Contacts of the strand formed by residues 616 - 623 (chain A) in PDB entry 3H44
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 LEU 616 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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530A PHE* 4.1 18.2 - - + +
611A ALA* 3.0 34.3 + - + +
612A GLU* 3.2 7.2 + - - +
614A ALA* 4.5 4.7 - - + +
615A GLY* 1.3 76.5 - - - +
617A SER* 1.3 61.5 + - - +
631A VAL* 4.2 7.6 - - + -
632A LYS 3.6 13.2 - - - +
634A TYR* 3.8 16.8 - - + +
637A LYS* 3.8 27.8 - - + +
638A GLN* 3.6 29.8 - - + +
641A LEU* 3.9 23.7 - - + +
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Residues in contact with SER 617 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A GLU* 3.9 27.6 - - - -
615A GLY 4.1 1.1 - - - -
616A LEU* 1.3 77.9 - - - +
618A TYR* 1.3 64.6 + - - +
630A SER 4.0 0.2 - - - +
631A VAL* 3.5 4.2 - - - +
632A LYS* 2.9 45.5 + - - +
641A LEU* 4.5 4.7 - - - -
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Residues in contact with TYR 618 (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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601A LYS* 3.4 37.2 + - + +
604A LEU* 3.7 20.5 - - + +
605A ASN* 5.2 0.7 + - - -
608A ALA* 4.0 24.0 - - + -
617A SER* 1.3 80.1 - - - +
619A ASP* 1.3 65.2 + - - +
620A LEU* 3.9 32.3 - - + -
629A LEU* 4.0 3.6 - - + -
630A SER 3.2 10.8 - - - +
631A VAL* 4.1 7.6 - - + -
641A LEU* 4.3 12.3 - - + -
645A ILE* 3.6 36.8 - - + -
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Residues in contact with ASP 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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601A LYS* 6.1 0.2 - - - -
618A TYR* 1.3 77.7 - - - +
620A LEU* 1.3 60.4 + - - +
621A GLN* 3.0 26.9 + - - +
628A TYR* 3.6 22.9 + - - +
629A LEU* 3.4 3.0 - - - +
630A SER* 2.8 40.8 + - - +
632A LYS* 5.5 5.4 - - - -
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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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578A PHE* 5.4 1.6 - - + -
597A LEU* 4.0 29.1 - - + +
600A LEU* 3.6 33.0 - - + -
601A LYS* 3.1 37.0 + - + +
618A TYR* 3.9 21.6 - - + -
619A ASP* 1.3 77.3 + - - +
621A GLN* 1.3 63.0 + - - +
627A MET* 4.9 6.1 - - + -
628A TYR 3.0 26.5 - - - +
629A LEU* 3.8 18.6 - - + -
645A ILE* 4.5 11.0 - - + -
649A MET* 4.9 11.0 - - - -
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Residues in contact with GLN 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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597A LEU* 3.4 12.5 - - - +
601A LYS* 4.7 7.6 + - - +
619A ASP* 3.0 26.2 + - - +
620A LEU* 1.3 73.6 - - - +
622A ASN* 1.3 72.4 + - - +
623A THR* 5.1 2.7 - - + +
627A MET* 3.5 1.2 - - - -
628A TYR* 2.7 58.4 + - + +
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Residues in contact with ASN 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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590A SER* 4.2 4.3 - - - +
593A ALA* 3.8 25.7 - - + +
594A TYR* 3.5 48.6 + - - +
597A LEU* 3.3 10.5 - - + +
598A GLU* 5.8 0.4 + - - -
621A GLN* 1.3 87.3 - - - +
623A THR* 1.3 64.2 + - - +
626A GLY 3.3 11.9 - - - +
627A MET* 5.2 0.2 - - + -
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Residues in contact with THR 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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577A GLU* 3.6 23.3 + - - +
583A ALA* 4.1 11.3 - - - +
584A TYR* 4.6 2.1 - - - -
621A GLN* 4.1 4.7 - - + +
622A ASN* 1.3 81.7 - - - +
624A ILE* 1.3 63.2 + - - +
625A TYR* 2.9 25.2 + - - +
626A GLY* 2.8 28.1 + - - +
627A MET 3.7 1.0 + - - -
628A TYR* 3.9 22.7 - - + +
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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