Contacts of the helix formed by residues 736 - 751 (chain H) in PDB entry 5A31
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 GLU 736 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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733H VAL* 3.3 28.3 + - + +
734H PRO 3.3 4.1 - - - +
735H LYS* 1.3 75.2 - - - +
737H SER* 1.3 66.9 + - - +
738H LEU* 3.3 27.7 + - + +
739H VAL* 3.5 27.0 + - + +
740H TYR* 3.7 11.8 + - - -
766H LEU* 3.9 0.9 - - - -
172L CYS* 3.5 19.8 - - - -
173L THR 2.3 31.8 + - - +
174L THR* 3.8 3.4 - - - -
177L PHE* 3.5 35.0 - - + +
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Residues in contact with SER 737 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735H LYS 3.4 3.4 + - - -
736H GLU* 1.3 73.6 + - - +
738H LEU* 1.3 67.0 + - - +
740H TYR* 3.2 5.9 + - - +
741H PHE* 3.0 21.7 + - - +
763H ALA* 3.5 22.2 + - - +
766H LEU* 3.6 27.1 - - - -
767H ASP* 5.2 3.7 - - - +
171L ARG 4.5 12.6 + - - -
173L THR* 4.7 14.4 - - - -
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Residues in contact with LEU 738 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704H LEU* 6.1 0.4 - - + -
707H PHE* 3.3 39.0 - - + -
736H GLU* 3.3 16.5 + - + +
737H SER* 1.3 81.7 + - - +
739H VAL* 1.3 51.3 - - - +
741H PHE* 3.6 9.7 - - + +
742H LEU* 2.7 34.3 + - + +
166L ILE* 5.9 4.9 - - + -
167L GLY* 6.2 1.8 - - - +
169L PHE* 3.3 45.3 - - + +
170L PRO 4.8 5.4 - - - +
171L ARG 4.5 9.3 + - - +
172L CYS* 5.9 2.7 - - - -
177L PHE* 3.9 24.2 - - + -
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Residues in contact with VAL 739 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707H PHE* 4.6 7.0 - - + -
726H LEU* 4.1 12.9 - - + +
729H LEU* 3.6 29.6 - - + -
730H LYS* 3.9 22.9 - - + +
733H VAL* 4.5 7.2 - - + +
736H GLU* 3.5 30.9 + - + +
737H SER 3.2 0.4 - - - -
738H LEU* 1.3 76.7 - - - +
740H TYR* 1.3 60.0 + - + +
742H LEU* 3.2 2.6 + - - +
743H ILE* 2.9 49.1 + - + +
177L PHE* 4.3 9.0 - - + -
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Residues in contact with TYR 740 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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730H LYS* 3.2 40.7 - - + +
734H PRO* 3.2 31.9 + - - +
736H GLU 3.7 7.5 + - - -
737H SER 3.2 5.8 + - - +
739H VAL* 1.3 79.9 - - + +
741H PHE* 1.3 62.0 + - - +
743H ILE* 3.1 5.0 + - + -
744H GLY 2.9 13.3 + - - -
759H ASN* 2.8 45.8 - - - +
762H TRP* 3.2 51.5 - + + -
763H ALA 4.3 2.9 - - - +
766H LEU* 3.6 27.8 - - + -
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Residues in contact with PHE 741 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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737H SER* 3.0 15.4 + - - +
738H LEU* 3.6 9.9 - - + +
740H TYR* 1.3 76.3 - - - +
742H LEU* 1.3 68.2 + - - +
744H GLY* 3.3 3.8 + - - -
745H LYS* 3.1 59.4 + - + +
759H ASN 4.7 1.8 - - - -
760H PHE* 4.2 28.3 - + - -
763H ALA* 3.8 23.1 - - + +
764H MET* 5.7 8.1 - - - -
169L PHE* 4.6 21.8 - - + -
170L PRO 5.2 12.1 - - - +
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Residues in contact with LEU 742 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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707H PHE* 3.3 35.2 - - + -
710H ALA* 4.7 7.6 - - + +
711H SER* 4.1 25.8 - - - +
714H PHE* 4.8 11.7 - - + -
726H LEU* 3.3 31.4 - - + -
738H LEU* 2.7 22.4 + - + +
739H VAL 3.7 3.4 - - - +
741H PHE* 1.3 79.3 - - + +
743H ILE* 1.3 63.3 + - - +
745H LYS* 3.1 17.9 + - + +
746H VAL* 3.1 18.0 + - + -
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Residues in contact with ILE 743 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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723H LEU* 3.8 21.3 - - + -
726H LEU* 3.5 36.3 - - + +
