Contacts of the helix formed by residues 132 - 141 (chain C) in PDB entry 5JTP
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 132 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A PHE* 6.2 0.4 - - - -
13A ILE* 6.5 0.4 - - + -
101A TYR* 3.6 22.9 + - - -
105A ILE* 4.0 17.2 - - - +
104C ASN* 4.7 5.9 - - - +
130C PRO 3.8 4.8 + - - +
131C VAL* 1.3 67.2 - - - +
133C PHE* 1.4 62.2 + - - +
134C ASP* 3.1 23.3 + - - +
135C ALA* 2.9 43.7 + - + +
136C LEU* 3.3 20.8 + - + +
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Residues in contact with PHE 133 (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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44C LEU* 4.3 19.5 - - + -
60C LEU* 5.3 11.9 - - + -
99C GLY 3.9 8.4 - - - +
100C ALA* 3.5 15.9 - - + +
103C PRO* 4.8 13.0 - - + -
104C ASN* 3.1 28.6 + - - +
107C PHE* 4.1 28.7 - + + -
131C VAL* 3.1 51.4 + - + -
132C ASN* 1.4 70.8 - - - +
134C ASP* 1.4 52.1 + - - +
136C LEU* 3.7 9.2 - - + +
137C PHE* 2.8 35.2 + - - +
460G LEU* 5.7 7.9 - - + -
461G PHE* 4.3 6.4 - + + -
462G TYR* 4.2 21.1 - + + -
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Residues in contact with ASP 134 (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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96C HIS* 3.2 33.8 + - + +
100C ALA* 3.3 8.3 - - - +
101C TYR* 3.9 13.1 + - - +
104C ASN* 2.8 27.3 + - - -
132C ASN* 3.1 14.2 + - - +
133C PHE* 1.4 74.2 - - - +
135C ALA* 1.3 61.1 + - - +
137C PHE* 3.0 17.8 + - - +
138C MET* 3.1 29.7 + - + +
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Residues in contact with ALA 135 (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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132C ASN* 2.9 29.0 + - + +
134C ASP* 1.3 74.7 - - - +
136C LEU* 1.3 65.6 + - + +
138C MET* 3.5 29.4 + - + +
139C ASN* 4.0 7.4 + - - +
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Residues in contact with LEU 136 (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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131C VAL* 3.6 24.9 - - + -
132C ASN 3.3 13.9 + - - +
133C PHE* 3.8 7.0 - - + +
134C ASP 3.2 0.4 - - - -
135C ALA* 1.3 81.6 - - + +
137C PHE* 1.3 58.3 + - - +
138C MET 3.3 0.2 - - - -
139C ASN* 2.8 38.0 + - - +
140C TYR 3.7 0.2 + - - -
461G PHE* 3.3 23.8 - - + -
462G TYR* 3.6 35.9 - - + -
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Residues in contact with PHE 137 (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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92C THR 4.4 1.6 - - - -
95C ALA* 3.3 26.0 - - + -
96C HIS* 3.3 45.8 - + + -
98C LEU* 5.2 2.9 - - + -
99C GLY* 3.4 22.9 - - - -
100C ALA* 4.4 0.4 - - + -
133C PHE 2.8 19.1 + - - +
134C ASP 3.0 6.4 + - - +
136C LEU* 1.3 75.6 - - - +
138C MET* 1.3 54.4 + - - +
140C TYR* 3.1 31.5 + + - -
141C LEU* 2.8 72.4 + - + +
142C GLN 5.4 0.2 - - - -
461G PHE* 3.5 25.1 - + - -
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Residues in contact with MET 138 (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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155A ALA* 5.1 2.9 - - - +
96C HIS* 5.2 2.9 - - + +
134C ASP* 3.1 35.0 + - + +
135C ALA* 3.6 19.1 - - + +
136C LEU 3.3 0.4 - - - -
137C PHE* 1.3 78.1 - - - +
139C ASN* 1.4 60.6 + - - +
140C TYR 4.5 0.2 - - - -
141C LEU 4.2 1.7 - - - -
142C GLN 3.2 20.9 + - - +
143C GLN* 3.4 32.8 + - + +
144C GLN* 3.7 47.1 - - + +
145C ALA 5.6 1.3 - - - +
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Residues in contact with ASN 139 (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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155A ALA* 4.0 8.0 - - - +
135C ALA 4.0 5.5 + - - +
136C LEU* 2.8 39.8 + - - +
138C MET* 1.4 75.8 - - - +
140C TYR* 1.3 85.6 + - - +
461G PHE* 4.5 5.4 - - - +
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Residues in contact with TYR 140 (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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155A ALA* 3.1 21.4 - - - +
136C LEU 4.0 0.2 - - - +
137C PHE* 3.1 45.4 + + - +
139C ASN* 1.3 85.6 + - - +
141C LEU* 1.3 76.5 + - + +
457G GLN* 5.0 2.9 + - - -
459G ASP* 3.3 41.8 + - + +
461G PHE* 3.8 31.0 - + + -
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Residues in contact with LEU 141 (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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154A ASP* 3.9 12.8 - - + +
155A ALA* 4.4 9.2 - - - +
92C THR* 3.9 32.1 - - + +
95C ALA* 3.6 31.2 - - + -
137C PHE* 2.8 40.9 + - + +
138C MET 4.2 0.7 - - - -
140C TYR* 1.3 94.2 - - + +
142C GLN* 1.4 75.2 + - - +
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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