Contacts of the strand formed by residues 616 - 622 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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530B PHE* 4.0 20.4 - - + +
608B ALA 4.7 0.5 - - - +
611B ALA* 2.9 31.9 + - + +
612B GLU* 3.3 6.9 + - - +
614B ALA* 3.3 4.2 - - + +
615B GLY* 1.3 79.2 - - - +
617B SER* 1.3 60.9 + - - +
631B VAL* 3.8 11.2 - - + -
632B LYS 3.7 13.0 - - - +
634B TYR* 4.0 14.4 - - + +
637B LYS* 3.8 29.2 - - + +
638B GLN* 3.8 29.8 - - + +
641B LEU* 3.9 21.6 - - + +
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Residues in contact with SER 617 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612B GLU* 3.2 32.8 + - - -
615B GLY 4.1 1.7 + - - -
616B LEU* 1.3 76.0 - - - +
618B TYR* 1.3 64.8 + - - +
630B SER 3.8 0.2 - - - +
631B VAL* 3.3 7.5 - - - +
632B LYS* 2.9 44.8 + - - +
641B LEU* 4.6 4.0 - - - -
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Residues in contact with TYR 618 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601B LYS* 3.5 39.2 + - + +
604B LEU* 3.4 39.3 - - + +
605B ASN* 4.8 2.2 + - - -
608B ALA* 3.7 27.2 - - + +
612B GLU* 6.2 2.9 - - + -
617B SER* 1.3 81.1 - - - +
619B ASP* 1.3 64.3 + - - +
620B LEU* 4.1 21.3 - - + -
629B LEU* 4.2 5.4 - - + -
630B SER 3.1 9.4 - - - +
631B VAL* 4.3 4.3 - - + -
641B LEU* 4.4 8.1 - - + -
645B ILE* 3.6 28.3 - - + -
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Residues in contact with ASP 619 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601B LYS* 6.0 0.2 + - - -
618B TYR* 1.3 75.4 - - - +
620B LEU* 1.3 62.0 + - - +
621B GLN* 4.3 14.0 + - - +
628B TYR* 3.7 20.7 + - + +
629B LEU* 3.2 6.3 + - - +
630B SER* 2.8 48.7 + - - +
632B LYS* 6.1 2.6 - - - -
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Residues in contact with LEU 620 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578B PHE* 5.8 0.9 - - + -
597B LEU* 3.8 23.9 - - + +
600B LEU* 3.7 29.8 - - + -
601B LYS* 2.6 55.7 + - + +
604B LEU* 6.0 0.2 - - + -
618B TYR* 4.1 19.1 - - + -
619B ASP* 1.3 77.1 + - - +
621B GLN* 1.3 57.5 + - - +
627B MET* 4.9 6.5 - - + -
628B TYR 3.3 15.0 - - - +
629B LEU* 4.0 21.5 - - + -
645B ILE* 4.9 3.6 - - + -
649B MET* 3.8 19.5 - - + -
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Residues in contact with GLN 621 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597B LEU* 3.5 10.3 - - - -
601B LYS* 4.6 6.6 + - - +
619B ASP* 4.7 12.8 + - - +
620B LEU* 1.3 75.6 - - - +
622B ASN* 1.3 71.6 + - - +
623B THR* 5.2 2.0 - - + +
628B TYR* 2.8 63.5 + - + +
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Residues in contact with ASN 622 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590B SER* 4.1 5.4 - - - +
593B ALA* 4.1 17.1 - - + +
594B TYR* 3.3 54.0 + - - +
597B LEU* 3.2 19.6 - - + +
621B GLN* 1.3 83.7 - - - +
623B THR* 1.3 65.1 + - - +
626B GLY 3.5 11.0 - - - +
627B MET* 5.2 0.2 - - + -
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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