Contacts of the helix formed by residues 609 - 621 (chain B) in PDB entry 1CQT
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 GLU 609 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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607B SER* 4.0 18.1 - - - +
608B ILE* 1.3 80.8 - - - +
610B THR* 1.3 63.1 + - - +
611B ASN* 3.2 24.1 - - - +
612B ILE* 2.7 28.7 + - + +
613B ARG* 2.9 13.5 + - - +
640B MET* 5.0 6.4 - - + +
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Residues in contact with THR 610 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608B ILE 4.2 0.6 + - - -
609B GLU* 1.3 75.4 + - - +
611B ASN* 1.3 66.0 + - - +
613B ARG* 3.3 21.7 - - - +
614B VAL* 3.2 25.9 - - + +
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Residues in contact with ASN 611 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609B GLU* 3.8 18.7 - - - +
610B THR* 1.3 79.7 + - - +
612B ILE* 1.3 74.7 + - - +
614B VAL* 3.0 22.9 - - - +
615B ALA* 3.5 10.4 - - - +
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Residues in contact with ILE 612 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608B ILE* 3.6 15.3 - - + -
609B GLU* 2.7 24.5 + - + +
611B ASN* 1.3 82.3 - - - +
613B ARG* 1.3 58.5 + - - +
615B ALA* 3.2 6.4 + - - +
616B LEU* 2.9 31.2 + - + +
638B LEU* 3.8 23.1 - - + +
640B MET* 5.0 11.7 - - + -
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Residues in contact with ARG 613 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608B ILE* 3.5 26.3 + - + +
609B GLU 2.9 8.1 + - - +
610B THR* 3.3 26.5 - - - +
612B ILE* 1.3 73.1 - - - +
614B VAL* 1.3 65.5 + - + +
616B LEU* 3.0 10.5 + - + +
617B GLU* 2.7 48.3 + - - +
648B TRP* 4.6 6.9 - - - +
652B ARG* 2.7 20.4 - - - +
707O C 5.3 0.4 + - - -
708O A 2.7 34.4 + - - -
709O A 4.4 11.4 + - - -
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Residues in contact with VAL 614 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610B THR 3.2 16.2 - - - +
611B ASN* 3.0 22.2 - - - +
613B ARG* 1.3 79.5 - - + +
615B ALA* 1.3 79.2 + - - +
617B GLU* 3.3 9.2 + - - +
618B LYS* 3.1 22.5 + - - +
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Residues in contact with ALA 615 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611B ASN 3.5 11.7 - - - +
612B ILE* 3.2 13.4 + - - +
614B VAL* 1.3 81.6 - - + +
616B LEU* 1.3 62.3 + - - +
618B LYS* 3.2 20.8 - - - +
619B SER* 3.5 8.3 + - - -
638B LEU* 4.7 17.7 - - + -
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Residues in contact with LEU 616 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608B ILE* 4.5 15.5 - - + -
612B ILE 2.9 19.3 + - - +
613B ARG* 3.0 13.6 + - - +
615B ALA* 1.3 74.8 - - - +
617B GLU* 1.3 60.4 + - - +
619B SER* 2.6 26.9 + - - +
620B PHE* 2.8 16.6 + - - +
634B ILE* 4.4 18.6 - - + -
638B LEU* 4.5 13.7 - - + -
645B ILE* 4.6 20.2 - - + +
648B TRP* 3.5 54.8 - - + +
649B PHE* 6.3 1.1 - - + -
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Residues in contact with GLU 617 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A GLN* 5.9 6.3 - - + +
613B ARG* 2.7 38.2 + - - +
614B VAL* 3.6 12.4 + - - +
616B LEU* 1.3 70.7 - - - +
618B LYS* 1.3 64.8 + - - +
620B PHE* 3.0 9.1 + - + +
621B LEU* 2.9 44.9 + - + +
648B TRP* 3.1 27.5 - - - -
652B ARG* 3.8 19.2 + - - +
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Residues in contact with LYS 618 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614B VAL 3.1 11.3 + - - +
615B ALA* 3.2 14.6 - - - +
617B GLU* 1.3 78.5 - - - +
619B SER* 1.3 57.5 + - - +
621B LEU* 3.7 2.6 + - - +
622B GLU* 3.1 26.5 + - - +
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Residues in contact with SER 619 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615B ALA 3.5 4.3 + - - -
616B LEU* 2.6 35.5 + - - +
618B LYS* 1.3 76.6 - - - +
620B PHE* 1.3 59.8 + - - +
622B GLU* 2.9 35.8 + - - +
623B ASN* 3.0 14.6 - - - +
634B ILE* 4.6 25.2 - - - +
648B TRP* 5.2 1.4 - - - -
649B PHE* 4.8 7.3 - - - -
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Residues in contact with PHE 620 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616B LEU 2.8 20.0 + - - +
617B GLU* 3.4 10.8 - - + +
619B SER* 1.3 69.6 + - - +
621B LEU* 1.3 76.0 + - + +
622B GLU 2.9 3.8 - - - -
623B ASN 2.8 30.0 + - - +
624B GLN* 3.4 45.0 + - + +
648B TRP* 3.5 29.2 - + + -
649B PHE* 4.1 13.0 - + - -
652B ARG* 3.4 44.6 - - + -
653B ARG* 3.8 7.0 - - - -
656B GLU* 4.2 17.5 - - + -
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Residues in contact with LEU 621 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ASN* 3.3 22.7 - - - +
115A ALA* 5.0 15.5 - - + -
137A GLN* 3.9 28.3 - - - +
138A LEU* 3.9 21.0 - - + +
617B GLU* 2.9 32.3 + - + +
618B LYS* 3.9 2.5 - - - +
620B PHE* 1.3 92.1 - - + +
622B GLU* 1.3 62.1 + - - +
623B ASN* 4.5 0.4 - - - -
624B GLN* 4.8 4.5 - - - +
656B GLU* 4.7 10.5 - - - +
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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