Contacts of the helix formed by residues 80 - 84 (chain C) in PDB entry 5EGU
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 ALA 80 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74C LEU 3.4 16.6 - - - +
75C TRP 3.2 23.1 - - - +
77C HIS* 3.0 19.5 + - - +
78C GLN 3.3 0.4 - - - -
79C PHE* 1.3 78.3 - - - +
81C TRP* 1.3 65.3 + - - +
82C PRO 3.3 0.4 - - - -
83C PHE* 2.8 19.8 + - - +
84C GLN* 3.4 16.9 - - - +
107C MET* 3.9 11.7 - - + -
153C LEU* 4.4 5.2 - - - -
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Residues in contact with TRP 81 (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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78B GLN 5.1 3.1 - - - +
81B TRP* 3.3 82.7 - + + +
84B GLN* 5.5 1.2 + - - -
201B 5NQ 4.0 36.1 - - + -
77C HIS 4.9 0.2 + - - -
78C GLN 3.9 17.6 + - - -
80C ALA* 1.3 77.1 - - - +
82C PRO* 1.3 107.0 - - + +
83C PHE 3.1 0.7 + - - -
84C GLN* 3.5 20.2 + - - +
85C GLN* 3.0 20.6 + - - +
92C LEU* 4.5 10.1 - - + -
149C MET* 3.7 13.6 - - + +
201C 5NQ 4.0 21.5 - - + +
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Residues in contact with PRO 82 (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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79C PHE 3.3 14.8 - - - +
80C ALA 3.4 1.3 - - - +
81C TRP* 1.3 123.1 - - + +
83C PHE* 1.3 62.1 + - + +
85C GLN* 3.3 11.5 + - - +
87C VAL* 5.2 0.7 - - - +
146C ILE* 3.4 34.1 - - + -
149C MET* 3.6 8.7 - - + -
201C 5NQ 3.2 40.6 - - + +
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Residues in contact with PHE 83 (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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79C PHE 3.5 25.6 - - - -
80C ALA 2.8 7.4 + - - +
82C PRO* 1.3 87.6 - - + +
84C GLN* 1.3 59.9 + - - +
85C GLN 3.3 4.8 + - - -
106C ASP* 3.7 3.8 - - - +
107C MET* 2.8 40.2 + - + +
132C MET* 3.9 33.9 - - + -
133C PHE* 5.7 1.6 - + - -
136C CYS* 4.3 15.3 - - + -
146C ILE* 3.9 20.9 - - + -
149C MET* 4.6 2.5 - - + -
150C ALA* 4.0 28.0 - - + -
153C LEU* 3.5 19.3 - - + -
201C 5NQ 3.4 21.5 - - + -
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Residues in contact with GLN 84 (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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78B GLN* 4.8 13.1 + - - +
75C TRP* 3.0 84.3 + - + +
80C ALA* 3.4 23.3 - - + +
81C TRP* 3.5 23.5 + - - +
83C PHE* 1.3 79.6 - - - +
85C GLN* 1.3 70.2 + - - +
107C MET* 4.3 1.8 - - + -
108C GLY* 3.4 13.4 - - - -
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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