Contacts of the helix formed by residues 854 - 858 (chain C) in PDB entry 5D4D
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 PRO 854 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30B ARG* 3.3 46.2 - - + +
31B GLY* 6.1 2.5 - - - -
692C GLU* 3.9 12.1 - - - +
852C ILE 4.0 5.4 - - - +
853C LEU* 1.3 94.3 - - + +
855C VAL* 1.3 66.7 + - - +
856C GLU* 3.1 21.1 - - - +
857C ASP* 2.9 34.2 + - - +
858C MET* 3.8 3.6 + - - +
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Residues in contact with VAL 855 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ARG* 4.8 2.4 + - - -
45A LEU* 4.3 35.2 - - + +
691C SER* 4.3 2.9 - - - -
692C GLU* 4.7 4.0 - - - +
693C GLU* 3.6 28.7 - - + +
696C LYS* 3.5 21.9 - - - +
853C LEU 3.8 1.4 + - - -
854C PRO* 1.3 70.5 - - - +
856C GLU* 1.3 72.5 + - - +
857C ASP 3.2 0.9 + - - -
858C MET* 3.3 25.2 + - - +
866C PRO* 3.7 31.6 - - + +
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Residues in contact with GLU 856 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ARG* 4.0 5.5 + - - +
42A ARG* 3.2 53.5 + - + +
45A LEU* 4.2 17.2 - - + +
46A SER* 3.6 28.0 + - - +
30B ARG* 4.5 14.2 + - - +
31B GLY* 5.1 1.4 - - - -
854C PRO* 3.4 22.9 - - - +
855C VAL* 1.3 89.2 + - - +
857C ASP* 1.3 68.8 + - - +
858C MET 3.5 0.2 - - - -
977C GLY* 3.2 20.0 - - - +
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Residues in contact with ASP 857 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ARG* 2.5 40.8 + - - +
31B GLY* 5.6 2.0 - - - -
34B VAL* 5.4 1.4 - - - +
679C PHE* 4.1 6.5 - - + -
853C LEU* 4.3 23.8 - - + +
854C PRO* 2.9 25.5 + - - +
856C GLU* 1.3 80.0 - - - +
858C MET* 1.3 65.9 + - - +
859C PRO* 3.6 5.2 - - - +
976C ASP* 4.5 0.2 - - - +
977C GLY* 4.1 6.8 + - - -
978C ARG* 3.9 29.7 - - - +
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Residues in contact with MET 858 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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689C VAL* 5.1 0.2 - - - -
690C ILE 4.4 2.2 - - - -
691C SER* 3.5 41.3 - - - +
853C LEU* 3.8 25.8 - - - -
854C PRO 4.0 6.3 - - - +
855C VAL* 3.3 18.0 + - - +
856C GLU 4.5 0.3 - - - +
857C ASP* 1.3 80.7 - - - +
859C PRO* 1.3 75.2 - - - +
860C HIS* 3.4 17.5 + - - +
866C PRO* 4.0 8.3 - - + -
867C VAL* 3.1 38.4 - - + +
868C ASP 3.9 7.9 - - - +
870C ILE* 3.9 20.9 - - + -
977C GLY* 3.6 4.0 + - - -
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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