Contacts of the helix formed by residues 28 - 32 (chain G) in PDB entry 4WFH
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 SER 28 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27E TYR* 5.9 0.7 - - - -
28E SER* 3.3 39.7 + - - -
31E GLY* 5.7 0.5 - - - -
32E TYR* 5.6 4.4 - - - -
27G TYR* 1.3 87.7 - - - +
29G PHE* 1.3 64.8 + - - +
30G THR* 3.2 6.8 + - - -
31G GLY* 3.0 24.3 + - - -
32G TYR* 3.8 3.6 - - - -
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Residues in contact with PHE 29 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24G VAL* 3.6 35.6 - - + +
27G TYR* 3.5 14.5 + - - -
28G SER* 1.3 71.2 - - - +
30G THR* 1.3 66.3 + - + +
31G GLY 3.3 1.2 + - - -
32G TYR 3.5 7.4 + - - +
34G MET* 4.2 17.7 - - + +
53G PRO* 3.5 29.2 - - + +
72G VAL* 3.7 25.1 - - + -
73G ASP 3.8 7.0 - - - -
74G LYS* 4.3 10.8 - - - +
77G SER* 3.2 37.6 - - - -
78G THR 3.3 36.1 - - - -
79G ALA* 3.9 2.9 - - + -
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Residues in contact with THR 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A PRO* 6.1 0.7 - - - +
78B CYS* 4.8 5.0 - - - +
32E TYR* 4.5 12.1 + - - -
28G SER* 3.1 7.5 + - - -
29G PHE* 1.3 86.3 - - + +
31G GLY* 1.3 59.4 + - - +
32G TYR 3.4 2.7 + - - +
52G ASN* 4.5 2.4 - - - +
53G PRO* 4.1 11.7 - - - +
54G ASN* 3.4 41.8 + - - +
74G LYS* 4.3 31.0 - - + +
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Residues in contact with GLY 31 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B PRO* 3.4 5.9 - - - +
78B CYS* 3.3 32.7 + - - +
31E GLY* 5.9 6.7 - - - -
28G SER* 3.0 18.9 + - - -
30G THR* 1.3 82.4 + - - +
32G TYR* 1.3 71.8 + - - +
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Residues in contact with TYR 32 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B PRO* 3.6 34.9 - - + +
78B CYS* 5.5 0.2 - - - -
28E SER* 5.8 2.5 - - - -
30E THR* 4.7 11.5 + - - -
54E ASN* 5.1 4.5 + - - -
27G TYR* 3.6 28.6 + + + +
28G SER* 4.4 3.6 - - - -
29G PHE 3.5 3.8 + - - +
30G THR 3.4 1.2 - - - -
31G GLY* 1.3 90.4 - - - +
33G ILE* 1.3 66.1 + - - +
34G MET* 4.7 1.6 - - - +
52G ASN* 5.8 0.2 - - - -
53G PRO* 3.1 26.7 - - - +
98G ARG* 3.6 57.0 + - + -
99G GLY* 5.3 4.3 - - - +
104G ASP* 5.4 0.9 - - - -
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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