Contacts of the helix formed by residues 621 - 630 (chain A) in PDB entry 3M6L
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 621 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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539A LEU* 3.4 9.9 - - - +
616A GLU* 3.5 25.0 + - - -
619A GLY 3.0 5.1 + - - -
620A PHE* 1.3 73.8 - - - +
622A VAL* 1.3 65.6 + - - +
623A SER* 3.8 5.1 + - - -
624A LYS* 3.2 30.8 + - - +
625A LEU* 3.0 22.5 + - - +
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Residues in contact with VAL 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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539A LEU* 3.5 9.1 - - + +
542A GLU* 3.4 33.7 - - + +
543A SER* 3.6 18.8 - - - +
546A GLU* 4.0 21.3 - - + -
621A SER* 1.3 74.2 - - - +
623A SER* 1.3 66.8 + - - +
625A LEU* 4.0 0.2 - - - +
626A VAL* 3.0 44.4 + - + +
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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
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621A SER* 3.3 5.8 + - - -
622A VAL* 1.3 80.0 - - - +
624A LYS* 1.3 66.5 + - - +
626A VAL* 4.0 4.0 - - - +
627A ASN* 3.1 35.2 + - - +
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Residues in contact with LYS 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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600A TYR* 3.6 8.1 + - - +
616A GLU* 3.0 43.9 + - - +
617A ARG* 4.9 3.6 + - - +
619A GLY* 3.6 28.8 - - - +
621A SER* 3.2 18.0 + - - +
623A SER* 1.3 80.1 - - - +
625A LEU* 1.3 64.1 + - - +
627A ASN* 3.5 8.8 + - - +
628A PHE* 3.0 22.9 + - - +
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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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530A LEU* 4.4 0.9 - - + -
539A LEU* 4.0 22.7 - - + -
540A CYS* 4.4 7.0 - - - -
543A SER* 3.5 26.2 - - - +
582A ILE* 4.6 0.7 - - + -
584A VAL* 4.0 24.7 - - + -
600A TYR* 3.9 41.0 + - + -
621A SER 3.0 16.3 + - - +
624A LYS* 1.3 74.8 - - - +
626A VAL* 1.3 67.0 + - - +
628A PHE* 3.2 5.3 + - + +
629A ILE* 2.9 48.9 + - + +
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Residues in contact with VAL 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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543A SER* 3.9 29.2 - - - +
546A GLU* 4.2 7.6 - - + -
547A LEU* 4.0 11.9 - - + -
550A GLN* 4.2 18.4 - - - +
622A VAL* 3.0 34.6 + - + +
623A SER* 4.0 4.7 - - - +
625A LEU* 1.3 75.9 - - - +
627A ASN* 1.3 68.5 + - - +
629A ILE* 3.1 9.3 + - - +
630A LEU* 2.9 43.8 + - + +
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Residues in contact with ASN 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 SER* 3.1 28.2 + - - +
624A LYS* 3.8 7.9 - - - +
625A LEU 3.3 0.2 - - - -
626A VAL* 1.3 82.1 - - - +
628A PHE* 1.3 59.0 + - - +
630A LEU* 3.5 3.3 + - - +
631A SER 3.1 3.5 + - - -
632A LYS 3.0 49.6 + - - +
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Residues in contact with PHE 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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582A ILE* 4.1 12.1 - - + -
598A LYS* 3.8 46.8 + - + -
599A VAL 4.1 13.2 - - - -
600A TYR* 3.4 45.5 - + + -
624A LYS 3.0 14.9 + - - +
625A LEU* 3.4 10.3 - - + +
627A ASN* 1.3 73.9 - - - +
629A ILE* 1.3 69.0 + - - +
631A SER* 3.0 14.5 + - - +
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Residues in contact with ILE 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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528A PHE* 3.7 52.3 - - + -
530A LEU* 3.8 30.5 - - + -
543A SER* 4.9 1.1 - - - -
547A LEU* 3.8 19.1 - - + -
580A GLU* 4.3 3.1 - - - +
582A ILE* 4.0 22.6 - - + +
598A LYS* 4.2 9.8 + - - +
625A LEU* 2.9 47.0 + - + +
626A VAL* 3.6 6.3 - - - +
628A PHE* 1.3 78.1 - - + +
630A LEU* 1.3 59.5 + - - +
631A SER* 3.3 3.8 + - - -
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Residues in contact with LEU 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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528A PHE* 3.9 26.0 - - + -
547A LEU* 3.8 18.4 - - + -
550A GLN* 3.7 22.9 - - - +
552A PHE* 3.8 33.2 - - + -
626A VAL* 2.9 23.3 + - + +
627A ASN* 4.2 4.3 - - - +
629A ILE* 1.3 75.9 - - - +
631A SER* 1.3 75.5 + - - +
632A LYS* 3.2 15.2 + - - +
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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