Contacts of the helix formed by residues 614 - 623 (chain A) in PDB entry 1TAQ
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 ILE 614 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611A TYR* 3.7 43.0 + - + +
612A SER 3.0 4.9 + - - +
613A GLN* 1.3 75.8 - - - +
615A GLU* 1.3 60.8 + - + +
617A ARG* 3.7 7.3 - - - +
618A VAL* 2.9 41.7 + - + +
757A ALA* 3.9 23.6 - - + +
760A LEU* 3.8 26.9 - - + -
785A ASP* 3.6 34.8 - - - +
817A LEU* 4.4 11.9 - - + -
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Residues in contact with GLU 615 (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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573A ARG* 4.8 5.2 - - - +
613A GLN* 3.1 1.6 + - - -
614A ILE* 1.3 81.0 - - + +
616A LEU* 1.3 58.1 + - + +
618A VAL* 3.5 5.2 + - - +
619A LEU* 2.9 27.8 + - - +
670A LEU* 3.8 29.9 - - + +
750A ASN* 5.4 0.5 - - - +
753A VAL* 3.6 25.0 - - + +
754A GLN* 3.1 37.1 + - + +
757A ALA* 4.4 16.2 - - + -
785A ASP* 5.1 7.1 - - - +
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Residues in contact with LEU 616 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613A GLN* 2.9 19.1 + - + +
615A GLU* 1.3 78.2 - - + +
617A ARG* 1.3 61.1 + - - +
618A VAL 3.0 1.6 - - - -
619A LEU* 3.2 24.0 + - + +
620A ALA* 2.9 30.5 + - - +
628A LEU* 4.8 7.5 - - + +
632A PHE* 3.5 16.9 - - + -
638A ILE* 4.0 28.9 - - + -
639A HIS* 4.5 5.8 - - - +
666A ASN* 3.5 40.8 - - + +
669A VAL* 5.0 1.1 - - + -
670A LEU* 4.0 11.4 - - + -
696A TYR* 5.2 2.2 - - - +
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Residues in contact with ARG 617 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A SER* 3.2 28.9 + - - -
613A GLN* 3.0 29.0 + - - +
614A ILE* 3.8 9.4 - - - +
616A LEU* 1.3 76.5 - - - +
618A VAL* 1.3 58.0 + - - +
620A ALA* 3.9 0.4 - - - +
621A HIS* 3.4 15.4 + - - +
632A PHE* 3.8 43.5 + - + -
635A GLY* 6.1 1.4 - - - -
813A LEU* 4.3 3.1 - - - +
815A VAL* 3.4 26.6 - - + +
816A PRO* 3.1 37.1 + - - +
817A LEU* 4.3 16.4 - - + +
818A GLU* 3.8 29.4 - - - +
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Residues in contact with VAL 618 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614A ILE* 2.9 29.2 + - + +
615A GLU* 3.6 4.7 - - - +
617A ARG* 1.3 78.4 - - - +
619A LEU* 1.3 60.1 + - - +
620A ALA 3.3 0.4 - - - -
621A HIS* 3.3 5.7 + - - +
622A LEU* 2.9 35.6 + - + +
753A VAL* 3.5 30.3 - - - +
756A THR* 3.7 34.5 - - + -
757A ALA* 4.4 4.5 - - - +
760A LEU* 3.7 20.0 - - + -
813A LEU* 4.5 5.6 - - + -
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Residues in contact with LEU 619 (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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615A GLU 2.9 17.2 + - - +
616A LEU* 3.2 18.4 + - + +
618A VAL* 1.3 74.7 - - - +
620A ALA* 1.3 52.9 + - - +
622A LEU* 4.7 3.1 - - - -
623A SER* 2.6 47.6 + - - -
628A LEU* 4.3 17.5 - - + -
669A VAL* 4.3 16.4 - - + -
670A LEU* 3.9 23.6 - - + -
696A TYR* 4.8 2.0 - - - +
703A VAL* 4.5 15.9 - - + -
706A TRP* 3.9 35.2 - - + -
707A ILE* 6.0 0.2 - - + -
753A VAL* 4.5 11.2 - - + -
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Residues in contact with ALA 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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616A LEU 2.9 16.2 + - - +
617A ARG 3.9 5.8 - - - +
619A LEU* 1.3 76.3 - - - +
621A HIS* 1.3 56.1 + - - +
623A SER* 3.3 6.2 + - - -
624A GLY* 2.8 28.4 + - - -
625A ASP 3.6 2.3 + - - -
628A LEU* 3.8 28.5 - - + +
629A ILE* 3.7 19.5 - - + +
632A PHE* 4.1 14.4 - - + -
815A VAL* 4.4 2.9 - - + -
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Residues in contact with HIS 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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617A ARG 3.4 12.7 + - - +
618A VAL* 3.3 9.8 + - - +
619A LEU 3.2 0.4 - - - -
620A ALA* 1.3 81.6 - - - +
622A LEU* 1.3 81.0 - - + +
624A GLY* 3.5 9.4 + - - -
723A LEU* 3.6 22.6 - - + +
811A TYR* 5.9 1.1 - + - -
812A PRO 4.5 3.8 - - - -
813A LEU* 3.5 27.5 - - + +
814A ALA* 3.0 43.3 + - + +
815A VAL* 5.3 0.4 - - + +
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Residues in contact with LEU 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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618A VAL* 2.9 26.2 + - + +
619A LEU* 4.1 2.7 - - - +
621A HIS* 1.3 91.9 - - + +
623A SER* 1.3 62.8 + - - +
706A TRP* 3.2 34.9 + - + +
722A THR 5.3 0.4 - - - -
723A LEU* 4.1 29.8 - - + +
752A PRO* 3.9 40.4 - - + +
753A VAL* 4.4 2.5 - - + +
756A THR* 4.1 5.2 - - + +
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Residues in contact with SER 623 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619A LEU* 2.6 31.5 + - - -
620A ALA* 3.3 5.7 + - - -
622A LEU* 1.3 75.4 - - - +
624A GLY* 1.3 60.9 + - - +
625A ASP* 3.2 17.7 + - - +
702A LYS* 3.8 24.4 - - - +
703A VAL* 3.9 15.0 - - - +
706A TRP* 3.8 29.4 - - - +
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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