Contacts of the helix formed by residues 619 - 625 (chain B) in PDB entry 4OSI
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 619 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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615B THR* 2.9 13.7 + - - +
616B VAL* 5.2 0.2 - - - -
617B GLN 2.4 19.4 + - - -
618B ARG* 1.3 101.4 - - - +
620B LEU* 1.3 57.5 + - - -
621B PRO* 3.0 11.4 - - + +
622B VAL* 3.1 37.4 + - + +
623B LEU* 3.2 30.1 - - + +
647B LEU* 4.3 26.0 - - + +
648B GLU* 4.6 13.9 - - + +
651B GLN* 4.8 15.0 - - + +
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Residues in contact with LEU 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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589B LEU* 6.2 2.0 - - + -
593B HIS* 3.9 40.2 - - + +
595B LEU* 4.9 17.7 - - + -
616B VAL* 2.9 31.5 + - + +
617B GLN* 3.9 2.0 - - - +
619B LEU* 1.3 69.9 - - - +
621B PRO* 1.3 76.8 - - + +
623B LEU* 4.6 3.8 - - - -
624B CYS* 3.5 35.9 + - + +
630B THR 5.1 0.7 - - - +
631B PRO* 5.1 7.0 - - + -
634B VAL* 4.1 25.1 - - + -
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Residues in contact with PRO 621 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593B HIS* 3.9 15.9 - - + +
617B GLN 3.2 14.6 - - - +
618B ARG* 4.4 4.3 - - - -
619B LEU* 3.9 9.4 - - + +
620B LEU* 1.3 98.1 - - + +
622B VAL* 1.3 57.8 + - + +
623B LEU 2.7 14.2 + - - -
624B CYS* 4.0 0.3 - - - +
625B GLN* 3.2 20.7 + - - +
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Residues in contact with VAL 622 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619B LEU* 3.1 36.2 + - + +
621B PRO* 1.3 74.9 - - + +
623B LEU* 1.3 63.5 + - + +
625B GLN* 3.2 32.1 - - - +
626B ALA* 3.7 9.7 + - + -
627B HIS* 3.1 21.8 + - + -
651B GLN* 4.7 13.0 - - + -
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Residues in contact with LEU 623 (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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616B VAL* 5.7 0.9 - - - +
619B LEU* 3.2 34.1 - - + +
620B LEU* 4.5 1.6 - - - +
621B PRO 2.7 9.5 + - - -
622B VAL* 1.3 84.8 - - + +
624B CYS* 1.3 52.1 + - - +
625B GLN 2.9 4.3 - - - -
627B HIS* 3.1 18.4 + - + +
628B GLY* 2.4 30.5 + - - -
629B LEU* 3.4 15.4 + - + +
634B VAL* 3.3 34.3 - - + -
637B ILE* 6.3 0.7 - - + -
647B LEU* 4.5 18.4 - - + +
650B VAL* 4.4 22.7 - - + -
651B GLN* 4.9 10.8 - - + +
654B LEU* 6.1 0.2 - - + -
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Residues in contact with CYS 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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620B LEU* 3.5 33.4 + - + +
621B PRO 3.5 1.6 + - - -
623B LEU* 1.3 79.9 - - - +
625B GLN* 1.3 56.6 - - - +
628B GLY* 3.3 11.9 - - - -
629B LEU* 2.7 36.5 - - - +
630B THR 3.3 20.9 - - - -
631B PRO* 4.3 3.1 - - - -
634B VAL* 5.2 1.8 - - - -
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Residues in contact with GLN 625 (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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621B PRO 3.2 19.7 + - - +
622B VAL* 3.2 22.8 - - - +
623B LEU 2.9 1.2 - - - -
624B CYS* 1.3 79.8 - - - +
626B ALA* 1.3 87.8 + - - +
627B HIS 3.0 9.6 + - - -
628B GLY* 3.2 7.8 + - - -
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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