Contacts of the helix formed by residues 605 - 613 (chain A) in PDB entry 1QU2
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 605 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A ASN* 6.2 2.9 - - + -
63A LEU 4.6 9.0 - - - +
64A HIS* 5.3 4.9 - - + -
65A MET* 4.1 4.5 - - - +
603A VAL* 4.0 15.9 - - + -
604A ILE* 1.3 78.6 - - - +
606A PRO* 1.3 79.1 - - + +
607A ASP* 3.3 24.9 - - + +
608A GLN* 3.0 26.5 + - + +
609A VAL* 3.2 13.3 + - - +
1993A MRC 6.3 0.9 - - + -
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Residues in contact with PRO 606 (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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63A LEU* 3.7 17.9 - - + +
64A HIS* 3.3 30.7 - - - +
65A MET* 3.4 33.3 - - + +
68A ALA* 4.1 16.4 - - + -
138A ASP* 6.5 0.9 - - + -
142A LEU* 4.9 10.5 - - + -
605A VAL* 1.3 91.9 - - + +
607A ASP* 1.3 62.8 + - - +
609A VAL* 3.0 4.8 + - + +
610A VAL* 3.0 29.0 + - + +
618A ALA* 6.4 0.2 - - + -
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Residues in contact with ASP 607 (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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138A ASP* 4.4 20.0 - - - +
605A VAL* 3.3 13.9 - - + +
606A PRO* 1.3 78.2 - - - +
608A GLN* 1.3 83.1 + - - +
610A VAL* 3.6 5.4 + - - +
611A LYS* 2.9 60.0 + - - +
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Residues in contact with GLN 608 (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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604A ILE* 5.9 1.8 - - + -
605A VAL* 3.0 23.7 + - + +
607A ASP* 1.3 103.2 + - - +
609A VAL* 1.3 65.2 + - + +
611A LYS* 4.6 8.8 - - - +
612A GLN* 2.7 69.9 + - - +
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Residues in contact with VAL 609 (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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65A MET* 4.5 8.3 - - + -
604A ILE* 4.1 14.4 - - + -
605A VAL 3.2 10.3 + - - +
606A PRO* 3.0 8.5 + - + +
608A GLN* 1.3 77.3 - - + +
610A VAL* 1.3 58.9 + - - +
612A GLN* 5.0 2.0 - - - -
613A LYS* 2.8 31.0 + - + +
614A GLY 2.9 8.6 + - - +
617A ILE* 4.8 7.6 - - + -
618A ALA* 3.6 39.0 - - + +
633A ILE* 4.5 7.0 - - + -
638A LEU* 3.8 31.4 - - + -
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Residues in contact with VAL 610 (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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21A PRO* 3.8 5.5 - - - +
141A ARG* 3.3 54.8 + - + +
142A LEU* 3.7 29.6 - - + -
606A PRO 3.0 16.5 + - - +
607A ASP* 3.9 5.8 - - - +
609A VAL* 1.3 78.1 - - + +
611A LYS* 1.3 66.6 + - + +
614A GLY* 2.9 30.1 + - - +
615A ALA* 4.3 11.9 - - - +
618A ALA* 5.0 2.2 - - + -
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Residues in contact with LYS 611 (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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21A PRO* 3.1 26.9 - - - +
137A LYS* 4.7 14.9 - - - +
141A ARG* 5.1 16.8 - - - +
607A ASP* 2.9 47.4 + - - +
608A GLN* 4.2 11.9 - - - +
610A VAL* 1.3 81.2 - - + +
612A GLN* 1.3 59.4 + - + +
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Residues in contact with GLN 612 (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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21A PRO* 4.1 5.2 - - - +
608A GLN* 2.7 62.8 + - - +
609A VAL* 5.0 0.7 - - - -
611A LYS* 1.3 79.8 - - + +
613A LYS* 1.3 73.2 + - + +
635A ASP* 5.8 0.2 - - - +
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Residues in contact with LYS 613 (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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20A LEU* 3.5 14.0 - - - +
21A PRO* 3.8 6.4 - - - +
609A VAL* 2.8 19.5 + - + +
610A VAL 3.8 0.4 - - - -
612A GLN* 1.3 88.5 - - + +
614A GLY* 1.3 57.5 + - - +
617A ILE* 3.0 41.0 - - + +
635A ASP 5.0 1.4 + - - -
638A LEU* 3.5 29.7 + - + +
639A LYS* 3.7 14.1 - - - +
642A SER* 2.8 29.1 + - - +
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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