Contacts of the helix formed by residues 610 - 623 (chain U) 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 ASP 610 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13T ASN* 4.8 2.0 - - - +
15T THR* 4.8 1.2 + - - -
608U LEU* 3.9 3.2 - - - +
609U GLU* 1.3 78.3 - - + +
611U ALA* 1.3 57.5 + - - +
612U ILE* 3.1 23.4 + - - +
613U GLU* 3.4 32.2 + - + +
614U ALA* 3.0 27.5 + - - +
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Residues in contact with ALA 611 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525U TYR* 3.1 14.2 + - - +
529U ARG* 4.4 12.8 - - - +
608U LEU* 4.0 16.1 - - + +
609U GLU 4.0 3.6 + - - -
610U ASP* 1.3 70.0 + - - +
612U ILE* 1.3 58.3 + - + +
615U ASP* 2.9 39.0 + - - +
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Residues in contact with ILE 612 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610U ASP* 3.1 10.9 + - - +
611U ALA* 1.3 77.9 - - + +
613U GLU* 1.3 61.4 + - - +
615U ASP* 3.3 13.4 + - - +
616U GLN* 3.2 23.6 + - + +
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Residues in contact with GLU 613 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13T ASN* 4.8 4.2 + - - +
15T THR* 3.0 33.0 - - - +
19T ARG* 4.8 6.4 + - - -
610U ASP* 3.4 32.0 + - - +
612U ILE* 1.3 78.0 - - - +
614U ALA* 1.3 59.7 + - - +
616U GLN* 3.4 11.5 - - + +
617U THR* 3.0 35.2 + - - +
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Residues in contact with ALA 614 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14T ILE* 4.4 5.2 - - + -
15T THR* 3.2 18.8 + - - +
525U TYR* 3.4 29.6 - - + +
608U LEU* 3.8 11.0 - - + -
610U ASP 3.0 18.2 + - - +
611U ALA 3.6 0.7 - - - +
612U ILE 3.3 0.2 - - - -
613U GLU* 1.3 73.4 - - - +
615U ASP* 1.3 63.9 + - - +
617U THR* 3.1 1.7 + - - -
618U PHE* 3.0 33.8 + - + -
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Residues in contact with ASP 615 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525U TYR* 3.0 13.5 + - - -
526U ARG* 3.1 35.9 + - - +
529U ARG* 3.2 13.5 + - - -
611U ALA* 2.9 25.5 + - - +
612U ILE* 3.3 16.4 + - - +
614U ALA* 1.3 74.1 - - - +
616U GLN* 1.3 61.1 + - - +
619U GLU* 3.3 24.8 + - - +
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Residues in contact with GLN 616 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19T ARG* 5.1 4.8 - - - +
612U ILE* 3.2 10.9 + - + +
613U GLU* 3.4 19.7 - - + +
614U ALA 3.2 0.2 - - - -
615U ASP* 1.3 76.9 - - - +
617U THR* 1.3 68.4 + - - +
619U GLU* 3.5 8.7 + - - +
620U MET* 2.9 56.8 + - - +
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Residues in contact with THR 617 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15T THR* 3.6 27.1 - - + +
18T MET* 4.1 9.4 - - + -
19T ARG* 3.4 35.8 + - + -
613U GLU* 3.0 20.2 + - - +
614U ALA 3.1 4.2 + - - -
616U GLN* 1.3 86.0 + - - +
618U PHE* 1.3 62.0 + - + +
620U MET* 3.4 4.6 + - + +
621U LEU* 3.0 46.6 + - + +
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Residues in contact with PHE 618 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14T ILE* 4.0 17.0 - - + -
15T THR* 5.5 0.9 - - - -
18T MET* 3.3 40.8 - - + -
465U GLU* 3.8 6.4 - - - +
521U LEU 3.7 4.0 - - - -
522U THR* 3.2 47.3 - - + -
525U TYR* 3.6 43.5 - + + -
526U ARG* 3.8 18.8 - - - +
614U ALA* 3.0 33.3 + - + +
617U THR* 1.3 73.1 - - + +
619U GLU* 1.3 58.7 + - - +
621U LEU* 5.0 0.2 - - - -
622U MET* 2.8 40.3 + - + +
623U GLY 3.5 0.3 + - - -
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Residues in contact with GLU 619 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465U GLU* 3.3 17.4 + - - +
526U ARG* 4.5 1.7 + - - +
615U ASP* 3.3 19.4 + - - +
616U GLN* 3.8 7.6 - - - +
618U PHE* 1.3 78.6 - - - +
620U MET* 1.3 57.4 + - - +
623U GLY* 3.1 27.3 + - - -
625U VAL* 5.3 7.8 + - + +
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Residues in contact with MET 620 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19T ARG* 3.7 17.5 - - + +
616U GLN* 2.9 39.9 + - - +
617U THR* 3.7 6.5 - - - +
618U PHE 3.2 0.2 - - - -
619U GLU* 1.3 76.9 - - - +
621U LEU* 1.3 88.7 + - + +
625U VAL 4.4 3.3 - - - +
628U ASN* 3.9 33.4 - - + +
629U ARG* 3.5 27.2 + - - +
632U PHE* 3.7 31.9 - - + -
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Residues in contact with LEU 621 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18T MET* 3.5 40.2 - - + +
19T ARG* 3.8 8.1 - - - +
22T PHE* 3.3 41.1 - - + -
617U THR* 3.0 27.9 + - + +
620U MET* 1.3 89.2 - - + +
622U MET* 1.3 70.3 + - + +
629U ARG* 2.8 22.2 + - + +
632U PHE* 3.3 38.6 - - + -
2016V C 5.0 0.7 + - - -
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Residues in contact with MET 622 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18T MET* 4.0 14.4 - - + -
22T PHE* 3.5 27.6 - - + -
463U ASN* 3.1 33.8 + - - +
465U GLU* 3.2 25.2 - - + +
466U LYS* 3.4 9.3 - - - +
515U HIS* 5.0 0.2 - - - +
518U THR* 3.7 18.2 - - - +
519U LEU* 3.7 27.4 - - + -
522U THR* 3.2 29.6 - - + +
618U PHE* 2.8 20.8 + - + +
621U LEU* 1.3 75.6 - - + +
623U GLY* 1.3 61.5 + - - +
629U ARG* 4.0 1.1 - - - +
2016V C 4.1 6.3 - - - +
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Residues in contact with GLY 623 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465U GLU* 3.7 14.4 - - - -
466U LYS* 3.4 6.3 - - - -
618U PHE 3.5 1.4 + - - -
619U GLU* 3.1 26.4 + - - -
621U LEU 3.6 1.0 - - - -
622U MET* 1.3 79.1 - - - +
624U ASP* 1.3 59.8 + - - -
625U VAL 3.3 3.4 - - - -
629U ARG* 2.8 27.4 + - - +
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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