Contacts of the strand formed by residues 550 - 556 (chain D) in PDB entry 3WF4
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 ALA 550 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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381D LYS* 4.0 13.2 - - - -
383D LYS 3.5 6.7 - - - +
384D THR* 3.7 13.9 - - + +
385D VAL 4.1 2.0 - - - +
548D LEU 3.2 9.8 + - - +
549D PRO* 1.3 75.4 - - - +
551D PHE* 1.3 62.2 + - - +
552D TYR* 3.4 28.3 - - + +
619D LEU* 3.4 10.3 - - - +
620D GLU 3.0 30.3 + - - -
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Residues in contact with PHE 551 (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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381D LYS* 3.9 1.9 - - - +
382D LEU* 2.9 30.6 + - + +
383D LYS 2.9 16.2 + - - +
384D THR 4.8 1.1 - - - -
385D VAL* 4.1 14.6 - - + -
392D LEU* 4.0 25.8 - - + -
516D THR* 4.3 16.6 - - + -
520D VAL* 3.9 20.2 - - + -
524D LEU* 3.3 37.7 - - + -
550D ALA* 1.3 73.2 - - - +
552D TYR* 1.3 62.4 + - - +
582D TRP* 4.2 4.3 - + - -
617D THR* 4.2 18.6 - - + -
618D VAL 3.1 9.0 - - - +
619D LEU* 3.9 38.4 - - + -
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Residues in contact with TYR 552 (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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379D LEU* 4.1 12.1 - - + +
380D GLU 3.3 10.8 - - - +
381D LYS* 3.4 46.1 + - + +
547D THR* 4.5 6.4 + - - +
548D LEU 4.4 5.4 + - - -
550D ALA* 3.4 36.9 - - + +
551D PHE* 1.3 74.1 - - - +
553D MET* 1.3 59.8 + - - +
576D TRP* 3.6 27.4 - + + -
616D ILE 3.7 0.5 - - - +
617D THR* 3.4 4.1 - - - -
618D VAL* 2.7 39.1 + - + +
620D GLU* 3.9 8.0 - - + +
624D ALA* 3.1 27.8 - - + +
626D CYS* 3.9 29.1 - - + +
634D CYS* 4.1 0.4 - - - -
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Residues in contact with MET 553 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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379D LEU* 3.9 4.9 - - - -
380D GLU* 2.8 37.3 + - - +
382D LEU* 3.8 35.6 - - + +
520D VAL* 4.6 2.9 - - - +
523D HIS* 3.4 57.7 - - + +
524D LEU* 6.4 0.2 - - + -
552D TYR* 1.3 73.9 - - - +
554D GLY* 1.3 63.3 + - - +
555D ASN* 4.9 3.8 - - - +
615D THR* 3.7 9.4 - - + -
616D ILE 3.1 12.1 - - - +
617D THR* 3.3 25.4 - - + +
703D NAG 5.4 4.0 - - - +
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Residues in contact with GLY 554 (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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377D VAL* 4.7 3.1 - - - -
378D THR 3.6 19.1 - - - -
379D LEU* 3.6 7.1 - - - +
380D GLU* 6.0 0.2 - - - -
553D MET* 1.3 77.6 - - - +
555D ASN* 1.3 69.6 + - - +
615D THR* 3.5 0.7 - - - -
616D ILE* 2.9 30.7 + - - +
703D NAG 5.6 2.7 - - - -
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Residues in contact with ASN 555 (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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377D VAL* 3.6 14.2 - - - +
378D THR 4.4 0.8 + - - +
523D HIS* 5.8 0.2 + - - -
553D MET* 4.9 3.5 - - - +
554D GLY* 1.3 81.8 - - - +
556D PHE* 1.4 64.0 + - - +
613D PRO* 4.2 14.7 - - + +
614D ASN 3.1 10.1 - - - +
615D THR* 3.7 14.9 + - - +
703D NAG 1.4 98.9 + - - +
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Residues in contact with PHE 556 (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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374D TYR* 4.1 30.3 - + + -
377D VAL* 3.9 16.8 - - + -
555D ASN* 1.4 75.0 - - - +
557D SER* 1.3 64.9 + - - +
558D ILE* 4.1 26.5 - - + -
583D ILE* 4.8 4.5 - - + -
608D LEU* 3.9 24.0 - - + -
613D PRO* 4.5 1.1 - - - -
614D ASN* 2.8 62.0 + - + -
616D ILE* 4.0 23.6 - - + -
638D PHE* 3.9 26.7 - + - -
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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