 3.7 11.3 + - - +
640A LEU 4.6 1.0 + - - -
642A CYS* 3.2 30.3 - - - +
645A HIS* 3.3 54.1 + - + +
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Residues in contact with MET 631 (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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382A TRP* 3.6 17.5 - - + -
450A LYS* 3.1 38.6 - - + +
451A ARG* 4.6 20.0 - - - +
616A PHE* 4.2 16.2 - - + -
628A GLU* 2.5 46.2 + - - +
630A ARG* 1.4 75.8 - - - +
632A ALA* 1.4 67.5 + - - +
633A ILE 3.0 0.7 - - - -
634A GLU* 2.7 19.1 + - + +
635A ALA* 2.9 11.4 + - - +
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Residues in contact with ALA 632 (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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612A ILE* 4.5 3.1 - - + +
616A PHE* 3.6 25.8 - - + -
624A MET* 3.8 27.8 - - + -
628A GLU 3.0 5.8 + - - +
629A MET* 3.3 8.1 - - - +
631A MET* 1.4 73.6 - - - +
633A ILE* 1.3 65.2 + - - +
634A GLU 2.8 1.0 + - - -
635A ALA* 3.1 13.8 + - - +
636A ALA* 3.1 12.8 + - - +
664A PHE* 4.0 20.6 - - + -
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Residues in contact with ILE 633 (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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629A MET* 2.7 54.5 + - + +
630A ARG 3.3 5.6 + - - +
631A MET 2.8 1.4 + - - -
632A ALA* 1.3 73.6 - - + +
634A GLU* 1.3 54.7 - - - +
636A ALA* 3.1 18.7 - - - +
638A PHE* 2.8 53.9 + - + +
640A LEU* 5.2 7.0 - - + -
645A HIS* 4.4 16.2 - - + +
648A ILE* 3.0 38.1 - - + -
667A CYS* 4.5 1.6 - - - -
668A LEU* 4.3 11.2 - - + -
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Residues in contact with GLU 634 (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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450A LYS* 3.2 38.6 + - - +
630A ARG 3.8 9.4 - - - +
631A MET* 2.7 10.6 + - - +
633A ILE* 1.3 81.7 - - - +
635A ALA* 1.3 50.5 + - - +
636A ALA 3.3 1.6 - - - -
637A GLY* 2.9 21.1 + - - -
638A PHE 3.1 17.2 + - - +
639A LYS* 3.4 36.8 - - + +
645A HIS* 6.3 0.4 - - + -
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Residues in contact with ALA 635 (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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612A ILE* 3.5 34.8 - - + +
615A LYS* 6.6 0.2 - - + -
616A PHE* 4.8 6.3 - - + -
631A MET 2.9 8.0 + - - +
632A ALA* 3.2 14.1 - - - +
634A GLU* 1.3 70.8 - - - +
636A ALA* 1.3 61.9 + - - +
637A GLY 3.2 1.3 + - - -
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Residues in contact with ALA 636 (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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521A LEU* 6.0 2.3 - - - +
609A TYR* 4.9 14.4 - - + -
612A ILE* 4.0 11.9 - - + -
632A ALA 3.1 6.4 + - - +
633A ILE 3.1 13.2 - - - +
635A ALA* 1.3 81.0 - - - +
637A GLY* 1.3 57.5 + - - +
638A PHE* 4.7 6.4 - - + +
668A LEU* 4.2 26.2 - - + -
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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