Contacts of the helix formed by residues 619 - 624 (chain B) in PDB entry 2R5N
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 TRP 619 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483B ARG* 3.7 8.9 - - - +
555B ILE* 3.8 21.8 - - + -
557B THR* 3.7 21.5 - - + -
583B MET* 4.4 5.8 - - + -
586B THR* 4.3 15.3 - - + -
610B ALA* 3.6 31.0 - - + -
611B VAL 5.8 0.9 - - - -
612B GLU* 2.9 52.9 + - + +
614B GLY 5.4 0.9 - - - -
615B ILE 4.0 16.1 + - - -
616B ALA* 3.0 10.8 + - - +
618B TYR* 1.3 84.2 - + - +
620B TYR* 1.3 64.8 + - - +
621B LYS 3.0 2.2 - - - -
622B TYR* 2.9 40.7 + + + +
623B VAL* 2.9 25.3 + - - +
629B ILE* 3.9 15.0 - - + -
631B GLY* 6.3 0.7 - - - -
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Residues in contact with TYR 620 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620A TYR* 3.7 10.8 - - - +
621A LYS* 3.5 54.1 - - + +
625A LEU* 4.6 0.3 - - - +
616B ALA* 4.8 1.1 - - + -
617B ASP* 3.2 44.6 + - - +
618B TYR 3.2 1.2 + - - -
619B TRP* 1.3 77.0 - - - +
621B LYS* 1.3 63.1 + - - +
623B VAL* 3.9 5.6 - - + -
624B GLY* 2.9 43.8 + - - -
625B LEU* 4.9 7.6 - - + -
629B ILE* 3.8 23.4 - - + +
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Residues in contact with LYS 621 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617A ASP* 2.7 47.2 + - + +
620A TYR* 3.5 37.0 - - + +
625A LEU* 3.4 19.1 - - - +
590B ASP* 2.5 33.5 + - - -
618B TYR* 3.3 34.1 + - + +
619B TRP 3.0 0.6 - - - -
620B TYR* 1.3 77.0 - - - +
622B TYR* 1.3 82.6 + - + +
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Residues in contact with TYR 622 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625A LEU* 4.2 2.8 - - - +
555B ILE* 3.9 18.7 - - + +
583B MET* 4.2 7.6 - - + -
586B THR* 3.3 27.8 + - + -
589B PHE* 4.0 16.3 - + - -
590B ASP* 2.6 37.7 + - - -
601B LEU* 3.8 18.8 - - + -
608B ARG* 2.8 35.1 + - - +
618B TYR* 3.7 20.6 - + - -
619B TRP* 2.9 29.9 + + + +
621B LYS* 1.3 101.1 - - + +
623B VAL* 1.3 60.7 + - + +
624B GLY 3.6 0.9 - - - -
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Residues in contact with VAL 623 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625A LEU* 4.2 6.8 - - - +
555B ILE* 4.5 5.6 - - + -
606B THR* 4.3 6.6 - - - +
608B ARG* 3.7 34.4 - - + +
610B ALA* 3.8 29.6 - - + +
619B TRP 2.9 22.6 + - - +
620B TYR* 3.9 1.8 - - + -
622B TYR* 1.3 80.8 - - + +
624B GLY* 1.3 73.2 + - - +
625B LEU 3.7 0.5 + - - -
626B ASN* 3.9 1.9 + - - +
627B GLY* 3.5 16.3 + - - -
628B ALA 3.9 6.3 - - - +
629B ILE* 3.7 25.1 - - + -
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Residues in contact with GLY 624 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624A GLY* 4.1 10.5 - - - -
625A LEU* 3.8 21.8 - - - +
620B TYR* 2.9 42.4 + - - -
622B TYR 3.6 1.2 - - - -
623B VAL* 1.3 86.6 - - - +
625B LEU* 1.3 62.7 + - - -
627B GLY 4.3 1.4 + - - -
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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
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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