Contacts of the strand formed by residues 639 - 643 (chain B) in PDB entry 5M5X
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 GLY 639 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584B CYS* 3.9 13.1 - - - +
585B CYS 3.1 21.5 - - - -
628B TYR* 3.6 9.2 - - - -
629B VAL* 2.9 36.5 + - - +
638B PRO* 1.3 77.7 - - - +
640B LEU* 1.3 64.5 + - - +
641B TYR* 4.9 0.7 - - - -
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Residues in contact with LEU 640 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565B LEU* 5.9 0.4 - - + -
584B CYS* 6.0 0.9 - - + -
585B CYS 2.8 19.4 + - - +
586B VAL* 3.2 18.3 - - + -
587B GLN 2.9 15.9 + - - -
601B GLY* 4.7 1.1 - - - +
604B ILE* 3.7 24.0 - - + -
605B ALA* 4.9 0.2 - - - -
608B LEU* 5.5 1.3 - - + -
609B ARG* 4.1 4.0 - - - +
626B ILE* 3.6 39.7 - - + -
627B GLY 3.2 13.7 - - - +
628B TYR* 3.9 28.3 - - + -
629B VAL 4.5 0.2 - - - +
639B GLY* 1.3 74.9 - - - +
641B TYR* 1.3 66.5 + - - +
642B LEU* 3.6 22.7 - - + -
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Residues in contact with TYR 641 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B HIS* 3.3 38.0 - + - +
214B PRO* 5.3 2.0 - - + -
376B PHE* 6.0 0.5 - - - -
380B LYS* 6.0 0.7 - - - +
585B CYS* 4.6 2.4 - - - -
587B GLN* 3.3 46.8 + - + +
627B GLY* 2.9 30.6 + - - -
629B VAL* 4.3 6.7 - - + -
636B GLN* 5.8 3.0 + - - +
637B TYR* 3.8 42.8 + - - +
638B PRO 4.1 1.2 + - - -
640B LEU* 1.3 82.2 - - - +
642B LEU* 1.3 66.8 + - - +
643B PHE* 3.6 9.9 - - + -
667B PHE* 3.5 35.2 - + + -
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Residues in contact with LEU 642 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B ARG* 4.4 4.2 + - - -
561B ILE* 4.2 20.6 - - + -
565B LEU* 4.0 17.7 - - + -
586B VAL* 3.8 14.8 - - + -
587B GLN 2.8 23.6 + - - +
588B ILE* 3.7 26.4 - - + -
589B ASP* 4.5 7.9 + - - -
608B LEU* 5.1 5.4 - - + -
620B LEU* 6.3 0.2 - - + -
624B LEU* 4.7 13.5 - - + -
625B GLU 3.5 7.4 - - - +
626B ILE* 4.2 15.5 - - + +
640B LEU* 3.6 25.1 - - + -
641B TYR* 1.3 75.7 - - - +
643B PHE* 1.3 78.5 + - - +
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Residues in contact with PHE 643 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B ARG* 3.2 49.4 - - - +
401B GLU* 4.8 2.0 - - - -
561B ILE* 5.1 1.6 - - - +
588B ILE* 4.7 6.8 - - - +
589B ASP* 4.8 10.7 - - - +
624B LEU* 3.2 21.2 - - - +
625B GLU* 2.9 63.2 + - + +
627B GLY 4.4 3.1 - - - -
641B TYR* 3.6 18.8 - - + -
642B LEU* 1.3 78.8 - - - +
644B GLY* 1.3 61.1 + - - +
645B GLY 3.8 0.4 - - - -
648B ARG* 3.5 22.4 - - + +
666B PRO* 6.4 0.7 - - + -
667B PHE* 3.5 36.1 - + + -
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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
------------------------------------------------------------
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