Contacts of the helix formed by residues 128 - 133 (chain B) in PDB entry 3NVN
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 THR 128 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B SER 3.8 4.7 - - - +
105B PHE* 3.2 28.2 + - - +
107B LYS* 3.5 18.6 - - - -
127B TRP* 1.3 73.2 - - - +
129B PHE* 1.3 73.4 + - - +
130B ASP 3.8 0.7 + - - -
131B ARG 3.8 2.8 + - - -
132B GLY 3.2 11.1 + - - -
155B SER 3.6 9.9 - - - +
156B CYS* 3.3 18.9 - - - +
157B HIS 3.4 32.5 - - - +
158B PRO* 3.7 10.6 - - + +
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Residues in contact with PHE 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B SER* 3.6 33.7 - - - -
81B ARG* 3.6 35.3 + - + +
82B ASP* 4.0 24.5 - - + -
90B PRO* 4.0 9.6 - - + -
105B PHE* 3.9 34.5 - + + -
127B TRP* 3.3 39.6 - + + +
128B THR* 1.3 80.2 + - - +
130B ASP* 1.3 72.2 + - - +
133B ALA* 3.0 21.5 + - - +
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Residues in contact with ASP 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ARG* 3.1 30.1 + - - -
128B THR 3.8 0.2 + - - -
129B PHE* 1.3 74.4 - - - +
131B ARG* 1.3 72.7 + - - +
132B GLY 3.4 0.2 + - - -
133B ALA* 3.6 13.2 + - + +
151B THR* 3.3 21.9 - - + +
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Residues in contact with ARG 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A HIS* 3.2 49.0 + - + +
297A THR* 4.5 5.9 - - - +
300A ASP* 2.8 37.2 + - - -
128B THR 3.8 2.0 + - - -
129B PHE 3.3 0.6 - - - -
130B ASP* 1.3 78.8 - - - +
132B GLY* 1.3 56.3 + - - +
151B THR* 4.5 7.0 - - + -
152B GLU* 2.9 38.5 + - + +
154B VAL 4.1 1.2 - - - +
156B CYS* 3.7 18.4 - - - +
193B ARG 4.8 11.1 + - - -
194B CYS* 4.4 27.2 + - + +
195B ASN 5.4 5.3 + - - -
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Residues in contact with GLY 132 (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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127B TRP 3.0 21.8 - - - -
128B THR 3.2 12.7 + - - -
131B ARG* 1.3 77.0 - - - +
133B ALA* 1.3 59.5 + - - +
152B GLU 3.9 0.4 - - - -
153B VAL 3.1 10.0 + - - -
154B VAL* 2.9 40.8 + - - -
156B CYS* 3.6 6.1 - - - +
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Residues in contact with ALA 133 (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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81B ARG* 3.7 18.4 - - - +
125B THR 4.1 0.7 - - - +
126B GLY* 3.4 0.9 - - - -
127B TRP* 2.9 28.6 + - - +
129B PHE 3.0 15.7 + - - +
130B ASP* 3.6 16.4 - - + +
131B ARG 3.5 0.6 - - - -
132B GLY* 1.3 77.2 - - - +
134B CYS* 1.3 60.0 + - - +
135B GLU* 4.5 6.3 - - - +
149B ASN* 5.4 3.4 - - - +
150B GLY 3.2 14.6 - - - +
151B THR* 4.0 7.2 - - + +
154B VAL* 5.1 0.2 - - - -
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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