Contacts of the strand formed by residues 713 - 717 (chain F) in PDB entry 6X34
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 SER 713 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686F TRP 3.5 11.9 - - - -
687F ALA* 3.9 17.9 - - - +
692F TYR* 4.4 17.5 - - - -
706F GLY 5.2 0.2 - - - -
707F VAL* 4.9 1.6 - - - -
708F GLY* 3.8 24.5 - - - +
710F ASP* 3.0 22.4 + - - +
711F LEU 3.4 0.2 - - - -
712F TYR* 1.3 78.7 - - - +
714F TYR* 1.3 74.2 + - - +
722F TRP 5.0 0.3 - - - +
724F GLY 5.0 1.2 + - - -
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Residues in contact with TYR 714 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685F GLY* 3.4 0.7 - - - -
686F TRP* 2.7 46.7 + - + +
707F VAL* 5.7 0.6 - - - +
708F GLY* 4.4 3.8 - - - -
711F LEU* 3.3 26.0 + - + +
712F TYR 4.6 1.8 - - - -
713F SER* 1.3 80.3 - - - +
715F GLY* 1.3 54.9 + - - +
722F TRP 4.6 2.2 - - - -
723F THR* 4.9 8.1 - - - -
755F ILE* 5.5 8.5 - - + -
768F PHE* 3.6 36.8 - + + -
771F PHE* 4.0 19.2 - + + +
772F ASN 5.3 2.1 + - - -
777F PHE* 4.1 30.7 - + - -
1470F ARG* 4.7 7.9 - - - -
1471F ALA 4.2 4.5 + - - -
1472F VAL* 3.5 44.9 - - + +
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Residues in contact with GLY 715 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683F ARG* 5.8 3.4 - - - -
684F VAL 3.7 2.2 - - - -
685F GLY* 3.7 15.3 - - - -
707F VAL* 5.2 4.9 - - - -
708F GLY* 4.1 10.0 - - - -
714F TYR* 1.3 75.6 - - - +
716F PHE* 1.3 62.3 + - - +
721F LEU* 4.5 1.4 - - - +
722F TRP* 3.2 36.0 + - - +
768F PHE* 4.9 5.5 - - - -
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Residues in contact with PHE 716 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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683F ARG* 5.3 1.9 - - - +
684F VAL* 3.2 26.2 + - - +
715F GLY* 1.3 74.8 - - - +
717F ASP* 1.3 65.1 + - - +
718F GLY 3.2 26.7 - - - -
719F LEU* 4.1 4.9 - - - -
720F HIS 3.5 37.7 - - - -
721F LEU* 3.6 17.5 - - + +
722F TRP* 4.9 1.8 - - - +
730F VAL* 5.0 5.2 - - + -
732F SER* 5.8 0.2 - - - -
744F VAL* 5.6 8.2 - - + +
757F PHE* 3.6 27.4 - - + -
759F ILE* 5.2 8.1 - - + -
764F VAL* 3.6 37.7 - - + -
766F GLY* 6.4 2.0 - - - -
768F PHE* 6.3 1.6 - - + -
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Residues in contact with ASP 717 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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682F LEU 3.3 26.0 - - - +
683F ARG* 3.7 21.4 - - + +
684F VAL* 4.4 3.6 - - + +
716F PHE* 1.3 83.3 - - - +
718F GLY* 1.3 62.0 + - - +
719F LEU 3.8 0.5 + - - -
720F HIS* 3.5 14.0 + - - +
722F TRP* 4.7 6.7 + - - -
737F LEU* 4.7 1.9 - - - +
744F VAL* 5.9 4.9 - - - -
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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