Contacts of the helix formed by residues 709 - 722 (chain A) 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 SER 709 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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705A SER* 5.2 1.7 - - - -
708A HIS* 1.3 79.1 - - - +
710A VAL* 1.3 64.9 + - - +
711A SER* 3.2 13.9 + - - -
712A GLU* 3.1 26.4 + - - +
713A LEU* 3.1 23.6 + - - +
751A GLU* 4.4 14.7 + - - -
380B ASN* 3.3 28.3 - - - +
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Residues in contact with VAL 710 (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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630A LEU* 5.1 0.4 - - + -
705A SER* 6.4 0.4 - - - -
709A SER* 1.3 72.4 - - - +
711A SER* 1.3 65.2 + - - +
713A LEU* 3.3 8.3 + - + +
714A ILE* 3.0 29.5 + - + +
747A ALA* 4.0 11.9 - - + +
750A TYR* 4.6 9.6 - - + -
757A GLY* 3.7 26.5 - - - +
758A LEU* 3.8 27.4 - - + +
761A PHE* 3.7 37.7 - - + -
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Residues in contact with SER 711 (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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709A SER* 3.2 12.2 + - - -
710A VAL* 1.3 78.5 - - - +
712A GLU* 1.3 66.2 + - - +
714A ILE* 3.4 2.0 + - - +
715A TRP 3.2 13.2 + - - -
744A TYR* 3.1 40.6 + - - -
747A ALA* 3.9 21.3 + - - +
748A ARG* 3.9 26.2 - - - -
751A GLU* 4.5 7.6 + - - -
357B ASP* 5.2 3.6 + - - -
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Residues in contact with GLU 712 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704A PHE* 3.9 9.0 - - + -
708A HIS* 3.2 27.2 - - + +
709A SER* 3.1 36.6 + - - +
710A VAL 3.2 0.6 - - - -
711A SER* 1.3 82.8 + - - +
713A LEU* 1.3 66.9 + - - +
715A TRP* 3.0 5.9 + - - +
716A GLU* 2.9 21.3 + - - +
357B ASP* 5.7 5.3 - - - +
360B LYS* 5.6 6.9 + - - +
361B GLU* 4.1 21.2 - - - +
380B ASN* 4.5 4.6 + - - +
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Residues in contact with LEU 713 (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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630A LEU* 4.5 9.0 - - + -
633A ILE* 3.9 23.3 - - + -
701A TRP* 3.8 26.9 - - + +
704A PHE* 3.6 29.0 - - + -
705A SER* 3.3 26.5 - - - +
709A SER 3.1 17.0 + - - +
710A VAL* 3.7 7.6 - - + +
712A GLU* 1.3 75.3 - - - +
714A ILE* 1.3 57.3 + - - +
716A GLU* 3.1 2.6 + - + +
717A VAL* 2.9 50.2 + - + +
758A LEU* 4.5 13.7 - - + -
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Residues in contact with ILE 714 (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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630A LEU* 4.0 32.8 - - + -
710A VAL* 3.0 22.6 + - + +
711A SER* 3.5 7.4 - - - +
713A LEU* 1.3 75.2 - - - +
715A TRP* 1.3 58.3 + - - +
717A VAL* 3.3 6.7 + - - +
718A TYR* 2.9 62.8 + - + +
743A LEU* 4.0 18.4 - - + +
744A TYR* 4.1 13.7 - - + -
747A ALA* 3.7 30.7 - - + -
761A PHE* 4.5 2.0 - - + -
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Residues in contact with TRP 715 (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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711A SER 3.2 9.2 + - - +
712A GLU 3.0 9.0 + - - +
714A ILE* 1.3 81.9 - - - +
716A GLU* 1.3 63.0 + - - +
718A TYR* 3.2 13.1 + + + +
719A ARG* 2.7 60.2 + - + +
744A TYR* 4.2 21.1 - + + -
321B ARG* 4.4 19.7 - - + -
325B GLU* 6.2 0.2 - - - -
358B MET* 5.2 6.5 - - + -
361B GLU* 3.4 46.9 - - + +
362B VAL* 4.1 15.3 - - + -
365B ASP* 2.9 23.2 + - - -
