Contacts of the helix formed by residues 733 - 744 (chain B) in PDB entry 4K44
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 SER 733 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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661B SER* 6.4 2.2 - - - -
719B GLN* 5.7 0.4 - - - +
724B VAL* 3.5 21.3 - - - +
731B PHE* 3.3 2.7 + - - +
732B ASP* 1.3 80.5 - - - +
734B LEU* 1.3 63.7 + - - +
735B VAL* 3.4 10.3 + - - +
736B ASP* 3.0 28.4 + - - -
737B LEU 3.0 18.2 + - - -
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Residues in contact with LEU 734 (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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661B SER* 5.5 1.3 - - - +
663B ALA* 3.7 21.0 - - + +
668B TRP* 4.1 6.5 - - + -
669B TYR* 3.8 31.2 - - + -
693B VAL* 4.4 14.4 - - + -
702B TYR* 4.3 25.1 - - + -
704B ILE* 6.5 0.4 - - + -
717B VAL* 3.9 31.0 - - + -
719B GLN* 5.1 3.8 + - - +
724B VAL* 3.8 17.0 - - + +
733B SER* 1.3 72.6 - - - +
735B VAL* 1.3 62.3 + - - +
737B LEU* 3.5 9.1 - - + +
738B ILE* 2.9 30.0 + - + +
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Residues in contact with VAL 735 (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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662B GLN* 4.1 10.8 - - + -
663B ALA* 3.7 33.3 - - + +
666B LYS* 4.0 31.4 - - + +
668B TRP* 4.1 7.5 - - + -
733B SER* 3.2 8.8 + - - +
734B LEU* 1.3 76.3 - - - +
736B ASP* 1.3 65.9 + - - +
738B ILE* 3.4 1.4 + - - +
739B SER* 2.9 40.8 + - - +
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Residues in contact with ASP 736 (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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731B PHE* 4.1 6.4 - - + -
732B ASP* 3.2 33.6 - - + +
733B SER* 3.0 25.2 + - - +
735B VAL* 1.3 79.9 - - - +
737B LEU* 1.3 65.3 + - - +
739B SER* 3.5 6.8 + - - -
740B TYR* 3.0 24.6 + - - +
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Residues in contact with LEU 737 (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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704B ILE* 3.7 28.5 - - + -
717B VAL* 4.0 20.2 - - + -
724B VAL* 3.7 16.8 - - + -
726B LEU* 4.1 16.2 - - + +
731B PHE* 3.7 39.4 - - + +
733B SER 3.0 13.4 + - - +
734B LEU* 3.5 12.6 - - + +
736B ASP* 1.3 77.2 - - - +
738B ILE* 1.3 73.6 + - + +
740B TYR* 3.2 3.1 + - - +
741B TYR* 3.1 38.9 + - + -
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Residues in contact with ILE 738 (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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668B TRP* 3.7 35.7 - - + +
691B PHE* 3.8 22.7 - - + -
693B VAL* 3.6 23.3 - - + -
704B ILE* 4.3 4.9 - - + -
734B LEU* 2.9 21.9 + - + +
735B VAL 4.0 0.4 - - - +
737B LEU* 1.3 89.9 - - + +
739B SER* 1.3 64.0 + - - +
741B TYR* 3.2 2.6 + - - +
742B GLU* 3.0 41.6 + - + +
752B LEU* 3.7 21.7 - - + +
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Residues in contact with SER 739 (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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735B VAL* 2.9 28.9 + - - +
736B ASP* 3.7 9.6 + - - -
738B ILE* 1.3 76.8 - - - +
740B TYR* 1.3 62.2 + - - +
742B GLU* 3.3 19.8 + - - -
743B LYS* 3.0 37.6 + - - +
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Residues in contact with TYR 740 (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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731B PHE* 3.6 21.5 - + + -
736B ASP 3.0 18.3 + - - +
737B LEU 3.5 4.5 - - - +
738B ILE 3.2 0.2 - - - -
739B SER* 1.3 77.6 - - - +
741B TYR* 1.3 95.2 + + - +
743B LYS* 3.0 5.6 + - - -
744B HIS* 2.8 79.6 + + + +
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Residues in contact with TYR 741 (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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764A ILE* 4.7 8.0 - - + +
726B LEU* 3.6 26.1 + - + +
729B SER* 3.9 13.9 + - - -
731B PHE* 3.5 29.3 - + - -
737B LEU* 3.1 32.4 + - + +
738B ILE 3.2 1.8 + - - -
740B TYR* 1.3 95.7 - + - +
742B GLU* 1.3 59.9 + - - +
743B LYS 3.3 0.9 - - - -
744B HIS 3.1 14.8 - - - +
745B PRO 3.5 26.0 - - - -
746B LEU* 3.7 23.5 + - + -
751B LYS* 3.6 0.7 - - - -
752B LEU* 2.8 47.7 + - + -
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Residues in contact with GLU 742 (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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668B TRP* 4.6 6.6 + - - -
691B PHE* 4.2 9.6 - - + -
738B ILE* 3.0 31.7 + - + +
739B SER* 3.6 13.4 + - - +
740B TYR 3.2 0.4 - - - -
741B TYR* 1.3 78.2 - - - +
743B LYS* 1.3 78.8 + - - +
744B HIS 3.7 0.2 - - - -
751B LYS* 3.8 13.4 - - - +
752B LEU* 3.4 30.5 - - + +
753B ARG* 5.7 0.4 - - - -
755B PRO* 5.6 3.6 - - - +
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Residues in contact with LYS 743 (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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739B SER* 3.0 35.2 + - - +
740B TYR* 3.0 8.6 + - - +
742B GLU* 1.3 102.0 + - + +
744B HIS* 1.3 77.3 + - + +
751B LYS* 3.4 20.5 + - - +
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Residues in contact with HIS 744 (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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740B TYR* 2.8 76.5 + + + +
741B TYR* 3.1 24.8 - - - +
742B GLU 3.7 0.2 - - - -
743B LYS* 1.3 97.5 + - + +
745B PRO* 1.3 79.2 - - + +
751B LYS* 3.6 5.6 - - - +
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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