Contacts of the helix formed by residues 752 - 767 (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 GLN 752 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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747H TYR* 3.4 22.2 + - + +
750H LEU* 3.3 19.5 + - + +
751H GLY* 1.3 73.2 - - - +
753H THR* 1.4 64.5 + - - +
754H HIS* 3.4 13.9 - - + -
755H LEU* 3.2 33.3 + - + +
756H ALA* 3.3 19.0 + - - +
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Residues in contact with THR 753 (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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748H LYS* 6.3 3.8 - - + +
751H GLY* 3.2 13.5 + - - +
752H GLN* 1.4 68.2 - - - +
754H HIS* 1.3 64.0 + - - +
756H ALA* 3.4 9.1 + - - +
757H LEU* 3.0 40.1 + - - +
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Residues in contact with HIS 754 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
752H GLN* 4.6 15.0 + - + +
753H THR* 1.3 83.7 + - - +
755H LEU* 1.3 90.5 + - + +
757H LEU* 3.4 9.3 + - - +
758H MET* 3.2 20.4 + - - +
428X VAL* 4.3 8.6 - - + +
432X ASN* 4.9 9.7 + - - +
435X LYS* 6.0 5.6 - - - -
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Residues in contact with LEU 755 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747H TYR* 3.4 38.4 - - + +
752H GLN* 3.2 32.8 + - - +
754H HIS* 1.3 116.6 - - + +
756H ALA* 1.3 66.1 + - - +
757H LEU 3.1 0.4 - - - -
758H MET* 3.5 8.1 + - + +
759H ASN* 3.2 24.1 + - - +
432X ASN* 6.1 1.1 - - - +
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Residues in contact with ALA 756 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744H GLY* 3.7 21.8 - - - +
747H TYR* 3.8 16.7 - - + +
748H LYS* 4.1 19.3 - - + +
752H GLN 3.3 7.8 + - - +
753H THR* 3.5 12.3 - - + +
755H LEU* 1.3 77.8 - - - +
757H LEU* 1.3 58.1 + - + +
759H ASN* 3.3 1.7 + - - +
760H PHE* 2.9 37.4 + - + -
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Residues in contact with LEU 757 (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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753H THR* 3.0 28.1 + - - +
754H HIS* 3.7 7.2 - - - +
755H LEU 3.1 0.4 - - - -
756H ALA* 1.3 75.4 - - + +
758H MET* 1.3 64.0 + - - +
760H PHE* 3.3 10.3 + - + +
761H SER* 2.9 25.3 + - - -
424X ARG* 3.6 35.0 - - - +
425X GLU* 6.6 0.2 - - - -
428X VAL* 3.9 31.2 - - + -
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Residues in contact with MET 758 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
754H HIS 3.2 13.7 + - - +
755H LEU* 3.8 10.8 - - + +
756H ALA 3.5 0.2 - - - -
757H LEU* 1.3 75.0 - - - +
759H ASN* 1.3 63.0 + - + +
761H SER* 3.5 6.0 + - - -
762H TRP* 3.2 42.0 + - + +
428X VAL* 4.1 5.3 - - - +
429X MET* 4.1 27.6 - - + +
432X ASN* 3.0 48.9 - - + +
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Residues in contact with ASN 759 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
730H LYS* 6.1 0.4 - - - +
740H TYR* 2.8 54.0 - - - +
743H ILE* 2.9 36.2 - - - +
744H GLY* 3.4 11.1 - - - +
747H TYR* 3.9 12.5 - - - -
755H LEU 3.2 11.5 + - - +
756H ALA 3.6 4.3 - - - +
757H LEU 3.2 0.2 - - - -
758H MET* 1.3 79.7 - - - +
760H PHE* 1.3 63.6 - - - +
762H TRP* 3.2 16.6 + - - +
763H ALA 3.4 8.3 + - - -
