Contacts of the helix formed by residues 703 - 709 (chain A) in PDB entry 4MSL
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 LEU 703 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644A PHE* 3.3 39.3 - - + +
645A GLY* 4.2 12.3 - - - +
646A TYR* 4.7 6.3 - - + +
657A GLU* 4.9 12.3 - - + +
661A LEU* 5.3 5.6 - - + -
669A CYS* 3.8 6.6 - - - -
677A LEU* 3.1 26.6 + - + +
679A THR* 3.9 12.3 - - + -
701A LYS* 4.9 11.2 - - + -
702A ASP* 1.3 78.1 + - - +
704A LYS* 1.3 64.4 + - - +
705A LYS 3.1 3.4 - - - -
706A LYS* 3.0 35.9 + - + +
707A CYS* 3.3 14.0 + - - -
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Residues in contact with LYS 704 (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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669A CYS* 4.7 1.6 - - - +
674A GLU* 5.3 12.5 - - - +
677A LEU* 3.7 35.5 - - + +
702A ASP* 3.1 35.1 + - - +
703A LEU* 1.3 77.0 - - - +
705A LYS* 1.3 55.4 + - + +
707A CYS* 3.1 23.2 - - - -
708A THR* 2.8 28.7 + - + +
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Residues in contact with LYS 705 (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 ASP* 3.8 17.7 + - - +
703A LEU 3.1 0.2 - - - -
704A LYS* 1.3 83.4 - - + +
706A LYS* 1.3 56.6 + - - +
708A THR* 3.1 7.7 + - - +
709A SER* 2.7 42.3 + - - -
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Residues in contact with LYS 706 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645A GLY 5.3 0.8 + - - -
657A GLU* 2.7 31.7 + - - +
658A GLN* 2.2 31.6 + - - +
659A PRO* 3.2 22.9 + - - +
660A GLU* 3.4 28.4 - - - +
661A LEU* 4.8 12.7 - - + +
702A ASP 4.7 1.3 + - - +
703A LEU* 3.0 28.8 + - + +
705A LYS* 1.3 83.7 - - - +
707A CYS* 1.3 57.9 + - - +
709A SER* 3.1 22.1 - - - -
710A ASN* 4.2 0.3 + - - -
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Residues in contact with CYS 707 (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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660A GLU* 4.3 7.2 - - - -
661A LEU* 4.5 1.8 - - + +
666A LEU* 4.4 8.5 - - + +
669A CYS* 2.0 61.2 - - + -
670A LEU* 4.1 12.6 - - + -
703A LEU 3.3 5.1 + - - -
704A LYS* 3.1 22.7 - - - -
706A LYS* 1.3 75.5 - - - +
708A THR* 1.3 66.6 + - - +
709A SER 3.0 5.9 + - - -
710A ASN* 3.5 10.7 + - - -
711A PHE* 3.3 19.0 - - - -
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Residues in contact with THR 708 (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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670A LEU* 5.3 7.9 - - + -
704A LYS* 2.8 25.0 + - + +
705A LYS* 3.1 11.3 + - - +
707A CYS* 1.3 77.3 - - + +
709A SER* 1.3 64.3 + - - +
710A ASN 3.1 2.1 + - - -
711A PHE* 3.1 34.1 + - + +
713A SER* 4.6 9.3 + - - -
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Residues in contact with SER 709 (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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660A GLU* 5.3 1.3 + - - -
705A LYS* 2.7 24.5 + - - -
706A LYS* 3.1 21.8 - - - -
707A CYS 3.0 0.2 - - - -
708A THR* 1.3 77.5 - - - +
710A ASN* 1.3 66.5 + - - +
711A PHE 3.9 4.2 - - - +
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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