Contacts of the strand formed by residues 64 - 69 (chain 7) in PDB entry 4UOW
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 LEU 64 (chain 7).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307 SER* 5.2 13.5 - - - -
317 CYS 3.6 9.2 - - - +
327 GLN* 4.6 14.1 - - + +
607 GLN* 3.1 5.9 - - - +
617 ASP* 2.9 47.5 + - + +
627 GLY 3.1 0.4 - - - -
637 ASP* 1.4 85.7 + - - +
657 TYR* 1.3 61.0 + - - +
667 ARG* 5.3 2.9 - - + +
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Residues in contact with TYR 65 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297 LEU 4.2 0.2 - - - +
307 SER* 3.4 3.8 - - - -
317 CYS* 2.9 38.5 + - - +
337 ILE* 3.3 46.6 + - + -
387 THR* 4.4 6.2 + - - -
397 PRO* 3.2 41.4 + - + +
417 VAL* 3.5 37.0 - - + -
437 TRP* 5.0 3.1 - - + +
597 ALA 3.8 4.3 - - - +
607 GLN* 3.1 41.2 + - + -
627 GLY 4.6 0.3 + - - -
637 ASP* 3.3 19.5 - - - -
647 LEU* 1.3 74.3 - - - +
667 ARG* 1.3 60.5 + - - +
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Residues in contact with ARG 66 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287 THR* 3.8 28.1 - - - +
297 LEU 3.4 9.6 - - - +
307 SER* 4.2 11.2 - - - -
437 TRP* 4.8 5.7 - - - +
577 ARG 3.7 1.9 - - - +
587 LEU* 3.6 3.0 - - - -
597 ALA* 2.8 62.7 + - - +
647 LEU* 5.3 3.4 - - + +
657 TYR* 1.3 75.7 - - - +
677 LEU* 1.3 59.8 + - - +
687 THR* 3.2 21.6 + - - +
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Residues in contact with LEU 67 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277 ALA 4.0 0.2 - - - +
287 THR* 3.4 2.6 - - - -
297 LEU* 2.8 43.9 + - + +
437 TRP* 3.7 41.4 - - + +
507 VAL* 3.8 15.5 - - + -
567 PHE* 3.8 36.3 - - + -
577 ARG 3.5 2.0 - - - +
587 LEU* 4.0 18.6 - - + +
667 ARG* 1.3 72.7 - - - +
687 THR* 1.3 62.6 + - - +
697 ILE* 4.0 4.0 + - + +
807 TYR* 4.0 30.3 - - + -
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Residues in contact with THR 68 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267 ASP* 4.2 15.9 - - + +
277 ALA 3.4 9.6 - - - +
287 THR* 3.5 12.0 - - + +
567 PHE* 3.3 7.4 - - - +
577 ARG* 2.7 47.6 + - + -
667 ARG* 3.2 31.8 + - - -
677 LEU* 1.3 71.9 - - - +
697 ILE* 1.3 63.5 + - - +
707 LEU* 3.7 22.4 + - + +
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Residues in contact with ILE 69 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267 ASP* 3.4 2.3 - - - -
277 ALA* 2.7 47.7 + - + +
297 LEU* 3.8 29.6 - - + -
557 ARG* 3.6 5.8 - - + +
567 PHE* 3.6 27.6 - - + -
677 LEU* 4.6 6.5 - - + +
687 THR* 1.3 74.1 - - - +
707 LEU* 1.3 63.9 + - - +
727 LEU* 4.3 6.2 + - + -
767 ASP* 3.4 34.8 - - + +
807 TYR* 3.8 22.4 - - + +
977 LEU* 3.8 14.4 - - + -
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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