Contacts of the helix formed by residues 616 - 622 (chain j) in PDB entry 5JPQ
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 616 (chain j).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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603j LEU* 4.2 19.0 - - + +
609j PRO 4.8 11.7 - - - +
610j ALA 5.4 1.3 - - - +
611j GLY 3.8 9.5 - - - +
612j ASP 2.6 31.8 + - - +
614j ILE 4.4 0.2 - - - -
615j PRO* 1.5 60.3 - - - +
617j LEU* 1.3 56.0 + - - +
618j VAL 3.8 1.1 - - - -
619j SER* 4.1 3.6 + - - -
620j GLN* 3.4 19.2 + - - +
628j ALA* 5.9 1.4 - - - +
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Residues in contact with LEU 617 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613j LEU 4.0 19.2 + - - +
616j TRP* 1.3 70.5 - - - +
618j VAL* 1.4 57.9 + - - +
619j SER 3.0 3.1 - - - -
620j GLN* 3.4 7.4 - - + +
621j GLN* 2.6 41.7 + - + +
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Residues in contact with VAL 618 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614j ILE 3.6 24.7 + - - +
615j PRO* 5.1 1.5 - - + -
616j TRP 3.8 1.4 - - - +
617j LEU* 1.4 74.1 - - - +
619j SER* 1.3 55.2 + - - +
621j GLN* 5.2 0.4 - - - -
622j PHE* 2.6 43.4 + - + +
627j PHE* 4.0 17.4 - - + +
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Residues in contact with SER 619 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599j ILE 4.2 9.0 - - - -
603j LEU* 5.2 0.9 - - - -
604j SER* 3.6 18.6 - - - +
615j PRO 5.8 1.2 + - - -
616j TRP 4.1 3.8 + - - -
617j LEU 3.0 0.2 - - - -
618j VAL* 1.3 78.2 - - - +
620j GLN* 1.4 68.3 + - - +
622j PHE 3.3 11.6 - - - +
624j ASP 3.5 23.0 - - - +
625j ASP 3.8 15.5 - - - -
627j PHE* 3.9 2.0 - - - +
628j ALA* 3.9 22.3 - - - +
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Residues in contact with GLN 620 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603j LEU* 3.7 24.2 + - + +
604j SER* 4.1 9.2 - - - +
606j GLY* 5.7 2.5 - - - -
616j TRP 3.4 16.1 + - - +
617j LEU* 3.1 8.1 + - + +
619j SER* 1.4 80.5 - - - +
621j GLN* 1.3 60.8 + - + +
622j PHE 4.0 2.4 - - - +
849j LEU* 4.8 11.4 - - + +
853j VAL* 4.9 5.7 - - - +
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Residues in contact with GLN 621 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617j LEU* 2.6 27.0 + - + +
618j VAL* 5.2 0.4 - - - -
620j GLN* 1.3 71.8 - - - +
622j PHE* 1.3 64.2 + - + +
746j TYR* 5.5 11.4 - - + -
853j VAL* 4.9 20.4 - - + +
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Residues in contact with PHE 622 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618j VAL* 2.6 34.1 + - + +
619j SER 3.3 11.9 - - - +
620j GLN 3.5 2.8 - - - +
621j GLN* 1.3 81.3 - - + +
623j GLN* 1.3 61.1 + - - +
624j ASP 3.6 5.4 - - - +
627j PHE* 5.6 1.8 - - + -
778j PHE* 4.9 17.9 - - + -
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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