727H GLU* 4.8 3.4 - - + +
730H LYS* 4.0 29.6 - - + +
739H VAL* 2.9 34.5 + - + +
740H TYR* 3.1 4.7 + - + +
742H LEU* 1.3 75.4 - - - +
744H GLY* 1.3 62.1 + - - +
746H VAL* 3.1 12.4 + - - +
747H TYR* 3.1 21.7 + - + +
759H ASN* 2.9 31.7 + - - +
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Residues in contact with GLY 744 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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740H TYR 2.9 10.9 + - - -
741H PHE 3.6 0.7 - - - -
742H LEU 3.3 0.2 - - - -
743H ILE* 1.3 75.4 - - - +
745H LYS* 1.3 62.1 + - - +
747H TYR* 3.2 2.9 + - - -
748H LYS* 3.2 17.8 + - - +
756H ALA* 3.7 10.8 - - - +
759H ASN* 3.4 17.1 - - - +
760H PHE* 3.3 31.8 - - - -
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Residues in contact with LYS 745 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714H PHE* 3.6 27.0 - - + -
741H PHE* 3.1 46.1 + - + +
742H LEU* 3.1 14.2 + - + +
744H GLY* 1.3 71.7 - - - +
746H VAL* 1.3 65.9 + - - +
748H LYS* 3.3 19.8 + - + +
749H LYS* 3.4 10.2 + - - +
760H PHE* 3.5 14.7 - - + -
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Residues in contact with VAL 746 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714H PHE* 3.6 18.1 - - + -
719H TYR* 4.1 25.0 - - + +
722H ALA* 4.5 6.3 - - + -
723H LEU* 3.3 32.1 - - + -
726H LEU* 3.6 31.6 - - + -
742H LEU* 3.1 17.6 + - + +
743H ILE 3.1 7.2 + - - +
745H LYS* 1.3 73.7 - - - +
747H TYR* 1.3 57.7 + - - +
749H LYS* 3.2 8.2 + - - +
750H LEU* 2.9 25.5 + - + +
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Residues in contact with TYR 747 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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723H LEU* 3.4 38.0 - - + +
727H GLU* 4.6 10.0 + - - -
743H ILE* 3.1 18.2 + - + +
744H GLY 3.7 6.5 - - - +
745H LYS 3.2 0.4 - - - -
746H VAL* 1.3 78.1 - - - +
748H LYS* 1.3 53.6 + - - +
750H LEU* 2.9 19.1 + - + +
751H GLY 2.6 32.9 + - - -
752H GLN* 3.4 22.6 + - - +
755H LEU* 3.4 52.3 - - + +
756H ALA* 3.8 15.9 - - + +
759H ASN* 3.9 15.9 - - - -
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Residues in contact with LYS 748 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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744H GLY 3.2 12.0 + - - +
745H LYS* 3.3 15.5 + - + +
747H TYR* 1.3 73.4 - - - +
749H LYS* 1.3 59.9 + - + +
751H GLY* 3.1 20.0 + - - -
752H GLN 6.0 0.2 - - - -
753H THR* 6.3 3.6 - - + +
756H ALA* 4.1 15.0 - - + +
760H PHE* 4.0 26.0 - - + -
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Residues in contact with LYS 749 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714H PHE* 4.1 19.7 - - + -
719H TYR* 3.3 49.5 - - + +
745H LYS 3.4 10.7 + - - +
746H VAL 3.2 7.5 + - - +
747H TYR 3.2 0.2 - - - -
748H LYS* 1.3 79.3 - - + +
750H LEU* 1.3 60.8 + - - +
751H GLY* 3.4 0.5 + - - -
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Residues in contact with LEU 750 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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719H TYR* 3.9 31.9 - - + -
720H LYS* 5.6 1.6 - - - +
723H LEU* 3.8 29.8 - - + -
746H VAL* 2.9 16.9 + - + +
747H TYR* 2.9 25.0 + - + +
749H LYS* 1.3 75.3 - - - +
751H GLY* 1.3 59.2 + - - +
752H GLN* 3.3 19.9 + - + +
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Residues in contact with GLY 751 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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747H TYR 2.6 11.6 + - - -
748H LYS* 3.1 14.8 + - - -
749H LYS 3.2 1.5 - - - -
750H LEU* 1.3 73.8 - - - +
752H GLN* 1.3 56.2 + - - -
753H THR* 3.2 19.6 + - - +
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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