Contacts of the helix formed by residues 85 - 95 (chain B) in PDB entry 3EHR
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 ASN 85 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80B ALA* 2.8 18.7 + - - +
83B ARG* 3.3 8.7 - - + +
84B GLY* 1.3 73.9 - - - +
86B LEU* 1.3 57.5 + - - +
87B SER* 3.4 9.5 + - - -
88B TRP* 3.0 42.2 + - + +
89B LEU* 2.9 26.5 + - - +
121B ILE* 3.7 1.8 - - - -
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Residues in contact with LEU 86 (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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84B GLY 3.4 5.5 + - - -
85B ASN* 1.3 71.4 + - - +
87B SER* 1.3 68.0 + - - +
89B LEU* 3.2 3.6 + - + +
90B ARG* 2.9 56.8 + - - +
120B ASP* 3.9 36.8 - - + +
121B ILE* 3.6 13.7 - - + -
124B MSE 3.6 37.0 - - + -
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Residues in contact with SER 87 (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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85B ASN* 3.4 6.8 + - - -
86B LEU* 1.3 78.6 - - - +
88B TRP* 1.3 63.0 + - - +
90B ARG* 3.4 11.5 + - - +
91B GLU* 3.1 21.5 + - - +
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Residues in contact with TRP 88 (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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18B ARG* 3.6 15.9 - - - -
38B ILE* 3.7 32.3 - - + +
40B TYR* 3.1 24.7 + - - -
73B ILE* 3.9 8.1 - - + -
76B PRO* 3.7 22.4 - - + +
79B GLU* 3.4 44.0 - - + -
80B ALA* 3.7 19.1 - - + -
83B ARG* 6.2 3.1 - - - -
85B ASN* 3.0 35.0 + - + +
87B SER* 1.3 74.6 + - - +
89B LEU* 1.3 67.2 + - - +
91B GLU* 3.1 12.3 + - - -
92B CYS* 2.9 31.0 + - - -
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Residues in contact with LEU 89 (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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77B LEU* 3.5 42.6 - - + +
80B ALA* 3.6 6.1 - - + +
81B ALA* 3.9 20.0 - - + +
85B ASN 2.9 18.8 + - - +
86B LEU* 3.2 5.4 + - + +
88B TRP* 1.3 75.2 - - - +
90B ARG* 1.3 62.1 + - - +
92B CYS* 3.2 4.3 + - - +
93B LEU* 3.1 28.7 + - + +
121B ILE* 3.9 25.4 - - + +
124B MSE 3.7 35.9 - - + -
125B LEU* 4.1 16.6 - - + -
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Residues in contact with ARG 90 (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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161A ALA* 3.7 22.0 + - - +
162A LYS* 4.0 31.3 - - - +
86B LEU* 2.9 51.4 + - + +
87B SER* 3.7 9.6 - - - +
88B TRP 3.3 0.2 - - - -
89B LEU* 1.3 75.4 - - - +
91B GLU* 1.3 57.5 + - - +
93B LEU* 3.3 10.7 + - - +
94B ASP* 2.9 38.7 + - - +
124B MSE 3.7 37.1 - - + +
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Residues in contact with GLU 91 (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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38B ILE* 4.0 10.5 - - - +
40B TYR* 2.7 37.6 + - + +
54B SER* 5.2 0.2 - - - -
55B LYS* 4.1 21.3 + - - +
56B GLY 4.8 2.9 + - - -
87B SER* 3.1 13.7 + - - +
88B TRP* 3.4 19.6 - - - +
90B ARG* 1.3 74.3 - - - +
92B CYS* 1.3 65.0 + - - +
94B ASP* 3.4 8.7 + - + +
95B ASN* 2.8 38.1 + - - +
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Residues in contact with CYS 92 (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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40B TYR* 3.7 9.4 + - - -
76B PRO* 3.8 35.9 - - - -
77B LEU* 3.7 16.6 - - + -
88B TRP* 2.9 42.5 + - - -
89B LEU* 3.2 8.5 + - - +
91B GLU* 1.3 75.8 - - - +
93B LEU* 1.3 61.4 + - - +
95B ASN 3.1 8.3 + - - -
97B VAL* 3.0 37.8 + - + +
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Residues in contact with LEU 93 (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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77B LEU* 3.8 23.8 - - + -
89B LEU* 3.1 33.9 + - + +
90B ARG* 3.6 6.1 - - - +
92B CYS* 1.3 75.3 - - - +
94B ASP* 1.3 63.2 + - - +
96B ARG* 3.0 14.7 + - - -
97B VAL 3.9 17.1 - - - +
99B VAL* 4.2 10.8 - - + +
124B MSE 4.3 16.2 - - + -
125B LEU* 4.7 3.1 - - + -
128B GLN* 3.8 47.5 - - + +
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Residues in contact with ASP 94 (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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160A LEU 5.2 5.2 - - - +
161A ALA* 5.9 3.8 - - - -
90B ARG* 2.9 28.0 + - - +
91B GLU* 3.5 9.8 - - + +
92B CYS 3.3 0.2 - - - -
93B LEU* 1.3 76.7 - - - +
95B ASN* 1.3 65.8 + - - +
96B ARG* 3.2 3.4 + - - +
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Residues in contact with ASN 95 (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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14B VAL* 3.4 21.3 - - + +
40B TYR* 3.5 44.5 - - + +
53B THR* 3.9 21.1 + - - +
91B GLU* 2.8 42.5 + - - +
92B CYS 3.1 2.6 + - - +
94B ASP* 1.3 82.0 - - - +
96B ARG* 1.3 67.3 - - - +
97B VAL 3.3 2.7 - - - -
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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