Contacts of the helix formed by residues 625 - 637 (chain s) in PDB entry 6QX2
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 VAL 625 (chain s).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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619s GLU 5.4 3.0 - - - +
620s MET* 4.3 3.1 - - - +
623s GLY* 3.3 1.9 - - - +
624s ASP* 1.3 84.6 - - - +
626s VAL* 1.3 64.1 + - - +
627s GLU* 4.1 11.0 - - + +
628s ASN* 3.3 35.9 + - - +
629s ARG* 3.8 20.7 + - - +
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Residues in contact with VAL 626 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178r GLY 3.7 15.7 - - - +
624s ASP 3.4 8.9 + - - +
625s VAL* 1.3 72.5 - - - +
627s GLU* 1.3 61.0 + - - +
629s ARG* 3.3 24.1 + - - +
630s ARG* 2.9 25.2 + - + +
2017w G 3.7 44.9 - - + +
2018w C 3.6 21.5 - - - +
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Residues in contact with GLU 627 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625s VAL* 3.4 9.6 - - + +
626s VAL* 1.3 78.2 - - - +
628s ASN* 1.3 60.2 + - - +
630s ARG* 3.1 43.3 + - - -
631s GLN* 2.9 37.2 + - + +
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Residues in contact with ASN 628 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619s GLU* 6.4 0.2 - - - -
620s MET* 3.9 25.4 - - + +
625s VAL* 3.3 33.9 + - - +
626s VAL 3.4 0.2 - - - -
627s GLU* 1.3 78.1 - - - +
629s ARG* 1.3 57.7 + - - +
631s GLN* 3.5 7.0 + - - +
632s PHE* 3.0 28.4 + - - +
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Residues in contact with ARG 629 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22r PHE* 3.7 27.8 - - + -
177r VAL* 4.1 4.3 - - - -
178r GLY* 4.8 0.9 - - - -
466s LYS* 3.8 8.6 - - - +
620s MET* 3.5 23.6 + - - +
621s LEU* 2.8 42.3 + - + +
622s MET 4.0 1.4 - - - -
623s GLY 2.8 30.3 + - - +
624s ASP 4.1 2.4 + - - -
625s VAL 3.8 5.6 + - - +
626s VAL* 3.3 25.2 + - - +
628s ASN* 1.3 75.3 - - - +
630s ARG* 1.3 65.2 + - - +
632s PHE* 3.4 9.7 + - - +
633s ILE* 3.2 33.4 + - + +
2016w C 4.2 1.7 + - - -
2017w G 2.6 43.4 + - - +
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Residues in contact with ARG 630 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178r GLY* 3.1 38.4 - - - +
179r MET* 4.2 2.5 - - + -
626s VAL 2.9 14.7 + - - +
627s GLU* 3.1 38.1 + - - +
629s ARG* 1.3 72.5 - - - +
631s GLN* 1.3 79.8 + - - +
633s ILE* 3.2 7.1 + - - +
634s GLU* 3.0 49.3 + - - +
701s JK8 3.0 59.0 + - - +
2018w C 5.9 0.7 - - - -
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Residues in contact with GLN 631 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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627s GLU* 2.9 24.0 + - - +
628s ASN* 3.5 9.6 - - - +
630s ARG* 1.3 97.6 + - - +
632s PHE* 1.3 57.2 - - - +
634s GLU* 3.3 11.4 + - - +
635s ASP* 2.9 66.3 + - - +
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Residues in contact with PHE 632 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19r ARG* 3.7 56.8 - - + -
22r PHE* 4.8 7.4 - + - -
23r LEU* 4.4 14.4 - - + -
620s MET* 3.7 26.5 - - + -
621s LEU* 3.3 26.2 - - + -
628s ASN 3.0 15.1 + - - +
629s ARG* 3.4 11.9 - - - +
631s GLN* 1.3 76.3 - - - +
633s ILE* 1.3 63.4 + - + +
635s ASP* 4.5 4.5 - - - -
636s ASN* 2.9 67.8 + - + +
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Residues in contact with ILE 633 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22r PHE* 4.7 1.8 - - + -
23r LEU* 4.1 18.1 - - + +
26r ALA* 3.8 25.4 - - + -
27r MET* 4.5 9.0 - - + -
30r ILE* 4.0 11.4 - - + -
177r VAL* 3.9 30.7 - - + +
178r GLY* 4.3 0.2 - - - -
179r MET* 6.1 0.2 - - + -
629s ARG* 3.2 26.3 + - + +
630s ARG* 3.2 9.4 + - + +
632s PHE* 1.3 81.6 - - + +
634s GLU* 1.3 55.0 + - - +
636s ASN 3.3 1.7 + - - -
637s ALA* 2.8 34.8 + - - +
701s JK8 3.5 25.1 - - + +
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Residues in contact with GLU 634 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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630s ARG* 3.0 28.7 + - - +
631s GLN* 3.7 12.7 + - - +
633s ILE* 1.3 76.3 - - - +
635s ASP* 1.3 66.9 + - - +
637s ALA* 3.4 12.1 + - - +
701s JK8 2.8 80.0 + - + +
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Residues in contact with ASP 635 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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631s GLN* 2.9 52.7 + - - +
632s PHE* 3.7 3.0 + - - +
634s GLU* 1.3 79.0 - - - +
636s ASN* 1.3 72.6 + - - +
637s ALA 3.8 1.9 + - - +
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Residues in contact with ASN 636 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19r ARG* 3.4 26.7 + - - +
23r LEU* 3.2 34.2 - - + +
632s PHE* 2.9 48.6 + - + +
633s ILE 3.5 1.3 - - - -
635s ASP* 1.3 86.4 - - - +
637s ALA* 1.3 64.8 + - - +
638s VAL* 3.3 8.9 + - - +
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Residues in contact with ALA 637 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27r MET* 3.9 11.7 - - + -
633s ILE 2.8 16.6 + - - +
634s GLU 3.4 9.8 + - - +
635s ASP 3.5 2.1 - - - +
636s ASN* 1.3 75.8 - - - +
638s VAL* 1.3 66.5 + - - +
701s JK8 3.5 52.2 - - + -
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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