Contacts of the helix formed by residues 138 - 142 (chain A) in PDB entry 3NA0
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 GLY 138 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A PRO 4.0 0.6 + - - -
137A ILE* 1.3 73.5 - - - +
139A VAL* 1.3 67.2 + - - -
140A LEU 3.0 4.9 + - - -
141A LEU* 3.0 11.6 + - - -
142A LYS* 3.3 17.3 + - - +
150A ASP* 4.4 0.2 - - - -
318A ALA* 3.9 7.6 - - - +
319A ASN* 3.2 19.5 - - - -
322A GLU* 3.0 20.7 + - - -
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Residues in contact with VAL 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A GLY* 1.3 70.7 - - - -
140A LEU* 1.3 65.3 + - - +
141A LEU 3.3 0.3 + - - -
142A LYS* 3.5 7.1 + - - -
147A TRP* 3.2 43.2 + - + +
150A ASP* 3.9 9.1 + - + -
151A ARG* 3.8 30.3 - - + +
154A LEU* 4.1 5.2 - - + -
319A ASN* 2.6 20.8 + - - +
322A GLU* 3.3 1.1 + - - +
460A ARG* 3.1 18.2 + - - -
463A LEU* 4.0 16.2 - - + -
601A HEM 3.9 34.7 - - + +
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Residues in contact with LEU 140 (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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120A ARG* 3.8 21.9 + - - +
122A LEU* 3.8 12.8 - - + +
126A TRP* 3.8 27.6 - - + -
130A HIS* 6.4 0.9 - - + -
138A GLY 3.0 1.2 + - - -
139A VAL* 1.3 80.9 - - - +
141A LEU* 1.3 66.8 + - + +
270A TRP* 5.7 2.0 - - + -
322A GLU* 3.1 20.0 + - - +
460A ARG* 3.4 12.0 + - - -
601A HEM 3.8 22.0 - - + -
602A 2DC 3.7 55.9 - - + -
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Residues in contact with LEU 141 (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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122A LEU* 3.8 33.0 - - + +
123A ILE 5.6 1.8 - - - +
126A TRP* 4.5 15.0 - - + +
127A VAL* 4.1 18.8 - - + -
130A HIS* 3.3 47.6 - - + +
137A ILE* 3.6 31.5 - - + +
138A GLY 3.0 3.8 + - - +
140A LEU* 1.3 93.2 - - + +
142A LYS* 1.3 62.9 + - - +
143A LYS 4.3 0.2 + - - -
322A GLU* 4.3 7.8 + - - +
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Residues in contact with LYS 142 (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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122A LEU* 5.8 0.7 - - - +
137A ILE* 3.2 39.9 - - + -
138A GLY 3.3 11.9 + - - +
139A VAL* 3.5 5.4 + - - +
141A LEU* 1.3 81.3 - - - +
143A LYS* 1.3 60.7 + - - +
146A ALA* 3.6 28.6 + - + +
147A TRP* 3.8 17.8 - - + +
150A ASP* 3.1 27.9 + - - +
315A ASP* 2.9 28.1 + - - -
460A ARG* 2.8 27.9 + - - -
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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