Contacts of the helix formed by residues 649 - 656 (chain B) in PDB entry 4YZ9
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 649 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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648B THR* 1.3 71.8 - - - +
650B GLN* 1.3 65.5 + - - +
652B TYR* 3.2 26.5 + - + -
653B VAL* 3.0 29.9 + - + +
668B LEU* 3.7 28.0 - - + -
672B THR* 5.4 0.2 - - - +
691B PRO* 3.0 17.6 + - + +
694B ILE* 2.7 41.1 + - + +
696B ILE* 4.6 3.8 - - + -
763B VAL* 3.7 31.0 - - + -
766B TYR* 5.0 0.2 - - + -
767B VAL* 4.0 13.2 - - + -
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Residues in contact with GLN 650 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648B THR* 3.3 9.6 + - - +
649B LEU* 1.3 76.3 - - - +
651B GLU* 1.3 63.7 + - - +
653B VAL* 3.2 2.4 + - - +
654B GLU* 2.9 54.4 + - - +
691B PRO* 3.3 21.6 + - + +
692B HIS* 2.9 39.5 + - + +
766B TYR* 3.6 20.9 - - + +
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Residues in contact with GLU 651 (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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646B ALA 4.7 0.7 - - - +
647B ALA* 3.1 30.3 - - + +
648B THR* 3.3 24.1 + - - +
649B LEU 3.3 0.4 - - - -
650B GLN* 1.3 83.2 - - - +
652B TYR* 1.3 62.5 + - - +
654B GLU* 4.5 6.3 - - - +
655B GLN* 3.0 53.9 + - + +
658B PHE* 3.5 3.0 - - + -
714B LEU* 5.0 4.3 - - - +
715B CYS 4.8 15.0 - - - -
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Residues in contact with TYR 652 (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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648B THR 3.2 13.2 + - - +
649B LEU* 3.2 28.1 + - + +
651B GLU* 1.3 80.3 - - - +
653B VAL* 1.3 71.8 + - + +
656B LYS* 3.8 12.0 + - - -
658B PHE* 3.3 60.1 - + + +
659B ALA* 5.8 0.7 - - - -
661B LEU* 5.5 1.1 - - + -
663B LEU* 2.9 34.9 + - + -
664B GLU 3.8 1.6 - - - -
665B PRO* 3.7 22.2 - - + +
668B LEU* 3.5 23.9 - - + +
696B ILE* 4.1 9.2 - - + -
767B VAL* 4.7 11.0 - - + -
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Residues in contact with VAL 653 (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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649B LEU* 3.0 15.9 + - + +
650B GLN 3.9 0.7 - - - +
652B TYR* 1.3 91.4 - - + +
654B GLU* 1.3 67.9 + - - +
656B LYS* 3.8 9.0 + - - +
766B TYR* 3.5 36.8 - - + +
767B VAL* 4.0 20.9 - - + +
770B GLU* 3.7 17.7 - - + +
771B GLY* 3.5 29.8 - - - +
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Residues in contact with GLU 654 (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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650B GLN* 2.9 46.4 + - - +
651B GLU* 4.3 5.3 - - - +
653B VAL* 1.3 78.2 - - + +
655B GLN* 1.3 68.6 + - + +
656B LYS* 3.3 4.0 + - - +
766B TYR* 3.9 12.0 + - - +
771B GLY* 6.1 2.5 - - - -
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Residues in contact with GLN 655 (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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651B GLU* 3.0 41.6 + - - +
654B GLU* 1.3 78.6 - - + +
656B LYS* 1.3 63.4 + - - +
657B ASP* 3.0 23.3 + - + +
658B PHE* 3.1 24.6 - - + -
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Residues in contact with LYS 656 (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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652B TYR 3.8 7.9 + - - -
653B VAL 3.8 9.6 + - - +
654B GLU 3.3 6.8 - - - +
655B GLN* 1.3 78.2 - - - +
657B ASP* 1.3 59.4 + - - +
658B PHE 3.3 2.9 + - - +
659B ALA* 3.8 16.8 + - - +
770B GLU* 6.1 0.4 - - - +
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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