Contacts of the helix formed by residues 754 - 763 (chain M) in PDB entry 3HOU
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 754 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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747M VAL* 3.9 16.4 - - - +
753M GLY* 1.3 74.5 - - - -
755M PHE* 1.3 70.1 + - - +
756M ILE* 3.7 12.1 + - - +
757M ASN* 2.8 30.9 + - - +
758M ILE* 3.4 8.4 + - - +
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Residues in contact with PHE 755 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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727M ASP* 3.5 41.1 - - + -
730M GLY* 3.8 9.6 - - - -
731M ARG* 3.4 30.7 - - + -
734M GLU* 3.3 42.4 + - + +
747M VAL* 4.7 3.6 - - - +
754M SER* 1.3 75.1 - - - +
756M ILE* 1.3 89.6 + - + +
757M ASN 2.7 2.3 + - - -
758M ILE* 2.8 20.3 + - + +
759M ALA* 3.0 15.2 + - + -
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Residues in contact with ILE 756 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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726M ARG* 4.1 31.0 - - - +
727M ASP* 5.9 0.4 - - - +
754M SER* 3.5 8.8 + - - +
755M PHE* 1.3 93.7 - - + +
757M ASN* 1.3 63.5 + - - +
759M ALA* 3.0 11.5 - - + +
760M GLN* 2.9 55.0 + - + +
1021N MET* 5.2 0.4 - - + -
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Residues in contact with ASN 757 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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743M VAL* 6.1 1.3 - - + -
747M VAL* 6.2 0.2 - - + -
753M GLY* 3.5 9.0 - - - -
754M SER* 2.8 43.9 + - - +
755M PHE 2.7 4.4 + - - -
756M ILE* 1.3 74.1 - - - +
758M ILE* 1.3 67.5 + - + +
759M ALA 3.0 1.6 + - - -
760M GLN 3.4 0.3 + - - -
761M MET* 3.1 32.4 + - + +
1018N PRO* 3.6 22.4 - - + +
1019N SER* 3.7 14.6 - - - +
1021N MET* 3.2 26.7 - - - +
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Residues in contact with ILE 758 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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733M ALA* 5.2 2.5 - - + +
734M GLU* 4.4 37.9 - - + +
737M LEU* 3.4 33.4 - - + -
743M VAL* 4.2 20.6 - - + -
744M LYS* 4.9 11.0 - - + -
747M VAL* 4.1 22.7 - - + -
754M SER 3.7 11.2 - - - +
755M PHE* 2.8 10.1 + - - +
757M ASN* 1.3 73.5 - - + +
759M ALA* 1.3 62.4 + - - +
761M MET* 4.6 8.9 - - - +
762M SER* 3.1 31.4 + - - +
763M ALA* 4.1 0.5 + - - +
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Residues in contact with ALA 759 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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726M ARG* 5.7 5.6 - - + +
727M ASP* 6.3 0.7 - - - -
730M GLY* 4.3 19.7 - - - -
733M ALA* 6.2 0.4 - - - -
755M PHE* 3.0 17.0 + - + +
756M ILE* 3.0 24.5 - - + +
757M ASN 3.0 0.4 - - - -
758M ILE* 1.3 72.7 - - - +
760M GLN* 1.3 61.2 + - + +
761M MET 2.9 5.3 + - - -
763M ALA* 2.7 37.7 + - + -
764M CYS 3.3 9.8 + - - +
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Residues in contact with GLN 760 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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726M ARG* 5.6 2.3 - - - +
756M ILE* 2.9 37.2 + - + +
759M ALA* 1.3 78.6 - - + +
761M MET* 1.3 57.3 + - - +
763M ALA 4.8 0.7 - - - -
764M CYS 3.9 9.4 - - - +
765M VAL* 3.1 44.0 + - - +
768M GLN* 5.6 2.8 - - - +
803M SER* 3.9 0.8 - - - -
804M TYR* 2.9 48.9 + - + -
816M HIS* 6.1 0.8 + - - -
1021N MET* 3.3 29.1 - - - +
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Residues in contact with MET 761 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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669M THR* 3.5 25.1 - - + +
743M VAL* 4.2 26.7 - - + -
757M ASN* 3.1 23.7 + - + +
758M ILE* 3.9 4.7 - - - +
759M ALA 2.9 1.2 + - - -
760M GLN* 1.3 80.8 - - - +
762M SER* 1.3 63.5 + - - +
803M SER* 3.7 0.2 - - - -
804M TYR* 3.5 8.2 + - + -
805M LEU* 3.0 33.4 + - - +
1017N ILE* 5.1 9.0 - - + +
1018N PRO* 4.2 16.2 - - + +
1021N MET* 3.6 32.1 - - + -
1022N THR 5.2 0.4 - - - -
1023N VAL* 3.7 26.1 - - + +
1026N LEU* 5.8 0.4 - - - -
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Residues in contact with SER 762 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668M ASP 5.0 0.5 + - - -
669M THR* 2.7 35.1 + - - +
671M ALA* 4.6 7.0 - - - -
676M MET* 2.9 31.4 - - - +
679M ILE* 4.5 0.9 - - - +
733M ALA* 4.5 14.1 - - - -
737M LEU* 5.3 3.9 - - - +
758M ILE* 3.1 22.9 + - - +
761M MET* 1.3 83.0 - - - +
763M ALA* 1.3 60.0 + - - +
803M SER* 3.6 8.6 - - - -
805M LEU* 4.8 1.1 - - - -
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Residues in contact with ALA 763 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676M MET* 5.6 1.7 - - - +
679M ILE* 4.2 19.2 - - + +
683M ILE* 4.8 1.0 - - - +
729M ALA* 3.4 36.8 - - + +
730M GLY* 3.7 10.8 - - - +
733M ALA* 4.4 4.7 - - + -
759M ALA* 2.7 17.2 + - + +
762M SER* 1.3 74.3 - - - +
764M CYS* 1.3 65.3 + - - +
801M GLU 4.2 2.6 - - - +
803M SER* 3.4 16.8 + - - -
806M ARG* 5.8 0.5 - - - -
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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