Contacts of the helix formed by residues 85 - 93 (chain B) in PDB entry 3EHW
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 ARG 85 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A GLY* 4.1 4.7 - - - -
161A THR* 3.2 8.1 + - - -
162A GLY 3.0 30.5 + - - -
163A LYS* 4.3 4.8 - - - +
777A DUP 2.7 58.1 + - - +
49B ASP* 4.4 6.0 + - - +
83B ALA 3.8 0.4 + - - -
84B PRO* 1.3 76.7 - - - +
86B SER* 1.3 64.1 + - - +
87B GLY 4.5 0.9 - - - +
88B LEU* 3.8 22.3 + - + +
89B ALA* 3.2 21.5 + - - +
94B ILE 5.0 0.2 - - - +
128B ARG* 3.1 50.4 + - - +
129B ILE 4.6 2.5 + - - -
130B ALA* 4.1 26.6 - - - +
131B GLN* 3.9 9.6 - - + +
165B MG 4.2 0.4 - - - -
98C ALA* 4.6 0.9 - - - -
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Residues in contact with SER 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A PHE* 3.0 36.6 + - - -
777A DUP 2.7 66.9 + - - -
84B PRO 3.9 0.2 + - - -
85B ARG* 1.3 70.3 - - - +
87B GLY* 1.3 57.6 + - - +
89B ALA* 3.4 1.2 - - - +
90B ALA* 2.8 33.8 + - - +
98C ALA* 3.6 11.0 - - - +
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Residues in contact with GLY 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A PHE* 3.4 27.6 - - - -
159A GLY* 3.6 4.0 - - - -
163A LYS* 5.6 0.7 - - - -
777A DUP 2.8 17.8 + - - -
86B SER* 1.3 73.3 + - - +
88B LEU* 1.3 57.7 + - - +
90B ALA* 5.0 0.4 - - - -
91B LYS* 2.8 46.5 + - - +
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Residues in contact with LEU 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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163A LYS* 4.1 29.4 - - + +
777A DUP 4.5 0.6 + - - -
85B ARG* 3.8 23.0 + - + +
86B SER 3.4 0.2 - - - -
87B GLY* 1.3 74.8 - - - +
89B ALA* 1.3 57.2 + - - +
92B HIS* 2.9 30.5 + - + +
93B PHE 3.2 5.9 + - - -
94B ILE* 3.2 26.6 + - + +
121B PHE* 4.1 24.7 - - + -
128B ARG 3.9 8.3 - - - +
129B ILE* 3.7 46.0 - - + +
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Residues in contact with ALA 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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84B PRO* 5.2 0.7 - - + -
85B ARG 3.2 16.9 + - - +
86B SER 3.2 4.9 + - - +
87B GLY 3.2 0.4 - - - -
88B LEU* 1.3 78.9 - - - +
90B ALA* 1.3 58.9 + - - +
93B PHE* 3.0 25.3 + - - -
94B ILE 3.3 21.7 + - - +
63C LYS* 3.6 7.3 - - - +
98C ALA* 3.9 27.8 - - + +
112C VAL* 4.4 9.9 - - + -
114C PHE* 4.4 5.4 - - + -
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Residues in contact with ALA 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A PHE* 3.7 22.9 - - + -
86B SER 2.8 19.1 + - - +
87B GLY* 4.1 1.8 - - - +
89B ALA* 1.3 74.2 - - - +
91B LYS* 1.3 62.2 + - + +
63C LYS* 2.8 26.6 + - - +
65C VAL* 3.7 25.5 - - + +
112C VAL* 4.6 6.7 - - + -
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Residues in contact with LYS 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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158A PHE* 3.1 30.1 + - - -
159A GLY* 4.1 13.9 + - - -
163A LYS* 4.3 23.3 - - - +
87B GLY* 2.8 19.6 + - - +
90B ALA* 1.3 82.2 - - + +
92B HIS* 1.3 82.6 + - + +
93B PHE 3.8 0.2 - - - -
63C LYS* 4.1 7.3 + - - -
164X ASN* 4.9 13.3 - - - +
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Residues in contact with HIS 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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163A LYS* 3.8 24.0 + - - -
88B LEU* 2.9 17.4 + - + +
91B LYS* 1.3 100.6 + - + +
93B PHE* 1.3 70.7 + - - +
94B ILE* 3.2 20.6 + - + +
115B ASN* 3.9 7.4 + - - -
117B GLY* 4.2 2.8 - - - -
121B PHE* 4.1 26.4 - + + -
63C LYS* 4.4 1.1 - - - -
164X ASN* 4.0 28.6 + - + -
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Residues in contact with PHE 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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89B ALA* 3.0 16.4 + - - -
92B HIS* 1.3 79.5 - - - +
94B ILE* 1.3 61.3 + - - +
95B ASP 3.9 0.3 + - - -
114B PHE 3.8 0.2 - - - +
116B PHE* 3.0 56.2 + - + +
117B GLY* 3.6 14.8 - - - +
61C MET* 3.4 26.2 - - + -
62C GLU* 3.8 32.3 - - - -
63C LYS* 3.6 25.2 - - + +
114C PHE* 3.3 40.8 - + + -
116C PHE* 4.1 11.4 - + - -
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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
------------------------------------------------------------
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