Contacts of the helix formed by residues 144 - 151 (chain C) in PDB entry 5T5W
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 ASN 144 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C PHE* 3.5 43.7 - - + +
44C PRO* 4.6 2.3 - - - +
45C ARG* 5.4 2.4 + - - -
64C GLU* 4.5 6.0 + - - +
68C THR* 5.0 1.4 + - - -
140C SER 3.4 17.7 + - - +
141C VAL 3.7 4.3 - - - +
142C THR 3.2 0.8 - - - -
143C PHE* 1.3 77.2 - - - +
145C LEU* 1.3 64.3 + - - +
146C PHE 3.4 2.0 - - - -
147C ARG* 2.9 36.3 + - - +
148C LEU* 3.0 33.9 + - - +
151C ARG* 5.0 1.2 + - - -
152C ASP* 4.9 2.5 + - - +
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Residues in contact with LEU 145 (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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20C PHE* 4.3 30.7 - - + +
23C ALA* 5.0 5.6 - - + -
24C LYS* 4.5 22.2 - - + +
27C LEU* 5.1 5.8 - - + -
68C THR* 4.1 24.9 - - + -
72C LEU* 4.6 12.6 - - + -
89C PRO* 6.2 0.2 - - + -
93C LEU* 4.4 16.6 - - + -
141C VAL 3.2 8.0 + - - +
142C THR* 3.2 17.9 + - - +
143C PHE 3.3 0.6 - - - -
144C ASN* 1.3 79.7 - - - +
146C PHE* 1.3 65.0 + - + +
148C LEU* 3.4 7.6 + - + +
149C LEU* 3.2 33.5 + - + +
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Residues in contact with PHE 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B TYR* 3.9 14.7 - - - +
100B LEU* 4.2 15.3 - - + -
101B PHE* 3.7 20.2 - + - -
184B PHE* 3.7 34.1 - + - -
17C LEU* 4.4 9.0 - - + -
20C PHE* 3.9 17.9 - - + -
21C LYS* 3.6 29.8 - - + -
24C LYS* 3.5 48.0 - - + +
142C THR 4.8 0.2 + - - -
143C PHE 4.8 1.8 + - - -
145C LEU* 1.3 80.3 - - + +
147C ARG* 1.3 61.1 + - - +
148C LEU 3.2 0.9 - - - -
149C LEU* 3.8 12.8 - - + +
150C ALA* 2.9 31.5 + - - +
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Residues in contact with ARG 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B PRO* 4.9 6.9 - - - +
71B ASP* 2.7 38.8 + - - -
73B TYR* 3.6 35.3 - - + +
74B ASN* 3.7 6.1 - - - +
43C PHE* 3.9 6.1 + - - +
44C PRO* 3.7 42.3 - - - +
140C SER 4.5 0.4 + - - -
143C PHE* 3.5 24.9 + - - +
144C ASN* 2.9 43.3 + - - +
146C PHE* 1.3 76.2 - - - +
148C LEU* 1.3 59.7 + - - +
151C ARG* 3.2 33.4 + - - +
152C ASP* 3.0 26.4 + - - +
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Residues in contact with LEU 148 (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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61C LEU* 3.9 18.2 - - + -
64C GLU* 4.1 11.0 - - + -
65C LEU* 3.8 46.0 - - + +
68C THR* 3.8 25.8 - - + +
93C LEU* 4.9 1.3 - - + -
96C ILE* 6.1 0.4 - - + -
144C ASN* 3.0 25.1 + - - +
145C LEU* 3.6 7.4 - - + +
146C PHE 3.2 0.2 - - - -
147C ARG* 1.3 78.0 - - - +
149C LEU* 1.3 74.1 + - + +
152C ASP* 3.4 11.7 + - + +
153C LEU* 2.6 40.3 + - + +
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Residues in contact with LEU 149 (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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184B PHE* 5.7 0.7 - - + -
9C PHE 5.2 1.9 - - - +
12C LEU* 4.2 24.5 - - + +
17C LEU* 4.5 10.8 - - + -
20C PHE* 3.7 46.2 - - + -
93C LEU* 3.9 23.3 - - + -
96C ILE* 4.4 5.6 - - + -
145C LEU* 3.2 21.5 + - + +
146C PHE* 3.6 13.2 + - + -
148C LEU* 1.3 90.3 - - + +
150C ALA* 1.3 61.8 + - + +
153C LEU* 3.7 26.4 - - + +
154C ASN* 4.0 5.0 + - - +
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Residues in contact with ALA 150 (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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73B TYR* 4.1 8.1 - - + -
100B LEU* 3.9 27.1 - - + -
132B PRO* 5.7 1.1 - - + -
133B PRO* 3.3 15.5 - - + +
184B PHE* 4.0 19.5 - - + -
146C PHE 2.9 18.0 + - - +
149C LEU* 1.3 78.2 - - - +
151C ARG* 1.3 57.7 + - - +
154C ASN* 3.3 18.0 + - - +
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Residues in contact with ARG 151 (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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73B TYR* 3.3 44.9 - - + +
133B PRO* 4.6 6.1 - - + +
44C PRO* 5.4 4.2 - - - +
45C ARG* 3.3 20.4 + - - +
47C TRP 5.1 0.8 + - - -
48C ASP* 2.9 30.6 + - - +
49C LEU* 5.5 0.2 - - - +
144C ASN* 5.0 1.8 + - - -
147C ARG* 3.2 41.1 + - - +
150C ALA* 1.3 79.2 - - - +
152C ASP* 1.3 87.7 + - - +
154C ASN* 3.4 3.1 + - - +
155C CYS* 2.9 31.2 + - + +
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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