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Residues in contact with PHE 760 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741H PHE* 4.2 30.7 - + - +
744H GLY* 3.3 34.8 - - - -
745H LYS* 3.5 17.5 - - + -
748H LYS* 4.0 25.1 - - + -
756H ALA* 2.9 25.6 + - + +
757H LEU* 3.8 13.0 - - + +
759H ASN* 1.3 72.8 - - - +
761H SER* 1.3 65.8 + - - +
763H ALA* 3.3 16.1 + - - +
764H MET* 3.3 20.5 + - + +
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Residues in contact with SER 761 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757H LEU 2.9 16.1 + - - -
758H MET* 3.7 9.2 - - - -
759H ASN 3.2 0.2 - - - -
760H PHE* 1.3 77.5 - - - +
762H TRP* 1.3 50.0 + - - +
764H MET* 3.4 3.7 + - - +
765H ASP* 2.6 43.6 + - - +
425X GLU* 2.7 40.7 + - - +
428X VAL* 6.1 2.2 - - - -
429X MET* 4.3 16.6 - - - -
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Residues in contact with TRP 762 (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* 5.1 6.5 - - + -
740H TYR* 3.2 61.2 - + + -
758H MET* 3.2 34.0 + - + +
759H ASN* 3.2 13.1 + - - +
761H SER* 1.3 74.6 - - - +
763H ALA* 1.3 53.1 + - - +
765H ASP* 3.3 25.4 + - + +
766H LEU* 2.5 47.1 + - + +
400X ILE* 5.6 4.6 - - - +
401X ARG* 5.9 4.0 - - - +
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Residues in contact with ALA 763 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737H SER* 3.5 29.3 + - - +
740H TYR* 4.3 1.4 - - - +
741H PHE* 3.8 42.6 - - + +
759H ASN 3.4 3.4 + - - +
760H PHE 3.3 10.0 + - - +
762H TRP* 1.3 78.3 - - - +
764H MET* 1.3 62.2 + - + +
766H LEU* 3.1 2.9 + - - -
767H ASP* 3.1 24.8 + - - +
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Residues in contact with MET 764 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741H PHE* 5.7 7.9 - - - -
760H PHE* 3.3 17.2 + - + +
761H SER* 4.2 3.4 - - - +
763H ALA* 1.3 80.5 - - + +
765H ASP* 1.3 59.4 + - - +
767H ASP* 3.6 21.7 + - - +
425X GLU* 4.9 9.2 - - - +
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Residues in contact with ASP 765 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761H SER* 2.6 27.1 + - - +
762H TRP* 3.3 32.0 + - - +
764H MET* 1.3 71.8 - - - +
766H LEU* 1.3 61.6 + - - +
767H ASP 4.8 1.4 - - - -
397X ARG* 5.1 18.0 + - - +
400X ILE* 4.1 20.7 - - - +
413X LEU* 4.9 1.4 - - - +
417X TYR* 3.6 25.1 + - - +
425X GLU* 4.9 2.3 + - - -
429X MET* 5.1 5.5 - - - +
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Residues in contact with LEU 766 (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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735H LYS* 3.3 37.0 - - + +
737H SER* 3.6 21.3 - - - +
740H TYR* 3.6 34.3 - - + -
762H TRP* 2.5 23.7 + - + +
763H ALA 3.1 5.1 + - - +
765H ASP* 1.3 76.6 - - - +
767H ASP* 1.3 67.4 + - - +
173L THR* 5.7 5.5 - - - -
401X ARG* 4.6 18.4 - - - +
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Residues in contact with ASP 767 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737H SER* 5.1 4.2 + - - +
763H ALA 3.1 12.3 + - - +
764H MET* 3.6 17.9 + - - +
765H ASP 3.5 3.4 - - - -
766H LEU* 1.3 80.8 - - - +
173L THR* 6.1 4.0 - - - -
397X ARG* 5.5 9.0 + - - -
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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