Contacts of the helix formed by residues 706 - 710 (chain B) in PDB entry 5M64
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 PHE 706 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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704B THR 3.5 1.2 + - - -
705B PRO* 1.3 74.1 - - - +
707B SER* 1.3 64.6 - - - +
708B ASP 3.0 3.6 - - - +
709B PHE* 3.0 41.8 + + + +
710B ASN* 3.7 9.5 + - - -
961B GLY* 5.2 1.7 - - - -
964B VAL* 3.6 43.7 - - + -
965B GLU* 3.1 25.1 - - + -
968B ALA* 4.7 0.9 - - + -
980B ASP 5.4 1.1 - - - -
981B SER* 3.7 27.1 - - - -
983B PRO* 4.9 14.1 - - + +
985B ILE* 4.7 5.4 - - + -
986B PHE* 3.5 35.2 - + - -
996B PHE* 4.0 15.3 - + - -
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Residues in contact with SER 707 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
995A TYR* 3.3 29.0 + - - -
697B LEU* 5.1 7.2 - - - -
701B ALA* 2.7 34.2 + - - -
704B THR* 2.8 27.1 + - - -
705B PRO 3.3 1.1 - - - -
706B PHE* 1.3 75.6 - - - +
708B ASP* 1.3 65.2 + - - +
709B PHE 3.5 0.3 + - - -
710B ASN* 3.8 12.6 + - - +
715B ASN* 4.2 10.2 + - - +
983B PRO* 4.6 8.4 - - - +
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Residues in contact with ASP 708 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
986A PHE* 3.6 10.2 - - - -
989A GLY* 6.1 1.1 - - - -
990A ILE* 3.4 24.3 - - + +
995A TYR* 4.1 13.7 - - - -
697B LEU* 5.2 2.1 - - - +
706B PHE 3.0 0.4 - - - -
707B SER* 1.3 83.0 - - - +
709B PHE* 1.3 71.0 + - + +
710B ASN 3.3 6.6 + - - +
983B PRO* 3.3 11.5 - - - +
984B TRP* 3.0 80.3 + - + -
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Residues in contact with PHE 709 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
986A PHE* 3.0 33.7 - - - -
987A TYR* 4.3 9.2 - - - -
988A SER 4.7 0.4 - - - -
989A GLY* 3.9 29.2 - - - -
706B PHE* 3.0 48.4 + + + +
708B ASP* 1.3 90.6 - - + +
710B ASN* 1.3 69.6 + - - +
958B MET* 5.6 0.3 - - - +
960B ILE* 3.2 31.0 - - + +
961B GLY* 3.6 1.3 + - - -
964B VAL* 4.6 13.0 - - + -
983B PRO* 6.2 0.7 - - + -
984B TRP 5.8 3.1 - - - -
986B PHE* 4.3 27.6 - + + -
992B PRO* 4.4 11.7 - - + -
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Residues in contact with ASN 710 (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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986A PHE* 4.2 15.6 - - - -
995A TYR* 4.9 4.7 - - - -
998A HIS* 4.5 1.6 + - - -
704B THR* 4.9 3.4 - - - +
706B PHE 3.7 15.4 + - - -
707B SER* 3.8 14.9 + - - +
708B ASP 3.3 8.3 - - - +
709B PHE* 1.3 89.5 - - - +
711B GLN* 1.3 70.5 + - - +
714B ARG* 4.7 3.1 - - + -
715B ASN* 4.4 7.4 + - - +
921B HIS* 3.9 43.8 + - - +
958B MET* 4.8 9.0 - - - +
959B THR* 4.2 7.0 - - - -
960B ILE 4.2 3.8 + - - -
961B GLY* 3.1 21.2 + - - -
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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