Contacts of the helix formed by residues 621 - 632 (chain A) in PDB entry 6QVC
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 THR 621 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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619A SER* 3.4 12.0 + - - +
620A TYR* 1.3 76.2 - - - +
622A TYR* 1.3 66.6 + - + +
623A GLY 3.4 2.8 + - - -
624A GLU* 2.9 12.9 + - - +
625A LEU* 2.9 37.3 + - - +
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Residues in contact with TYR 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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621A THR* 1.3 86.6 - - + +
623A GLY* 1.3 58.4 + - - +
625A LEU* 3.3 11.3 + - + +
626A ARG* 3.0 37.6 + - - +
668A GLU* 6.2 0.2 - - - -
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Residues in contact with GLY 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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621A THR* 3.2 1.8 + - - -
622A TYR* 1.3 76.1 - - - +
624A GLU* 1.3 56.8 + - - +
626A ARG* 3.3 11.0 + - - +
627A THR* 2.7 37.8 + - - -
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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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615A PHE* 5.2 3.1 - - - +
620A TYR* 3.1 57.2 - - + +
621A THR* 2.9 13.9 + - - +
623A GLY* 1.3 76.8 - - - +
625A LEU* 1.3 56.9 + - - +
627A THR* 3.3 11.6 + - + +
628A LEU* 2.8 54.9 + - - +
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Residues in contact with LEU 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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616A VAL* 5.5 2.0 - - + -
617A SER 4.7 4.9 - - - +
618A ALA 5.8 0.2 - - - +
620A TYR* 3.9 23.6 - - + +
621A THR* 2.9 23.3 + - - +
622A TYR* 3.8 9.2 - - + +
623A GLY 3.2 0.4 - - - -
624A GLU* 1.3 77.9 - - - +
626A ARG* 1.3 60.6 + - + +
628A LEU* 3.3 24.1 + - + +
629A LEU* 3.0 31.0 + - - +
661A LEU* 4.4 28.4 - - + +
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Residues in contact with ARG 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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622A TYR* 3.0 24.8 + - - +
623A GLY* 3.7 8.5 - - - +
625A LEU* 1.3 76.5 - - + +
627A THR* 1.3 57.7 + - - +
629A LEU* 3.2 17.7 + - + +
630A GLN* 3.0 53.0 + - - +
661A LEU* 6.3 0.7 - - + -
665A LEU* 4.1 26.6 - - + +
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Residues in contact with THR 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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623A GLY 2.7 19.0 + - - -
624A GLU* 3.4 18.0 - - + +
626A ARG* 1.3 74.7 - - - +
628A LEU* 1.3 54.8 + - + +
630A GLN* 3.2 8.7 + - - +
631A THR* 2.6 54.3 + - + +
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Residues in contact with LEU 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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615A PHE* 4.1 17.0 - - + +
616A VAL* 3.9 36.3 - - + -
620A TYR* 4.8 0.4 - - + -
624A GLU* 2.8 49.5 + - - +
625A LEU* 3.3 20.4 + - + +
627A THR* 1.3 71.1 - - + +
629A LEU* 1.3 65.5 + - - +
631A THR* 3.7 5.4 - - - +
632A THR* 2.6 45.0 + - + +
637A LEU* 6.1 1.6 - - + -
654A ARG* 2.8 4.2 + - - +
657A LEU* 6.5 0.7 - - + -
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Residues in contact with LEU 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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625A LEU 3.0 18.0 + - - +
626A ARG* 3.4 19.1 - - + +
628A LEU* 1.3 77.6 - - - +
630A GLN* 1.3 64.3 + - + +
631A THR 3.5 0.2 + - - -
632A THR 3.7 2.4 - - - +
654A ARG* 2.5 28.2 + - + +
657A LEU* 5.8 1.8 - - + -
658A GLN* 3.8 34.5 - - + +
661A LEU* 3.7 35.4 - - + -
662A GLN* 5.5 11.2 - - + +
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Residues in contact with GLN 630 (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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626A ARG* 3.0 41.3 + - - +
627A THR* 4.0 7.3 + - - +
629A LEU* 1.3 80.4 - - + +
631A THR* 1.3 62.6 + - + +
632A THR 5.0 0.2 - - - -
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Residues in contact with THR 631 (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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627A THR* 2.6 44.5 + - + +
628A LEU* 3.7 7.8 - - - +
630A GLN* 1.3 79.1 - - + +
632A THR* 1.3 69.7 + - - +
633A THR* 5.2 3.1 - - - +
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Residues in contact with THR 632 (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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614A LYS* 5.5 11.4 - - + -
628A LEU* 2.6 23.7 + - + +
629A LEU 3.7 2.1 - - - +
630A GLN 5.0 0.2 - - - -
631A THR* 1.3 93.2 - - - +
633A THR* 1.3 67.3 + - - +
634A VAL* 5.0 6.1 - - - -
637A LEU* 5.7 2.6 - - - +
654A ARG* 2.2 53.1 + - - -
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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