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Residues in contact with GLU 716 (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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700A LYS* 5.5 9.1 - - + -
701A TRP* 5.0 5.8 - - + -
704A PHE* 3.9 39.3 - - + -
712A GLU 2.9 11.7 + - - +
713A LEU* 3.4 9.4 - - + +
715A TRP* 1.3 78.1 - - - +
717A VAL* 1.3 57.4 + - - +
719A ARG* 2.9 38.6 + - - +
720A ASP* 2.9 57.1 + - - +
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Residues in contact with VAL 717 (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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629A VAL* 3.8 27.4 - - + -
630A LEU* 4.8 5.6 - - + -
633A ILE* 3.9 27.1 - - + -
650A ILE* 5.7 0.9 - - + -
701A TRP* 4.0 20.4 - - + +
713A LEU* 2.9 28.4 + - + +
714A ILE* 3.6 7.0 - - - +
716A GLU* 1.3 74.6 - - - +
718A TYR* 1.3 63.6 + - + +
720A ASP* 4.5 0.2 - - - -
721A THR* 2.7 49.5 + - + +
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Residues in contact with TYR 718 (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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626A ALA* 4.5 9.6 - - + -
714A ILE* 2.9 36.7 + - + +
715A TRP* 3.2 16.8 + + + +
717A VAL* 1.3 87.0 - - + +
719A ARG* 1.3 56.6 + - - +
721A THR* 4.1 2.2 - - - -
722A LYS* 3.0 26.9 + - - -
723A TYR* 3.6 12.7 + + + +
724A MET* 4.2 30.9 + - + +
725A ASP* 5.2 1.6 - - - +
740A LEU* 2.6 65.8 + - + +
741A ARG* 4.8 0.9 - - - -
743A LEU* 3.5 17.7 - - + +
744A TYR* 4.7 6.7 - + + -
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Residues in contact with ARG 719 (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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715A TRP* 2.7 47.7 + - - +
716A GLU* 2.9 42.8 + - - +
718A TYR* 1.3 75.5 - - - +
720A ASP* 1.3 67.7 + - - +
722A LYS* 4.0 21.6 + - - +
725A ASP* 5.9 1.6 - - - -
361B GLU* 3.1 23.6 + - - -
364B ALA* 3.9 15.0 - - - +
365B ASP* 3.0 27.6 + - - +
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Residues in contact with ASP 720 (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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697A HIS* 4.0 29.7 + - + -
700A LYS* 5.0 5.5 - - - +
701A TRP* 3.1 30.9 + - + +
716A GLU* 2.9 42.0 + - - +
717A VAL 4.0 2.7 - - - +
718A TYR 3.4 0.2 - - - -
719A ARG* 1.3 83.7 - - - +
721A THR* 1.3 61.2 + - - +
722A LYS* 3.7 4.2 + - - +
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Residues in contact with THR 721 (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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650A ILE* 3.7 35.3 - - + +
697A HIS* 5.7 3.4 - - + +
701A TRP* 3.6 33.2 - - + -
717A VAL* 2.7 29.2 + - + +
718A TYR* 3.9 0.5 + - - -
720A ASP* 1.3 76.0 - - - +
722A LYS* 1.3 69.4 + - - +
723A TYR* 3.1 26.3 + - - +
726A TYR* 5.6 0.7 - - - +
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Residues in contact with LYS 722 (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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718A TYR 3.0 14.5 + - - -
719A ARG* 4.1 16.6 + - - +
720A ASP 3.3 4.4 + - - +
721A THR* 1.3 79.9 - - - +
723A TYR* 1.3 59.3 + - - +
724A MET 3.3 2.2 - - - -
725A ASP* 3.3 26.4 + - + +
726A TYR* 2.9 29.9 + - - +
719B LYS* 4.1 7.1 - - - +
720B SER* 4.1 19.0 + - - +
723B GLN* 3.3 28.7 - - - +
758B GLN* 4.2 22.3 - - - +
762B LEU* 4.1 19.2 - - + +
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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