Contacts of the strand formed by residues 46 - 50 (chain C) in PDB entry 1HWG
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 PHE 46 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C ARG 3.5 14.6 - - - +
40C SER* 3.9 4.0 - - - +
41C PRO* 4.7 1.8 - - - -
45C THR* 1.3 79.5 - - - +
47C SER* 1.3 78.3 + - - +
48C CYS* 3.9 10.1 - - - -
95C TYR* 3.5 6.0 - - - -
96C PHE* 2.8 78.2 + + + +
101C THR* 3.6 26.2 - - + -
107C TYR* 4.1 25.1 - + - -
109C ILE* 5.5 1.3 - - + -
123C PHE* 3.6 26.9 - + - -
125C VAL* 4.4 7.4 - - + -
128C ILE* 3.6 24.2 - - + -
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Residues in contact with SER 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C LYS 3.9 0.7 - - - +
38C CYS* 3.0 21.3 - - - -
39C ARG* 3.1 15.3 + - - +
41C PRO* 6.0 0.5 - - - +
46C PHE* 1.3 82.7 - - - +
48C CYS* 1.3 66.9 + - - +
49C HIS* 3.4 20.2 + - - -
89C ALA* 4.5 10.0 - - - +
94C CYS 3.1 14.6 - - - -
95C TYR* 4.1 14.6 - - - -
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Residues in contact with CYS 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C PHE* 4.3 4.5 - - + -
37C LYS 3.3 4.0 - - - -
38C CYS* 2.3 44.0 - - - -
46C PHE* 3.9 16.6 - - - -
47C SER* 1.3 73.7 - - - +
49C HIS* 1.3 65.3 + - - +
50C TRP* 4.0 1.8 - - - -
66C LEU* 4.0 19.7 - - + -
93C SER* 2.9 27.2 - - - -
94C CYS 3.0 11.3 + - - +
96C PHE* 4.5 6.1 - - - -
109C ILE* 3.7 14.8 - - + -
123C PHE* 4.6 0.2 - - - -
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Residues in contact with HIS 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C PHE* 3.5 8.1 - - - -
36C THR* 2.7 44.5 + - + +
37C LYS* 2.9 24.7 + - + -
39C ARG* 5.4 5.6 - - + +
47C SER* 3.4 22.2 + - - -
48C CYS* 1.3 80.7 - - - +
50C TRP* 1.3 59.8 + - - +
89C ALA* 4.3 14.3 + - + -
91C GLU 4.9 2.4 + - - -
92C ASN 3.3 9.0 + - - +
93C SER* 3.6 22.1 - - - -
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Residues in contact with TRP 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C LYS 3.0 17.5 - - - +
35C PHE* 4.0 15.3 - + + -
36C THR* 3.3 10.7 + - - -
48C CYS 4.0 0.9 - - - -
49C HIS* 1.3 81.0 - - - +
51C THR* 1.3 74.3 + - - +
64C ILE* 3.5 36.6 - - + +
66C LEU* 3.6 26.7 - - + -
86C TYR* 3.9 24.9 - + - -
92C ASN* 2.8 58.1 + - + +
93C SER* 3.4 33.4 - - - -
111C LEU* 3.6 19.1 - - + -
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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