Contacts of the helix formed by residues 85 - 90 (chain A) in PDB entry 2HUE
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 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A GLY 4.0 9.4 - - - +
47A SER* 4.3 0.7 - - - -
53A HIS* 3.9 35.0 - - + +
83A LEU 3.9 6.1 - - - +
84A ILE* 1.3 88.5 - - + +
86A ALA* 1.3 67.3 + - - +
87A SER* 3.1 5.2 - - - +
88A GLU* 2.8 42.8 + - + +
89A LEU 3.2 8.5 + - - -
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Residues in contact with ALA 86 (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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84A ILE 3.0 7.3 + - - +
85A PRO* 1.3 69.9 - - - +
87A SER* 1.3 59.2 + - - +
88A GLU 3.3 1.0 + - - -
89A LEU* 3.4 21.5 + - - +
90A VAL* 4.6 1.9 + - - +
128A ALA 4.9 9.4 - - - +
130A VAL* 3.9 27.1 - - + +
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Residues in contact with SER 87 (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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49A ARG* 4.9 11.6 + - - -
85A PRO* 2.9 4.4 + - - +
86A ALA* 1.3 78.0 - - - +
88A GLU* 1.3 72.5 + - - +
89A LEU 3.5 0.2 - - - -
90A VAL 5.3 1.3 + - - -
91A SER* 4.9 5.7 + - - -
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Residues in contact with GLU 88 (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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46A GLY 4.1 12.8 - - - +
47A SER* 2.6 33.3 + - - -
48A SER* 3.4 17.0 + - - -
49A ARG* 3.8 28.3 + - - +
84A ILE* 4.3 3.4 - - - +
85A PRO* 2.8 25.7 + - + +
87A SER* 1.3 89.3 + - - +
89A LEU* 1.3 64.2 + - - +
90A VAL 3.6 0.9 - - - -
91A SER* 2.8 27.7 + - - +
92A VAL 5.2 0.7 - - - +
93A THR* 5.7 2.6 - - - -
122B LYS* 6.0 1.1 - - - +
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Residues in contact with LEU 89 (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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18A PHE* 3.6 23.0 - - + -
44A TYR* 4.9 1.5 + - - +
81A ALA* 4.1 22.0 - - + +
84A ILE* 3.5 38.4 - - + -
85A PRO 3.2 8.0 + - - +
86A ALA* 3.4 16.3 + - - +
88A GLU* 1.3 79.0 - - - +
90A VAL* 1.3 60.2 + - + +
91A SER 3.1 5.6 + - - -
115A ASN* 3.6 19.1 + - - +
130A VAL* 3.5 37.7 - - + -
132A VAL* 4.4 0.7 - - + -
135A ILE* 4.1 16.3 - - + +
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Residues in contact with VAL 90 (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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86A ALA 4.6 2.0 + - - +
87A SER 5.3 0.8 + - - -
88A GLU 3.6 0.4 - - - -
89A LEU* 1.3 77.2 - - + +
91A SER* 1.3 55.2 + - - +
115A ASN* 3.5 21.1 - - - +
116A GLU* 4.0 1.6 - - - -
117A TYR* 3.8 55.2 - - + +
126A PRO* 6.4 0.4 - - + -
130A VAL* 4.3 9.6 - - + -
135A ILE* 3.7 28.9 - - + -
501A GOL 2.7 23.1 + - - +
402B SO4 4.7 0.7 + - - -
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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