Contacts of the helix formed by residues 644 - 654 (chain A) in PDB entry 2Y48
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 PRO 644 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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595A TYR* 4.9 1.1 - - - +
642A PRO 3.6 3.3 - - - +
643A LEU* 1.3 88.9 - - + +
645A GLU* 1.3 66.7 + - - +
646A TRP* 3.4 42.2 - - + +
647A LYS* 2.9 14.7 + - + +
648A THR* 3.2 7.8 + - - -
780A ILE* 3.5 33.7 - - + -
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Residues in contact with GLU 645 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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643A LEU 3.7 1.8 + - - -
644A PRO* 1.3 72.0 - - - +
646A TRP* 1.3 66.2 + - - +
647A LYS 3.0 0.3 + - - -
648A THR* 3.3 10.7 + - - +
649A SER* 2.7 52.0 + - - +
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Residues in contact with TRP 646 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644A PRO* 3.4 23.4 - - + +
645A GLU* 1.3 82.8 - - - +
647A LYS* 1.3 108.8 + - - +
649A SER* 4.3 4.2 - - - -
650A ALA* 3.6 17.2 + - - +
653A ARG* 4.8 0.7 + - - -
775A LEU* 3.4 42.6 - - + +
778A GLN* 3.7 29.4 - - + -
779A PRO 4.3 6.7 - - - -
780A ILE* 3.7 18.4 - - + -
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Residues in contact with LYS 647 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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643A LEU* 4.2 24.2 - - + -
644A PRO* 2.9 17.6 + - + +
646A TRP* 1.3 103.8 - - + +
648A THR* 1.3 68.3 + - - +
649A SER 3.2 0.4 - - - -
650A ALA* 3.1 7.8 + - - +
651A VAL* 3.0 23.4 + - + +
775A LEU 3.1 9.3 + - - +
776A MET* 3.0 42.9 + - + -
778A GLN 2.8 25.8 + - - -
780A ILE* 3.9 4.0 - - - -
798A PHE* 3.3 23.5 - - + -
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Residues in contact with THR 648 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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643A LEU* 3.9 36.2 + - + +
644A PRO 3.2 2.4 + - - +
645A GLU* 3.3 19.8 + - - +
647A LYS* 1.3 76.3 - - - +
649A SER* 1.3 57.6 + - - +
651A VAL* 3.3 10.9 + - + +
652A GLN* 3.0 42.2 + - - +
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Residues in contact with SER 649 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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645A GLU* 2.7 43.6 + - - -
646A TRP* 4.3 4.9 - - - -
648A THR* 1.3 76.1 + - - +
650A ALA* 1.3 59.5 + - - +
652A GLN* 3.8 7.2 - - - +
653A ARG* 2.9 53.5 + - - +
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Residues in contact with ALA 650 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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646A TRP 3.6 12.2 + - - +
647A LYS* 3.1 11.5 + - - +
649A SER* 1.3 77.2 - - - +
651A VAL* 1.3 64.5 + - - +
653A ARG* 3.7 13.6 - - - +
654A MET* 3.0 30.7 + - - +
772A ASP* 4.3 9.2 - - + +
775A LEU* 4.1 21.5 - - + -
776A MET* 4.0 16.2 - - - -
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Residues in contact with VAL 651 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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627A LEU* 3.8 15.9 - - + +
630A LEU* 3.6 33.0 - - + +
631A LYS* 2.8 43.2 + - + -
643A LEU* 5.9 3.4 - - + -
647A LYS* 3.0 21.0 + - + +
648A THR* 3.5 13.2 - - + +
649A SER 3.2 0.2 - - - -
650A ALA* 1.3 78.3 - - - +
652A GLN* 1.3 61.7 + - + +
654A MET 3.7 2.4 + - - -
776A MET* 3.7 24.9 - - + -
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Residues in contact with GLN 652 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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631A LYS* 3.2 19.5 + - + +
633A GLN* 5.1 11.5 - - - +
648A THR* 3.0 30.0 + - - +
649A SER* 3.9 6.7 - - - +
650A ALA 3.2 0.2 - - - -
651A VAL* 1.3 80.9 - - + +
653A ARG* 1.3 63.3 + - + +
654A MET 3.3 0.9 - - - +
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Residues in contact with ARG 653 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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646A TRP 4.8 1.0 + - - -
649A SER* 2.9 39.2 + - - +
650A ALA* 3.7 10.4 - - - +
652A GLN* 1.3 76.4 - - + +
654A MET* 1.3 64.3 + - - +
655A GLY 3.7 0.2 + - - -
765A ALA* 3.8 15.2 - - - +
766A ALA 5.0 1.9 - - - +
767A GLY 3.7 20.4 - - - +
768A SER* 4.0 9.7 + - - +
772A ASP* 2.6 44.4 + - - +
775A LEU* 3.5 19.0 - - - +
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Residues in contact with MET 654 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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627A LEU* 3.9 26.7 - - + -
631A LYS* 2.8 24.1 + - - -
650A ALA 3.0 17.6 + - - +
651A VAL 4.1 1.8 - - - +
652A GLN 3.3 1.9 - - - +
653A ARG* 1.3 80.2 - - - +
655A GLY* 1.3 60.0 + - - +
762A SER* 4.6 2.7 - - - -
763A TYR 4.8 0.4 - - - -
765A ALA* 4.7 0.2 - - - +
768A SER* 4.0 9.4 - - - +
772A ASP* 3.7 28.5 - - + +
773A TYR* 3.7 40.4 - - + +
776A MET* 3.3 31.9 - - - +
802A HIS* 3.7 13.2 - - + +
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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