Contacts of the helix formed by residues 53 - 58 (chain P) in PDB entry 3J7Y
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 53 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1546 TYR* 3.5 27.9 + - + +
1556 TYR* 3.2 29.9 + - + -
3206 GLN* 5.1 0.8 - - - +
51P ASN* 3.2 13.6 + - - +
52P PRO* 1.3 76.5 - - - +
54P ASN* 1.3 65.3 + - - +
55P LEU 3.5 1.8 - - - -
56P GLU* 3.3 17.8 + - - +
57P LEU* 3.2 65.2 + - + +
78P HIS* 3.3 31.3 + - - -
101P VAL* 6.2 0.2 - - - +
139P GLY 3.0 24.7 + - - -
140P ILE* 3.4 22.2 - - - +
141P ASN 4.6 1.4 - - - +
142P PHE* 5.4 3.2 + - - +
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Residues in contact with ASN 54 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2646 GLY* 3.5 7.4 - - - -
2656 ILE* 3.6 4.4 + - - +
49P ASN* 2.9 41.2 + - - +
51P ASN* 3.1 29.2 + - - +
52P PRO 3.4 0.4 - - - -
53P ARG* 1.3 77.6 - - - +
55P LEU* 1.3 71.4 + - + +
56P GLU 3.1 1.9 + - - -
57P LEU* 3.2 6.0 + - - +
58P LEU* 3.1 41.9 + - - +
142W PHE* 3.5 22.8 - - - -
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Residues in contact with LEU 55 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3446 PHE* 3.7 31.2 - - + -
49P ASN 5.4 2.7 - - - +
51P ASN 5.3 2.0 - - - +
52P PRO 4.8 3.1 + - - +
53P ARG 3.5 0.4 - - - -
54P ASN* 1.3 101.0 - - + +
56P GLU* 1.3 58.0 + - + +
58P LEU* 4.1 12.1 - - + -
59P SER 3.4 0.3 + - - -
60P VAL* 2.9 31.4 + - + -
61P ALA* 2.8 45.4 + - + +
139W GLU* 4.7 13.0 - - + +
140W GLY* 5.3 1.6 - - - -
142W PHE* 5.1 4.3 - - + -
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Residues in contact with GLU 56 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1546 TYR* 2.7 24.5 + - - -
52P PRO 3.9 9.7 - - - +
53P ARG* 3.4 27.8 - - + +
54P ASN 3.1 0.2 + - - -
55P LEU* 1.3 77.2 - - - +
57P LEU* 1.3 61.2 + - - +
59P SER* 3.1 18.5 + - - -
61P ALA* 4.8 4.7 - - + -
77P TRP* 3.4 47.4 - - + +
78P HIS* 3.1 22.9 + - - -
95P HIS* 2.7 25.2 + - - -
174P PRO* 5.8 1.4 - - - +
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Residues in contact with LEU 57 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1926 GLU* 4.9 8.1 - - + -
2656 ILE* 3.2 44.4 - - + -
3206 GLN* 4.2 17.3 - - - +
3226 ARG* 3.9 24.5 + - - +
51P ASN* 4.5 0.9 - - - +
53P ARG* 3.2 55.2 + - + +
54P ASN 3.2 2.8 + - - +
56P GLU* 1.3 74.8 - - - +
58P LEU* 1.3 65.0 + - - +
59P SER* 3.1 4.5 + - - -
139P GLY 5.0 1.6 - - - +
141P ASN* 6.3 1.1 - - - +
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Residues in contact with LEU 58 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2626 GLY* 5.9 2.5 - - - +
2646 GLY* 4.0 18.4 - - - +
2656 ILE* 5.5 4.7 - - + -
3446 PHE* 4.9 4.0 - - + -
54P ASN* 3.1 35.4 + - - +
55P LEU* 4.2 15.7 - - + +
57P LEU* 1.3 76.0 - - - +
59P SER* 1.3 74.7 + - - +
60P VAL* 3.6 18.4 - - + +
177P ILE* 4.8 1.4 - - - +
142W PHE* 3.8 27.4 - - + -
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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
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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