Contacts of the helix formed by residues 755 - 765 (chain B) in PDB entry 3U44
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 ASP 755 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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719B LYS* 3.4 31.6 + - - +
723B GLN* 5.4 0.4 - - - -
750B LEU* 4.6 0.7 - - - +
753B GLU* 3.1 19.1 - - - +
754B GLN* 1.3 97.3 + - + +
756B ARG* 1.3 67.9 + - - +
757B LEU* 3.0 5.4 - - - +
758B GLN* 2.9 25.0 + - + +
759B SER* 3.4 16.4 + - - -
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Residues in contact with ARG 756 (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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750B LEU 3.8 10.5 - - - +
751B MET* 3.3 31.1 + - + +
752B SER* 3.8 4.0 + - - +
753B GLU* 2.8 42.8 + - - +
754B GLN* 3.0 9.0 + - - +
755B ASP* 1.3 76.6 + - - +
757B LEU* 1.3 64.8 + - - +
759B SER* 3.1 5.0 + - - -
760B LYS* 2.8 26.2 + - - +
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Residues in contact with LEU 757 (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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754B GLN 4.3 5.0 + - - +
755B ASP* 3.0 3.6 - - - +
756B ARG* 1.3 76.6 - - - +
758B GLN* 1.3 62.9 + - - +
760B LYS* 3.1 22.8 - - + +
761B LYS* 3.0 36.8 + - + +
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Residues in contact with GLN 758 (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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722A LYS* 4.2 30.1 - - - +
719B LYS* 4.9 7.2 - - - +
723B GLN* 5.5 3.1 - - - +
755B ASP* 2.9 18.2 + - + +
757B LEU* 1.3 75.4 - - + +
759B SER* 1.3 68.4 + - - +
761B LYS* 2.7 36.5 + - + +
762B LEU* 2.8 12.5 + - - +
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Residues in contact with SER 759 (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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723B GLN* 3.0 27.5 + - - +
750B LEU* 4.1 15.2 + - - +
751B MET* 3.6 20.4 - - - -
755B ASP* 3.4 12.0 + - - -
756B ARG 3.1 7.9 + - - -
758B GLN* 1.3 76.2 - - - +
760B LYS* 1.3 58.5 + - - +
762B LEU* 3.1 10.2 + - - +
763B PHE* 2.8 44.8 + - - -
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Residues in contact with LYS 760 (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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978A ILE 5.5 4.9 - - - +
979A ARG 3.1 11.0 + - - +
980A ARG* 3.1 47.3 + - - +
751B MET* 4.4 7.3 - - + +
756B ARG 2.8 13.2 + - - +
757B LEU* 3.1 26.9 - - + +
759B SER* 1.3 75.1 - - - +
761B LYS* 1.3 64.9 + - + +
763B PHE* 3.1 9.5 + - - +
764B SER* 2.9 21.9 + - - -
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Residues in contact with LYS 761 (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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651A VAL 5.8 1.2 + - - -
690A LYS* 5.5 11.8 - - - +
726A TYR* 3.6 5.6 - - + -
757B LEU* 3.0 26.1 + - + +
758B GLN* 2.7 30.7 + - + +
760B LYS* 1.3 74.2 - - + +
762B LEU* 1.3 57.3 + - - +
764B SER* 2.5 41.2 + - - -
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Residues in contact with LEU 762 (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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722A LYS* 4.1 21.3 - - + +
725A ASP* 3.7 15.3 - - + +
726A TYR* 3.6 40.9 - - + +
723B GLN* 3.5 49.4 - - + +
724B SER 4.5 0.9 - - - +
727B ALA* 4.3 7.6 - - + +
758B GLN 2.8 14.1 + - - +
759B SER* 3.3 9.2 - - - +
761B LYS* 1.3 72.2 - - - +
763B PHE* 1.3 62.1 + - + +
765B SER* 2.6 35.3 + - - -
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Residues in contact with PHE 763 (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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978A ILE* 4.5 20.6 - - + +
723B GLN* 4.1 2.9 - - - -
726B THR* 3.0 32.5 - - - -
727B ALA* 3.4 28.5 - - + -
730B LEU* 3.8 17.9 - - + -
747B TYR* 3.9 18.2 - + - +
750B LEU* 4.4 13.0 - - + -
751B MET* 3.7 27.6 - - + -
759B SER* 2.8 32.7 + - - +
760B LYS* 3.5 5.6 - - - +
761B LYS 3.0 0.2 - - - -
762B LEU* 1.3 82.8 - - + +
764B SER* 1.3 60.8 + - - +
765B SER* 3.0 7.9 - - - -
766B LEU* 3.0 24.1 + - - +
767B PHE* 4.6 2.9 - - - -
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Residues in contact with SER 764 (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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726A TYR* 3.5 13.8 + - - -
760B LYS* 2.9 10.0 + - - -
761B LYS* 2.5 29.1 + - - -
763B PHE* 1.3 67.4 - - - +
765B SER* 1.3 65.1 + - - +
766B LEU 3.0 2.7 - - - -
767B PHE* 3.0 43.8 + - - +
768B PHE* 3.7 1.6 + - - +
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Residues in contact with SER 765 (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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726A TYR* 3.1 54.1 + - - -
729A GLY* 2.9 23.0 - - - +
730A MET* 3.7 9.6 - - - +
727B ALA* 4.8 3.6 - - - +
762B LEU 2.6 23.0 + - - -
763B PHE* 4.1 2.1 - - - -
764B SER* 1.3 82.8 + - - +
766B LEU* 1.3 65.6 + - - +
767B PHE 3.2 0.7 + - - -
768B PHE* 3.4 9.7 + - - +
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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