Contacts of the helix formed by residues 59 - 63 (chain A) in PDB entry 3NJ0
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 59 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A LEU 4.8 5.4 - - - +
56A ARG* 3.1 24.2 + - + +
58A ASP* 1.3 89.0 + - - +
60A PRO* 1.3 65.3 - - - +
61A GLU* 3.0 35.2 + - - +
62A ARG* 2.8 45.0 + - - +
63A TYR 4.7 0.2 + - - -
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Residues in contact with PRO 60 (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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56A ARG 4.4 1.9 - - - +
57A PHE 3.6 6.3 - - - +
58A ASP 3.3 6.3 - - - -
59A ASN* 1.3 90.5 - - - +
61A GLU* 1.3 65.9 + - - +
62A ARG 3.0 0.2 - - - -
63A TYR* 3.0 17.2 + - + -
64A LYS* 2.9 51.7 + - + +
67A VAL* 4.9 6.1 - - + -
70A CYS* 3.4 24.5 - - + -
83A ARG* 4.0 22.2 - - - +
85A VAL* 4.6 7.9 - - + -
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Residues in contact with GLU 61 (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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58A ASP 4.7 1.1 - - - +
59A ASN* 3.0 26.9 + - - +
60A PRO* 1.3 89.5 - - - +
62A ARG* 1.3 58.2 + - + +
63A TYR 3.1 0.2 - - - -
64A LYS 3.9 8.7 - - - +
67A VAL* 3.7 28.9 - - + +
68A LYS 6.0 0.4 - - - -
69A ARG* 4.7 2.9 - - - -
70A CYS* 3.4 28.6 + - - +
176A LYS* 2.9 28.4 + - - -
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Residues in contact with ARG 62 (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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53A LEU* 3.4 36.2 - - + +
56A ARG* 6.5 0.2 - - - -
59A ASN* 2.8 39.9 + - - +
60A PRO 3.0 1.0 - - - -
61A GLU* 1.3 81.3 - - + +
63A TYR* 1.3 61.3 + - + +
176A LYS* 3.7 12.6 - - - +
180A ALA* 4.3 19.4 + - - +
184A ALA* 4.6 11.3 - - - +
185A PRO 2.9 26.9 + - - -
186A MET* 4.2 17.1 - - - +
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Residues in contact with TYR 63 (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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53A LEU* 3.7 26.9 - - + -
54A ILE* 4.0 30.5 + - + +
59A ASN 5.1 0.7 - - - -
60A PRO* 3.0 18.3 + - + -
62A ARG* 1.3 80.2 - - + +
64A LYS* 1.3 96.6 + - + +
112A PHE* 5.6 2.1 - - - -
128A THR* 5.0 6.1 + - - +
147A GLU* 5.1 6.4 + - - -
173A ASN* 3.0 38.1 - - + +
174A LEU* 4.8 11.2 - - + -
176A LYS* 3.4 17.6 - - - +
177A LEU* 3.7 38.6 - - + -
180A ALA* 5.4 1.3 - - + -
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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