Contacts of the strand formed by residues 607 - 612 (chain B) in PDB entry 1GXD
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 TYR 607 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602B PHE 3.9 1.0 - - - +
604B LYS* 3.0 25.2 + - - +
606B ALA* 1.3 101.0 - - + +
608B TYR* 1.3 60.8 + - - +
609B LEU* 4.1 6.3 - - - +
621B PHE* 3.5 42.6 - + + -
622B GLY 3.7 4.7 - - - +
623B SER* 4.2 13.0 - - - -
624B ILE* 3.7 7.2 - - - +
136D ILE* 3.3 44.6 - - + +
152D VAL* 4.7 9.1 - - + +
153D THR 5.4 1.8 - - - -
155D LYS* 4.4 23.1 + - - -
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Residues in contact with TYR 608 (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 TYR* 3.7 28.0 - + - -
602B PHE 3.1 11.4 - - - +
603B PHE* 3.9 14.1 - - + +
607B TYR* 1.3 74.1 - - - +
609B LEU* 1.3 63.4 + - - +
610B LYS* 4.9 0.7 - - + -
620B LYS* 3.3 41.4 + - + +
621B PHE* 3.2 5.7 - - - +
622B GLY* 2.4 72.3 + - - -
623B SER 3.4 11.9 - - - -
624B ILE* 3.4 19.4 - - + +
627B ASP* 3.2 33.5 + - + +
628B TRP* 3.3 17.7 - - + -
137D PRO* 5.3 2.1 - - - +
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Residues in contact with LEU 609 (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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582B ASN 5.1 0.4 - - - +
583B ALA* 2.7 39.9 - - + +
584B ILE* 4.0 11.4 - - + -
585B PRO* 4.9 9.0 - - + -
588B LEU* 6.1 0.4 - - + -
601B TYR* 3.1 4.6 - - - -
602B PHE* 2.5 57.9 + - + +
604B LYS* 5.2 9.2 - - + -
607B TYR 4.1 7.4 - - - +
608B TYR* 1.3 80.0 - - - +
610B LYS* 1.3 61.9 + - - +
611B LEU* 3.4 3.9 + - + +
619B VAL* 5.3 10.3 - - + -
620B LYS 3.6 3.4 - - - -
621B PHE* 4.1 24.9 - - + -
149D MET* 4.5 10.3 - - + -
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Residues in contact with LYS 610 (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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599B HIS* 3.7 40.9 - - + +
601B TYR* 3.6 38.7 + - + +
608B TYR* 4.9 1.1 - - + -
609B LEU* 1.3 69.6 - - - +
611B LEU* 1.3 52.2 + - - +
618B SER* 2.5 32.2 - - - +
619B VAL* 2.9 11.3 - - - +
620B LYS* 2.9 65.5 + - + +
139D TYR* 5.0 4.6 - - + -
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Residues in contact with LEU 611 (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 TRP* 5.3 3.6 - - + -
581B TRP* 3.4 41.7 - - + -
582B ASN 5.4 2.9 - - - +
584B ILE* 4.3 13.9 - - + -
599B HIS* 3.1 9.9 - - - +
600B SER* 2.8 55.4 + - - +
602B PHE* 3.7 19.5 - - + -
609B LEU* 3.4 2.7 + - + -
610B LYS* 1.3 73.5 - - - +
612B GLU* 1.3 89.6 + - - +
613B ASN* 4.8 2.2 - - - +
616B LEU* 3.9 18.6 - - + +
618B SER 3.4 4.0 - - - -
619B VAL* 5.0 4.0 - - + -
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Residues in contact with GLU 612 (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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598B GLY 3.8 10.8 - - - +
599B HIS* 4.5 4.3 - - + +
611B LEU* 1.3 102.4 - - - +
613B ASN* 1.3 70.3 + - - +
614B GLN* 5.0 2.0 - - + +
615B SER* 2.7 33.4 - - - +
616B LEU* 3.3 6.7 - - - +
617B LYS* 3.4 22.3 - - - +
618B SER* 3.1 34.4 + - - +
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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