Contacts of the helix formed by residues 109 - 115 (chain B) in PDB entry 3N2E
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 109 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45B ARG* 4.5 1.6 + - - +
107B ARG 3.4 2.9 + - - +
108B LEU* 1.3 75.6 - - - +
110B GLN* 1.3 71.1 + - - +
111B LYS* 3.4 15.4 + - - +
112B GLU* 2.7 55.4 + - - +
113B ARG* 3.3 9.1 + - - +
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Residues in contact with GLN 110 (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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142A PHE* 5.3 2.9 - - + -
159A GLN* 5.6 0.2 - - - +
160A PHE* 3.4 26.0 - - - -
163A LEU* 3.1 45.8 - - + +
164A GLN* 4.8 16.6 - - - +
109B ASN* 1.3 74.4 - - - +
111B LYS* 1.3 62.3 + - + +
113B ARG* 2.2 41.8 + - - +
114B ALA* 3.0 22.1 + - - +
26C LYS* 4.7 8.3 - - - +
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Residues in contact with LYS 111 (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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45B ARG* 3.6 41.9 + - - +
109B ASN* 3.0 14.1 + - - +
110B GLN* 1.3 76.4 - - + +
112B GLU* 1.3 62.5 + - - +
114B ALA* 3.4 18.9 + - - +
115B LYS* 4.3 5.9 + - - +
1001B OSA 4.7 2.4 + - - -
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Residues in contact with GLU 112 (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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10B MET* 4.8 17.1 - - + +
45B ARG* 3.2 23.1 + - - +
107B ARG 3.7 4.3 - - - +
108B LEU* 3.3 27.9 - - + +
109B ASN* 2.7 48.8 + - - +
111B LYS* 1.3 76.8 - - - +
113B ARG* 1.4 59.2 + - - +
115B LYS* 4.3 1.6 + - - +
116B ARG* 3.5 28.1 - - - +
119B LEU* 4.3 3.1 - - - +
1001B OSA 3.9 13.9 + - - +
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Residues in contact with ARG 113 (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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159A GLN* 4.4 3.8 - - - +
160A PHE* 3.6 6.6 - - + -
163A LEU* 4.2 1.2 - - - +
105B ILE* 5.5 0.4 - - - +
108B LEU* 4.1 18.2 - - + -
109B ASN 3.3 10.2 + - - +
110B GLN* 2.2 50.4 + - - +
112B GLU* 1.4 75.3 - - - +
114B ALA* 1.3 62.9 + - - +
115B LYS 3.2 4.4 + - - -
116B ARG* 3.3 10.2 + - - +
119B LEU* 3.7 27.9 + - + -
120B ASN* 3.3 42.9 + - - +
23C LEU* 3.0 32.7 + - - +
24C ALA* 3.0 18.6 + - - +
26C LYS* 3.7 26.8 - - - +
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Residues in contact with ALA 114 (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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141A SER 3.5 20.6 - - - +
142A PHE* 3.3 26.2 - - + +
143A ILE 2.9 28.1 + - - +
160A PHE* 4.0 3.8 - - - -
110B GLN 3.0 12.3 + - - +
111B LYS* 3.4 17.3 + - - +
113B ARG* 1.3 77.8 - - - +
115B LYS* 1.3 64.0 + - + +
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Residues in contact with LYS 115 (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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137A GLU* 2.9 31.9 + - - +
138A LYS 4.7 0.2 + - - -
140A ALA* 3.2 23.1 + - - +
141A SER 4.3 9.4 - - - +
143A ILE* 3.7 32.9 - - + +
45B ARG* 5.7 3.8 - - + -
49B GLU* 3.8 32.8 - - + +
111B LYS 4.3 5.5 + - - +
112B GLU 4.3 1.4 + - - +
113B ARG 3.2 0.4 - - - -
114B ALA* 1.3 85.1 - - + +
116B ARG* 1.3 67.5 + - + +
117B PRO* 3.4 10.9 - - - +
1001B OSA 4.5 26.4 + - + +
2001B TLA 6.1 0.5 - - - -
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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