Contacts of the helix formed by residues 687 - 692 (chain 4) in PDB entry 5U8T
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 PRO 687 (chain 4).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6864 LEU* 1.3 113.7 - - + +
6884 VAL* 1.3 63.8 - - + +
6894 THR* 4.8 9.2 - - - +
6904 GLU* 4.9 4.8 - - + +
6914 ASN* 3.3 10.8 + - - +
8384 THR* 4.5 2.5 - - + -
8514 GLN* 5.2 9.6 - - - +
8544 LYS* 4.2 30.1 - - + +
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Residues in contact with VAL 688 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6824 TYR* 6.4 0.9 - - + -
6864 LEU 4.5 0.4 - - - -
6874 PRO* 1.3 72.8 - - + +
6894 THR* 1.3 62.5 + - + +
6904 GLU 3.6 0.2 - - - -
6914 ASN* 2.9 10.6 + - + +
6924 ILE* 2.8 36.7 + - + +
7074 LEU* 5.1 7.2 - - + -
8354 ASP 3.1 26.7 - - - +
8364 TYR* 3.4 52.9 - - + +
8384 THR* 3.5 11.2 - - + -
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Residues in contact with THR 689 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6874 PRO* 3.6 3.5 - - - +
6884 VAL* 1.3 78.8 + - + +
6904 GLU* 1.3 51.5 + - - +
6924 ILE* 2.8 22.9 + - - +
6934 ASP 2.7 27.1 - - - +
6944 LEU 4.3 1.6 - - - -
6964 PRO* 3.5 39.0 - - + +
6994 LEU* 5.1 9.6 - - + -
8364 TYR* 6.4 2.0 - - + -
8514 GLN 2.4 32.1 + - - -
8534 GLY* 4.5 6.7 + - - -
8544 LYS* 5.9 0.7 - - - +
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Residues in contact with GLU 690 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6784 ILE* 3.1 21.2 - - + +
6864 LEU* 3.8 20.7 - - + +
6874 PRO* 4.8 5.9 + - + +
6894 THR* 1.3 81.1 + - - +
6914 ASN* 1.3 65.0 + - - +
6924 ILE 3.1 0.2 - - - -
6934 ASP* 2.8 26.3 + - - -
6944 LEU 4.5 3.3 + - - -
8514 GLN* 3.6 26.8 - - + +
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Residues in contact with ASN 691 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6774 PRO* 4.2 10.9 - - - +
6784 ILE* 4.3 10.3 + - - +
6824 TYR* 2.3 70.1 + - - +
6834 ASN* 3.8 3.9 + - - -
6854 ASN 4.6 2.2 + - - -
6864 LEU* 3.3 20.4 - - + +
6874 PRO 3.3 15.0 + - - +
6884 VAL* 2.9 17.1 + - + +
6904 GLU* 1.3 80.3 + - - +
6924 ILE* 1.3 56.9 + - - +
6934 ASP 3.0 6.8 + - - -
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Residues in contact with ILE 692 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5654 LEU* 6.1 4.7 - - + +
5674 CYS* 5.2 12.1 - - - -
6354 ASP* 3.0 29.6 - - - +
6774 PRO* 5.8 1.3 - - - -
6884 VAL* 2.8 16.2 + - + +
6894 THR* 2.8 9.2 + - - +
6914 ASN* 1.3 77.0 - - - +
6934 ASP* 1.3 64.7 + - - +
6944 LEU* 4.8 3.7 - - + +
6994 LEU* 3.4 32.8 - - + -
7054 VAL* 3.5 33.7 - - + -
7074 LEU* 5.2 8.1 - - + -
8364 TYR* 3.6 21.8 - - + -
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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