Contacts of the helix formed by residues 5140 - 5146 (chain d) in PDB entry 3A0B
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 PRO5140 (chain d).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5468b ALA* 3.6 23.8 - - + +
5472b PHE* 3.0 35.2 - - + -
5476b PHE* 4.1 17.5 - - + -
5130d PHE* 3.1 30.7 - - + -
5133d ALA* 4.6 4.5 - - + -
5138d VAL 3.3 0.6 - - - -
5139d ARG* 1.3 83.0 - - + +
5141d TYR* 1.3 60.7 + - + +
5142d ASN 3.2 6.1 - - - +
5143d ALA 3.7 2.2 + - - +
5144d ILE* 3.0 30.7 + - + +
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Residues in contact with TYR5141 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5217a SER* 2.8 34.8 + - - +
5220a THR* 3.2 33.7 - - + -
5221a SER* 3.9 4.5 - - - -
5465b TRP* 3.8 19.5 - + - -
5476b PHE* 3.7 23.4 - + - -
6060b MGE 3.1 40.3 + - - -
5139d ARG* 2.8 50.1 + - + -
5140d PRO* 1.3 80.0 - - + +
5142d ASN* 1.3 57.3 + - - +
5144d ILE* 3.0 28.1 - - + +
5145d ALA* 3.3 7.4 - - - +
5272d LEU* 4.1 9.1 - - + +
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Residues in contact with ASN5142 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5214a MET* 4.6 4.9 - - - -
5217a SER* 2.8 17.4 + - - +
5218a LEU* 4.4 8.4 - - + +
5221a SER* 4.7 1.6 - - - -
5254a TYR* 2.7 42.2 + - + +
5258a LEU* 3.4 10.8 - - - +
6039a PHO 2.8 22.0 + - - +
5129d GLN* 2.6 39.0 + - - +
5139d ARG 4.4 0.8 + - - -
5140d PRO 3.2 0.4 - - - -
5141d TYR* 1.3 74.0 - - - +
5143d ALA* 1.3 57.2 + - - +
5145d ALA* 2.7 26.3 + - - +
5146d PHE 3.1 8.5 + - - -
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Residues in contact with ALA5143 (chain d).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5254a TYR* 4.9 0.2 - - - +
5126d MET* 2.8 46.7 - - + +
5129d GLN* 3.6 20.6 - - + -
5130d PHE* 3.4 42.2 - - + -
5133d ALA* 6.3 0.2 - - + -
5140d PRO 3.7 2.1 + - - +
5142d ASN* 1.3 76.7 - - - +
5144d ILE* 1.3 66.1 + - - +
5146d PHE* 3.1 2.8 + - - -
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Residues in contact with ILE5144 (chain d).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5461b PHE* 5.0 8.2 - - + -
5464b ILE* 4.0 15.0 - - + +
5465b TRP* 3.2 62.4 - - + +
5468b ALA* 4.8 4.9 - - + -
6060b MGE 4.8 11.8 - - + +
5126d MET* 4.8 0.3 - - - +
5130d PHE* 4.7 0.4 - - - -
5140d PRO* 3.0 17.0 + - + +
5141d TYR* 3.0 39.3 - - + +
5143d ALA* 1.3 76.7 - - - +
5145d ALA* 1.3 73.3 + - + +
5146d PHE 3.0 5.5 + - - -
5147d SER* 3.1 23.7 + - - -
5272d LEU* 4.4 10.8 - - + -
5276d VAL* 4.9 0.3 - - - +
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Residues in contact with ALA5145 (chain d).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5213a ALA 4.4 8.5 - - - +
5217a SER* 4.4 0.9 - - - -
6039a PHO 4.2 13.8 - - + +
5141d TYR 3.3 12.3 - - - +
5142d ASN 2.7 11.9 + - - +
5144d ILE* 1.3 81.7 - - - +
5146d PHE* 1.3 57.4 + - - -
5147d SER 3.1 2.9 + - - -
5148d ALA* 3.6 18.5 - - - +
5149d PRO* 3.7 2.4 - - - +
5272d LEU* 3.3 24.0 - - + -
5276d VAL* 3.6 18.7 - - + +
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Residues in contact with PHE5146 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6039a PHO 3.5 40.6 - + - -
5122d LEU* 3.6 34.3 - - + -
5125d PHE* 3.5 30.3 - + - -
5126d MET* 3.6 19.7 - - + -
5129d GLN* 3.8 9.0 - - - +
5142d ASN 3.1 5.0 + - - +
5143d ALA 3.5 11.9 - - - +
5144d ILE 3.0 2.0 + - - -
5145d ALA* 1.3 74.8 - - - +
5147d SER* 1.3 62.7 + - - +
5148d ALA 3.1 2.2 - - - -
5149d PRO* 3.3 20.4 - - + +
5150d ILE* 2.8 59.0 + - + +
6004d CLA 4.4 3.4 - - + -
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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