Contacts of the strand formed by residues 619 - 629 (chain B) in PDB entry 2G5T
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 VAL 619 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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528B MET* 5.3 0.7 - - + -
539B LYS* 4.1 14.2 + - - +
540B TYR 3.5 4.0 - - - +
542B LEU* 3.8 40.2 - - + -
574B ILE* 4.6 3.8 - - + -
613B PHE* 3.1 27.4 - - + +
614B SER* 3.6 26.2 - - - +
616B MET* 5.8 0.2 - - - -
617B GLY 3.5 2.4 - - - +
618B PHE* 1.3 102.2 - - + +
620B ASP* 1.3 60.7 + - - +
621B ASN* 3.0 9.0 + - - +
624B ILE* 4.2 13.9 - - + -
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Residues in contact with ASP 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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539B LYS* 3.8 28.4 - - + +
540B TYR 2.8 20.7 + - - +
619B VAL* 1.3 70.5 - - - +
621B ASN* 1.3 57.9 + - - +
622B LYS* 2.8 39.7 + - - +
623B ARG* 2.8 61.5 + - + +
624B ILE* 3.6 2.9 - - - +
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Residues in contact with ASN 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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614B SER* 3.6 24.9 + - - +
615B LYS* 5.3 13.5 - - - +
619B VAL 3.0 9.0 + - - +
620B ASP* 1.3 70.6 + - - +
622B LYS* 1.3 73.5 + - - +
623B ARG 3.4 0.7 - - - -
624B ILE* 3.8 20.6 + - + +
646B VAL 4.5 7.6 - - - +
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Residues in contact with LYS 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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620B ASP* 2.8 20.4 + - - +
621B ASN* 1.3 91.4 + - - +
623B ARG* 1.3 64.0 + - + +
624B ILE 3.8 1.8 - - - -
648B LYS* 3.4 25.8 - - - +
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Residues in contact with ARG 623 (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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539B LYS 3.7 18.0 + - - -
541B PRO* 3.3 27.8 - - + +
542B LEU 3.0 23.4 + - - -
620B ASP* 2.8 34.6 + - - +
622B LYS* 1.3 87.2 - - + +
624B ILE* 1.3 56.4 + - - +
648B LYS* 4.6 5.2 - - + -
762B CYS 4.6 4.7 - - - +
763B PHE* 2.8 69.3 + - + +
764B SER* 4.9 3.2 - - - +
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Residues in contact with ILE 624 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542B LEU* 3.3 21.3 - - + +
610B ALA* 4.2 12.8 - - + +
613B PHE* 6.0 0.2 - - + -
614B SER* 3.7 30.5 - - - +
619B VAL* 4.2 13.7 - - + -
620B ASP 3.6 10.3 - - - +
621B ASN* 3.8 14.8 - - + +
622B LYS 3.8 2.2 + - - -
623B ARG* 1.3 79.7 - - - +
625B ALA* 1.3 62.7 + - - +
646B VAL* 3.8 20.1 + - + +
647B PHE* 3.4 31.7 - - + -
648B LYS* 2.9 31.2 + - - +
763B PHE* 3.9 1.3 - - - -
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Residues in contact with ALA 625 (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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542B LEU 2.8 8.0 + - - +
543B LEU* 4.0 9.9 - - + -
544B LEU* 2.9 25.7 + - - +
624B ILE* 1.3 75.3 - - - +
626B ILE* 1.3 65.1 + - - +
647B PHE* 3.8 5.7 - - - -
649B CYS* 3.2 33.2 - - - +
650B GLY* 5.1 0.2 - - - -
759B ILE* 4.4 10.1 - - + -
763B PHE* 3.6 17.9 - - + -
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Residues in contact with ILE 626 (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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543B LEU* 3.9 2.7 - - - +
544B LEU* 3.4 32.3 - - + +
546B VAL* 3.8 18.2 - - + -
606B GLN* 4.6 3.1 - - + -
625B ALA* 1.3 80.5 - - - +
627B TRP* 1.3 64.2 + - - +
636B THR* 3.5 20.6 - - + +
639B VAL* 4.0 33.0 - - + -
640B LEU* 4.0 18.6 - - + -
647B PHE* 3.9 17.5 - - + -
649B CYS 3.2 10.3 + - - +
650B GLY* 2.9 25.6 - - - -
651B ILE* 2.9 3.3 + - - +
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Residues in contact with TRP 627 (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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543B LEU* 3.4 33.9 - - + +
544B LEU 3.1 6.3 + - - -
545B ASP* 3.8 34.6 + - - +
546B VAL* 3.0 26.3 + - - +
563B TRP* 3.5 30.4 - + + -
567B LEU* 5.7 0.2 - - - +
575B VAL* 5.5 0.6 - - - +
626B ILE* 1.3 76.0 - - - +
628B GLY* 1.3 76.9 + - - +
629B TRP* 3.9 25.4 - + + -
636B THR* 3.1 7.0 - - - -
651B ILE* 3.0 29.2 - - + +
653B VAL* 4.3 6.5 - - + -
752B TYR* 4.2 19.7 - + - -
755B MET* 3.1 31.2 - - + -
759B ILE* 5.9 0.9 - - + -
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Residues in contact with GLY 628 (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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545B ASP* 5.5 0.7 - - - -
546B VAL 3.4 16.2 - - - -
627B TRP* 1.3 89.4 - - - +
629B TRP* 1.3 59.0 + - - -
632B GLY 3.4 8.1 - - - -
633B GLY* 3.3 12.6 - - - -
636B THR* 3.1 4.2 + - - -
651B ILE 3.2 2.2 + - - +
652B ALA* 3.8 0.3 - - - -
653B VAL* 3.0 25.6 + - - +
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Residues in contact with TRP 629 (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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546B VAL 4.3 1.4 + - - -
547B TYR* 3.9 11.7 - - + -
627B TRP* 3.9 23.0 - + + -
628B GLY* 1.3 73.7 - - - -
630B SER* 1.3 72.7 + - - +
631B TYR 3.0 1.7 + - - -
632B GLY* 2.8 24.0 + - - -
633B GLY 3.5 0.7 - - - -
653B VAL* 3.3 33.4 - - + +
654B ALA* 3.9 5.7 - - + +
740B HIS* 2.9 43.3 + + - -
741B GLY* 3.6 22.9 - - - -
742B ILE* 3.7 18.6 - - + -
748B HIS* 6.2 0.2 - - - -
751B ILE* 4.1 13.7 - - + -
752B TYR* 3.7 28.7 - + - -
755B MET* 5.6 0.7 - - - -
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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