Contacts of the strand formed by residues 607 - 609 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603A PHE* 5.2 0.7 - - - -
604A LYS* 2.6 53.7 + - - +
605A GLY* 5.3 2.2 - - - -
606A ALA* 1.3 96.8 - - + +
608A TYR* 1.3 58.3 + - - +
621A PHE* 3.2 39.0 - + + -
622A GLY 3.0 22.7 - - - +
623A SER* 4.1 2.7 - - - -
624A ILE* 3.7 7.2 - - - +
136C ILE* 3.8 12.1 - - + -
152C VAL* 3.9 15.4 + - + -
153C THR* 3.2 39.9 + - + +
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Residues in contact with TYR 608 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A ARG* 4.9 0.5 + - - -
601A TYR* 3.6 36.3 - + + -
602A PHE 3.3 16.2 - - - +
603A PHE* 4.0 19.3 - - + +
607A TYR* 1.3 74.3 - - - +
609A LEU* 1.3 64.3 + - - +
610A LYS 4.1 2.9 - - - -
620A LYS* 3.6 32.3 - - + -
621A PHE* 3.6 14.9 - - - -
622A GLY* 2.8 55.1 + - - -
623A SER 3.9 0.7 - - - -
624A ILE* 3.9 13.0 - - + +
627A ASP* 2.6 50.9 + - + +
628A TRP* 4.1 13.5 - + - -
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Residues in contact with LEU 609 (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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583A ALA* 3.6 32.5 - - + +
584A ILE* 3.9 18.2 - - + +
585A PRO* 4.3 13.0 - - + -
602A PHE* 3.0 36.9 + - + +
604A LYS* 6.5 0.9 - - - -
608A TYR* 1.3 79.2 - - - +
610A LYS* 1.3 66.3 + - - +
611A LEU* 3.4 13.8 + - + -
618A SER* 5.0 3.6 - - - +
619A VAL 4.7 4.0 - - - +
620A LYS 3.9 3.1 - - - -
621A PHE* 3.8 27.8 - - + -
147C LEU* 4.8 3.8 - - + -
149C MET* 3.8 17.3 - - + -
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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
------------------------------------------------------------
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