Contacts of the strand formed by residues 716 - 721 (chain D) in PDB entry 5DFV
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 ASP 716 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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523D CYS 3.6 3.4 - - - +
551D ARG* 3.1 48.6 + - - +
710D GLY* 3.2 4.3 - - - -
711D SER 3.2 26.3 + - - +
715D THR* 1.3 93.0 + - - +
717D PHE* 1.3 61.9 + - - +
718D THR* 5.4 0.2 - - - -
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Residues in contact with PHE 717 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522D SER* 3.5 3.3 - - - -
523D CYS* 3.0 39.9 + - + +
562D VAL* 3.3 35.4 - - + -
596D SER* 3.9 18.2 - - - -
598D MET* 3.9 33.2 - - + -
601D TRP* 4.3 11.0 - - + +
694D ALA* 3.9 16.8 - - + -
709D SER 3.4 5.2 - - - +
710D GLY* 3.5 17.9 - - - -
711D SER* 3.5 26.2 - - - -
712D GLY 3.6 9.9 - - - -
715D THR 3.8 13.7 - - - -
716D ASP* 1.3 75.0 - - - +
718D THR* 1.3 66.4 + - - +
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Residues in contact with THR 718 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520D THR* 3.4 14.4 - - - +
521D ILE 3.2 12.5 + - - +
522D SER* 4.3 8.5 + - - +
601D TRP* 4.1 4.9 + - - -
707D SER 4.0 0.2 - - - +
708D GLY* 3.4 4.2 - - - -
709D SER* 2.7 47.7 + - - +
716D ASP 5.4 0.3 - - - -
717D PHE* 1.3 77.9 + - - +
719D LEU* 1.3 59.9 + - - +
720D ASN* 3.3 26.9 + - - +
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Residues in contact with LEU 719 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519D ALA 4.8 0.2 - - - -
521D ILE* 2.9 39.7 + - + +
601D TRP* 3.6 49.8 - - + +
613D LEU* 5.3 1.1 - - + -
614D ILE* 4.0 24.0 - - + -
706D PHE* 4.5 7.9 - - + -
707D SER 3.4 11.4 - - - +
708D GLY* 4.6 0.2 - - - -
718D THR* 1.3 72.9 - - - +
720D ASN* 1.3 86.0 + - - +
721D ILE* 4.7 8.3 - - + -
732D TYR* 3.7 37.9 - - + -
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Residues in contact with ASN 720 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518D ARG* 3.3 39.1 + - - +
519D ALA 3.5 2.5 - - - -
520D THR* 3.0 22.6 + - - -
705D ARG 3.1 5.6 - - - +
706D PHE* 3.4 3.1 - - - -
707D SER* 2.7 51.3 + - - +
709D SER* 5.7 0.6 + - - -
718D THR* 3.3 13.9 + - - +
719D LEU* 1.3 91.3 + - - +
721D ILE* 1.3 64.6 + - - +
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Residues in contact with ILE 721 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517D GLN 3.5 3.6 - - - +
518D ARG* 3.6 0.6 - - - -
519D ALA* 2.8 48.1 + - + +
521D ILE* 5.3 4.7 - - + -
705D ARG* 3.6 6.3 - - - +
706D PHE* 3.6 32.8 - - + -
719D LEU* 4.7 9.6 - - + -
720D ASN* 1.3 78.3 - - - +
722D HIS* 1.3 65.5 + - - +
723D PRO 4.4 1.8 - - - +
724D VAL* 4.1 12.8 - - + -
728D ASP* 3.6 24.5 - - + +
732D TYR* 3.7 14.6 - - + +
807D LEU* 3.4 30.5 - - + -
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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