Contacts of the helix formed by residues 713 - 722 (chain A) in PDB entry 1MUK
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 ASP 713 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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711A THR* 3.2 15.6 + - - +
712A ASP* 1.3 73.8 - - - +
714A PRO* 1.3 72.5 - - - +
715A ASP* 3.2 24.6 + - - +
716A VAL* 3.2 23.9 + - + +
717A LEU* 2.9 24.0 + - - +
755A ASN* 4.1 12.2 + - - -
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Residues in contact with PRO 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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712A ASP 3.0 12.1 - - - +
713A ASP* 1.3 85.6 - - - +
715A ASP* 1.3 61.1 + - - +
717A LEU* 3.3 8.1 + - + +
718A ARG* 2.9 51.1 + - - +
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Residues in contact with ASP 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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713A ASP* 3.2 12.4 + - - +
714A PRO* 1.3 76.3 - - - +
716A VAL* 1.3 61.6 + - - +
718A ARG* 3.0 19.1 + - - +
719A LEU* 2.9 26.0 + - - +
752A THR* 3.6 31.2 + - + +
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Residues in contact with VAL 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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711A THR* 4.1 7.4 - - + +
713A ASP* 3.2 31.2 + - + +
715A ASP* 1.3 75.4 - - + +
717A LEU* 1.3 61.4 + - - +
719A LEU* 3.8 1.8 - - - +
720A MET* 3.0 51.2 + - + +
752A THR* 3.9 15.9 - - + +
755A ASN* 3.7 28.9 - - + +
756A ASP* 4.2 10.5 - - + -
759A LEU* 3.9 15.9 - - + -
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Residues in contact with LEU 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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708A PRO* 3.7 37.9 - - + +
711A THR* 3.9 18.6 - - + +
712A ASP* 3.7 36.8 - - - +
713A ASP 2.9 14.6 + - - +
714A PRO* 3.6 7.2 - - + +
716A VAL* 1.3 77.9 - - - +
718A ARG* 1.3 61.6 + - + +
720A MET* 3.8 5.0 - - - +
721A LYS* 3.1 24.8 + - - +
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Residues in contact with ARG 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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714A PRO* 2.9 38.2 + - - +
715A ASP* 3.0 20.5 + - - +
717A LEU* 1.3 74.8 - - - +
719A LEU* 1.3 68.3 + - - +
721A LYS* 3.2 8.0 + - - +
722A SER* 3.1 21.4 + - - -
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Residues in contact with LEU 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 ASP 2.9 14.6 + - - +
716A VAL 3.8 3.8 - - - +
718A ARG* 1.3 75.8 - - - +
720A MET* 1.3 66.5 + - - +
722A SER* 2.7 30.1 + - - +
723A LEU* 3.4 16.5 - - + +
740A ILE* 4.0 26.2 - - + -
748A VAL* 3.9 22.4 - - + -
752A THR* 4.0 18.4 - - + +
753A ILE* 3.9 35.2 - - + -
756A ASP* 3.8 22.0 - - + +
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Residues in contact with MET 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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702A PHE* 3.6 11.9 - - + -
703A LEU* 3.9 38.9 - - + +
707A GLY* 3.7 30.5 - - - +
708A PRO* 3.8 9.6 - - + -
711A THR* 4.8 2.2 - - - -
716A VAL* 3.0 44.2 + - + +
717A LEU* 3.8 6.1 - - + +
719A LEU* 1.3 78.8 - - - +
721A LYS* 1.3 64.5 + - - +
723A LEU* 3.0 30.2 + - - +
756A ASP* 3.2 27.5 + - - +
759A LEU* 3.8 10.1 - - + -
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Residues in contact with LYS 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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703A LEU 5.5 2.0 - - - -
717A LEU 3.1 16.0 + - - +
718A ARG* 3.2 7.2 + - - +
720A MET* 1.3 79.4 - - - +
722A SER* 1.3 57.3 + - - +
723A LEU 3.1 9.5 + - - +
724A THR* 5.0 1.9 + - - -
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Residues in contact with SER 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 ARG 3.1 9.7 + - - -
719A LEU* 2.7 32.3 + - - +
721A LYS* 1.3 75.6 - - - +
723A LEU* 1.3 63.1 + - - +
724A THR* 5.4 0.6 - - - -
728A ASN* 3.5 13.7 + - - +
740A ILE* 6.0 0.2 - - - +
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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