Contacts of the helix formed by residues 711 - 715 (chain B) in PDB entry 4MS0
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 ILE 711 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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768A GLY 5.0 4.7 - - - +
770A GLU 5.9 0.2 - - - +
709B GLN 3.9 0.2 + - - -
710B PRO* 1.3 76.2 - - - +
712B PRO* 1.4 77.5 - - + +
713B MET* 3.9 27.1 - - + +
714B MET* 2.9 43.7 + - + -
715B ASP 3.4 5.4 + - - -
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Residues in contact with PRO 712 (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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768A GLY 3.6 20.6 - - - +
769A GLU* 4.1 17.5 - - + +
770A GLU 4.1 6.5 - - - +
771A THR* 3.9 18.3 - - + +
697B TRP* 5.0 0.3 + - - -
710B PRO 4.2 2.7 - - - +
711B ILE* 1.4 87.4 - - + +
713B MET* 1.3 62.2 + - - +
715B ASP* 3.0 29.4 + - + +
718B LYS* 3.9 27.0 - - + +
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Residues in contact with MET 713 (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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770A GLU* 3.5 37.0 + - + +
771A THR* 3.4 33.0 - - - +
772A ALA* 3.5 15.1 + - - +
773A THR* 5.2 2.9 - - - +
693B TYR* 4.9 1.6 - - - -
696B PHE* 3.5 44.8 - - + +
697B TRP* 3.9 8.2 + - - -
711B ILE* 3.0 26.9 + - + -
712B PRO* 1.3 78.9 - - - +
714B MET* 1.3 66.9 + - + +
715B ASP 3.4 0.4 + - - -
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Residues in contact with MET 714 (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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696B PHE* 3.5 47.6 - - + +
697B TRP* 3.6 10.8 - - - +
699B GLU* 3.5 35.9 - - + +
700B GLY* 3.1 31.8 - - - -
703B MET* 6.1 1.6 - - + -
704B LYS* 4.5 0.7 + - - -
710B PRO* 3.9 8.5 - - + -
711B ILE* 2.9 35.9 + - + +
713B MET* 1.3 81.4 - - + +
715B ASP* 1.3 59.0 + - - +
716B ARG 3.8 0.7 + - - -
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Residues in contact with ASP 715 (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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697B TRP* 3.5 7.9 + - - -
704B LYS* 3.0 20.0 + - - +
709B GLN* 2.6 30.7 + - - -
710B PRO* 4.1 6.5 - - + +
711B ILE 3.7 8.7 - - - +
712B PRO* 3.0 19.9 + - + +
713B MET 3.4 1.2 + - - -
714B MET* 1.3 76.3 - - - +
716B ARG* 1.3 60.4 + - - +
717B ASP* 3.0 28.1 + - - +
718B LYS* 2.9 38.5 + - + +
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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