Contacts of the strand formed by residues 615 - 619 (chain Q) in PDB entry 3RWR
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 615 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59N MET* 4.3 1.8 - - - -
61N MET* 3.8 22.7 - - + -
65N LYS* 6.3 0.7 - - - -
69N GLU* 5.7 2.5 - - + -
99N LYS* 3.9 22.0 - - + +
101N LEU* 3.5 29.2 - - + -
106N PHE* 3.5 50.7 - - + -
108N LEU* 4.0 16.6 - - + -
611Q GLU* 3.7 2.6 - - - -
612Q LEU 2.9 31.1 + - - +
613Q SER* 3.0 6.2 + - - +
614Q GLY* 1.3 80.6 - - - +
616Q PRO* 1.3 69.6 - - + +
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Residues in contact with PRO 616 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59N MET* 2.8 31.6 - - + +
60N ALA* 2.9 21.3 - - + +
61N MET* 4.0 10.3 - - + -
106N PHE* 3.2 33.2 - - + -
565Q LEU* 5.8 0.2 - - - +
610Q SER 4.6 5.6 - - - +
611Q GLU* 4.8 4.9 - - - +
612Q LEU* 4.6 0.7 - - - +
614Q GLY 3.9 2.4 - - - +
615Q LEU* 1.3 99.2 - - + +
617Q PHE* 1.3 61.9 + - - +
618Q TYR* 4.0 17.0 - - + +
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Residues in contact with PHE 617 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562Q ASN* 3.6 9.0 - - - +
565Q LEU* 5.0 7.2 - - + -
572Q PHE* 3.1 49.8 - + - -
575Q HIS* 3.7 35.7 - - + -
576Q LEU* 4.8 8.7 - - + -
579Q LEU* 3.9 8.5 - - + -
608Q VAL 4.0 0.2 - - - +
609Q ARG* 3.7 0.7 - - - -
610Q SER* 3.1 49.4 + - - +
611Q GLU 4.2 2.7 - - - -
612Q LEU* 3.8 31.9 - - + -
616Q PRO* 1.3 79.4 - - - +
618Q TYR* 1.3 81.7 + - - +
619Q TRP* 5.0 1.6 - - + -
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Residues in contact with TYR 618 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59N MET 5.1 0.4 - - - -
60N ALA* 3.2 26.8 - - + +
561Q LEU* 4.0 20.9 - - + +
562Q ASN* 2.7 42.6 + - + +
608Q VAL 3.7 5.8 - - - +
609Q ARG* 3.0 52.5 - - + -
610Q SER 6.1 0.9 - - - -
616Q PRO* 4.0 21.9 - - + +
617Q PHE* 1.3 89.4 - - - +
619Q TRP* 1.3 66.6 + - - +
620Q ASN* 5.7 2.0 - - - +
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Residues in contact with TRP 619 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534Q TYR* 3.1 30.5 - + - -
549Q VAL* 5.0 1.1 - - + -
554Q VAL* 3.8 23.8 - - + -
557Q ARG* 4.0 22.7 - - + -
558Q ALA* 3.7 26.9 - - - -
561Q LEU* 4.7 6.9 - - + +
562Q ASN* 5.1 0.2 - - - -
572Q PHE* 3.5 31.6 - + + -
576Q LEU* 3.6 25.9 - - + +
608Q VAL* 2.7 51.4 + - + +
617Q PHE* 5.0 2.2 - - + -
618Q TYR* 1.3 80.4 - - - +
620Q ASN* 1.3 95.6 + - - +
621Q PHE* 3.1 24.5 - + - -
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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