Contacts of the helix formed by residues 619 - 629 (chain A) in PDB entry 3T9K
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 619 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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583A PRO* 3.6 30.6 - - - +
585A LEU* 5.0 0.5 - - - +
614A ALA 3.0 12.1 + - - -
617A ALA* 4.2 3.6 - - - -
618A ASN* 1.3 73.7 - - - +
620A LEU* 1.3 62.8 + - - +
621A LEU* 3.6 6.8 + - - +
622A ALA* 3.0 27.0 + - - +
623A CYS* 3.0 28.8 + - - -
655A LEU* 4.3 2.7 - - - +
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Residues in contact with LEU 620 (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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468A GLU* 4.0 29.8 - - + -
471A LYS* 6.1 3.1 - - + -
618A ASN 3.8 4.8 + - - -
619A SER* 1.3 72.4 - - - +
621A LEU* 1.3 65.8 + - + +
623A CYS* 3.5 1.6 + - - +
624A GLU* 2.9 31.8 + - - +
654A GLY* 4.6 10.8 - - - +
655A LEU* 3.5 25.8 - - + +
658A LEU* 4.0 21.5 - - + -
717A ARG* 6.1 2.5 - - - +
725A ASP* 5.4 8.9 + - - +
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Residues in contact with LEU 621 (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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468A GLU* 4.1 10.1 - - - +
471A LYS* 3.9 34.3 - - + +
472A LEU* 3.9 19.2 - - + +
475A GLU* 3.7 31.4 - - + -
585A LEU* 4.1 17.0 - - + -
619A SER* 3.2 6.4 + - - +
620A LEU* 1.3 86.6 - - + +
622A ALA* 1.3 60.2 + - - +
624A GLU* 3.3 4.9 + - - +
625A PHE* 2.9 28.9 + - - +
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Residues in contact with ALA 622 (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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579A SER 4.3 1.3 - - - +
583A PRO* 4.1 12.3 - - + -
585A LEU* 4.1 5.5 - - + +
588A MET* 3.8 26.5 - - + -
614A ALA* 3.8 19.5 - - + -
619A SER* 3.0 20.5 + - - +
621A LEU* 1.3 73.3 - - - +
623A CYS* 1.3 66.5 + - - +
625A PHE* 3.4 2.5 + - - +
626A LEU* 3.0 28.2 + - - +
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Residues in contact with CYS 623 (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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611A LEU* 3.8 23.3 - - + -
614A ALA* 3.7 26.9 - - - -
615A THR* 4.0 0.7 - - - -
619A SER 3.0 25.4 + - - +
620A LEU 3.8 4.0 - - - +
622A ALA* 1.3 76.4 - - - +
624A GLU* 1.3 58.1 + - - +
626A LEU* 3.3 1.9 + - - +
627A LEU* 2.8 37.0 + - + +
655A LEU* 4.0 10.8 - - + -
658A LEU* 3.8 17.9 - - + -
659A PHE* 3.9 16.8 - - + -
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Residues in contact with GLU 624 (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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466A GLU* 5.7 1.4 - - - +
468A GLU* 3.9 23.0 - - + +
469A LEU* 3.8 23.4 - - - +
472A LEU* 4.0 15.9 - - + -
620A LEU 2.9 19.4 + - - +
621A LEU* 3.7 5.8 - - - +
622A ALA 3.3 0.2 - - - -
623A CYS* 1.3 74.3 - - - +
625A PHE* 1.3 59.1 + - - +
627A LEU* 3.3 4.7 + - - +
628A GLN* 2.9 51.1 + - + +
658A LEU* 3.5 21.4 - - + +
662A ARG* 2.7 33.7 + - - -
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Residues in contact with PHE 625 (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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434A ASN 3.4 15.7 - - - -
435A LEU 4.6 2.0 - - - -
472A LEU* 3.7 16.3 - - + +
476A LEU* 3.5 28.7 - - + -
585A LEU* 3.6 25.1 - - + -
588A MET* 3.8 15.7 - - + -
589A ALA* 3.8 38.1 - - + -
592A LEU* 3.5 24.9 - - + -
621A LEU 2.9 16.3 + - - +
622A ALA 3.7 3.4 - - - +
623A CYS 3.3 0.2 - - - -
624A GLU* 1.3 76.5 - - - +
626A LEU* 1.3 61.3 + - - +
628A GLN* 3.4 2.5 + - + +
629A ASN* 3.0 48.8 + - - +
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Residues in contact with LEU 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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575A LEU* 4.3 10.3 - - + -
579A SER* 3.8 7.6 - - - +
588A MET* 3.6 17.0 - - + -
592A LEU* 5.0 3.1 - - + -
598A VAL* 4.0 23.8 - - + +
610A PRO* 3.4 51.1 - - + +
611A LEU* 3.5 13.2 - - + +
614A ALA* 4.0 7.9 - - + -
622A ALA 3.0 20.7 + - - +
623A CYS 3.6 3.4 - - - +
625A PHE* 1.3 75.4 - - - +
627A LEU* 1.3 63.7 + - - +
629A ASN* 3.0 11.1 + - - +
630A GLY 3.3 0.5 + - - -
631A ALA* 3.0 31.5 + - + +
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Residues in contact with LEU 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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456A LYS* 5.8 0.2 - - - -
611A LEU* 4.0 21.5 - - + -
623A CYS 2.8 24.9 + - - +
624A GLU* 3.8 4.3 - - - +
626A LEU* 1.3 71.3 - - - +
628A GLN* 1.3 62.4 + - - +
630A GLY* 3.3 12.5 + - - -
631A ALA 3.9 20.9 + - - +
633A VAL* 4.1 18.2 - - + -
658A LEU* 3.8 32.3 - - + -
659A PHE* 4.3 12.8 - - + -
662A ARG* 3.9 40.6 + - + +
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Residues in contact with GLN 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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433A ILE* 3.3 53.4 - - - +
434A ASN* 3.3 19.1 + - - +
456A LYS* 3.5 29.2 + - - +
469A LEU* 4.3 12.4 - - + +
472A LEU* 4.6 2.2 - - + -
624A GLU* 2.9 48.4 + - + +
625A PHE* 3.6 6.7 - - - +
626A LEU 3.3 0.2 - - - -
627A LEU* 1.3 75.5 - - - +
629A ASN* 1.3 58.3 + - - +
630A GLY 3.4 1.4 + - - -
662A ARG* 3.3 16.0 - - - +
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Residues in contact with ASN 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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434A ASN* 3.0 45.4 + - - +
435A LEU* 5.8 2.2 - - - +
592A LEU* 4.3 21.5 - - + +
598A VAL* 3.3 29.9 - - + +
625A PHE* 3.0 32.9 + - - +
626A LEU 3.0 9.7 + - - +
628A GLN* 1.3 80.1 - - - +
630A GLY* 1.3 53.7 + - - -
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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