Contacts of the strand formed by residues 598 - 603 (chain D) in PDB entry 5ED1
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 PHE 598 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345D PRO 3.6 19.3 - - - -
346D HIS* 3.9 26.2 - + + -
348D ARG* 3.4 56.1 - - + -
373D THR* 4.8 3.1 + - - -
374D GLY* 4.1 10.9 - - - -
375D THR 5.1 0.2 + - - -
596D PRO* 3.1 22.2 - - + +
597D ASN* 1.3 85.7 - - + +
599D SER* 1.3 64.6 + - - +
600D VAL* 4.0 16.6 - - + -
611D VAL* 4.0 17.0 - - + -
612D ILE 3.3 14.1 - - - +
613D ASN* 5.0 1.3 - - - -
614D ALA* 4.9 2.0 - - - -
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Residues in contact with SER 599 (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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373D THR 3.1 17.4 + - - -
374D GLY* 4.2 1.6 - - - -
393D CYS* 3.5 41.9 + - - +
398D ILE* 3.8 14.0 - - - +
598D PHE* 1.3 76.6 - - - +
600D VAL* 1.3 64.8 + - - +
601D ASN* 4.9 1.0 + - - -
610D GLU 3.8 0.9 - - - +
611D VAL* 3.8 0.5 - - - -
612D ILE* 2.9 38.8 + - - +
614D ALA* 4.7 2.7 - - - +
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Residues in contact with VAL 600 (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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335D PHE* 4.3 16.8 - - + -
338D LEU* 6.3 0.2 - - + -
346D HIS* 3.7 31.2 - - + +
371D VAL* 5.2 2.0 - - + +
372D SER* 3.1 9.9 - - - -
373D THR* 3.0 43.2 + - + +
398D ILE* 4.0 0.3 - - - +
598D PHE* 4.0 15.5 - - + -
599D SER* 1.3 78.9 + - - +
601D ASN* 1.3 67.2 + - - +
602D TRP* 5.9 0.2 - - + -
609D ILE* 3.8 33.0 - - + -
610D GLU 3.5 2.9 - - - -
611D VAL* 4.2 7.4 - - + -
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Residues in contact with ASN 601 (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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371D VAL 3.4 6.7 - - - +
398D ILE* 3.6 22.8 - - + +
402D SER* 4.1 5.0 + - - +
599D SER* 4.9 1.2 + - - -
600D VAL* 1.3 78.7 - - - +
602D TRP* 1.3 63.5 + - - +
603D THR* 5.2 1.2 + - - -
609D ILE* 3.4 1.7 - - - -
610D GLU* 2.9 74.5 + - - +
612D ILE* 4.2 10.5 - - - +
626D ARG* 3.1 25.1 + - - -
627D LEU* 3.5 22.5 - - + +
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Residues in contact with TRP 602 (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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334D LYS* 3.8 39.0 - - + -
338D LEU* 3.5 44.3 - - + +
368D VAL* 4.0 21.1 - - + -
369D ILE 4.1 2.0 - - - -
370D SER* 3.2 9.0 - - - -
371D VAL* 2.9 41.1 + - + +
402D SER* 4.2 2.0 + - - -
600D VAL* 5.9 0.2 - - + -
601D ASN* 1.3 78.1 - - - +
603D THR* 1.3 67.6 + - - +
604D VAL* 3.4 35.2 - - + -
605D GLY 4.1 4.5 - - - -
606D ASP* 2.9 33.5 + - + -
608D ALA 3.3 23.1 - - - -
609D ILE* 4.2 4.9 - - + -
626D ARG* 4.0 4.3 - - - +
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Residues in contact with THR 603 (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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369D ILE 3.6 8.3 - - - +
370D SER* 4.4 0.4 - - - -
402D SER* 3.2 44.2 + - - +
405D ARG* 3.3 29.3 + - + +
406D PHE* 3.9 22.7 - - + +
601D ASN* 5.2 0.9 + - - -
602D TRP* 1.3 77.3 + - - +
604D VAL* 1.3 76.5 + - - +
606D ASP* 2.9 30.6 + - - +
627D LEU* 4.9 0.5 - - - +
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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