Contacts of the helix formed by residues 129 - 139 (chain C) in PDB entry 4B94
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 ARG 129 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125C PRO 4.6 0.4 + - - -
126C ASP 5.5 4.9 + - - -
127C ASP 3.6 2.4 - - - -
128C ALA* 1.3 75.3 - - - +
130C ASP* 1.4 63.5 + - - +
132C PHE* 3.2 7.3 + - - +
133C GLN* 3.0 36.8 + - - +
149C PHE* 4.2 9.2 - - + -
152C PHE* 3.9 25.8 - - + -
153C GLU* 2.7 41.5 + - - +
156C GLN* 4.6 7.5 - - - +
158C ASN* 3.3 14.3 - - - +
161C LYS* 6.0 2.4 - - - +
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Residues in contact with ASP 130 (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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95A ILE* 4.2 13.4 - - + +
98A LEU 4.9 0.7 - - - +
100A PRO* 3.4 27.1 - - + +
109A PHE* 4.4 0.9 - - - -
113A GLN* 3.4 13.6 + - - -
134A MET* 3.5 17.7 - - - +
138A ASN* 2.9 34.0 + - - +
127C ASP 4.8 1.2 + - - +
128C ALA 3.2 1.0 + - - -
129C ARG* 1.4 77.4 - - - +
131C TYR* 1.3 67.9 + - + +
132C PHE 3.3 0.2 - - - -
133C GLN* 3.4 8.7 - - - +
134C MET* 2.9 33.8 + - - +
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Residues in contact with TYR 131 (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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95A ILE 3.9 12.3 - - - -
96A GLU* 3.3 46.9 + - - +
98A LEU 4.4 0.2 - - - -
99A PRO* 3.4 36.2 - - - +
100A PRO* 4.0 5.7 - - + +
113C GLN 4.5 1.0 - - - +
116C PHE* 3.6 15.3 - + + -
117C ALA* 3.7 23.1 - - + +
120C LYS* 3.6 42.6 + - + -
127C ASP* 3.7 21.2 + - - -
128C ALA* 3.1 20.0 + - - +
130C ASP* 1.3 79.0 - - + +
132C PHE* 1.4 60.0 + - - +
134C MET 3.6 0.2 + - - -
135C ALA* 3.1 27.0 + - - +
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Residues in contact with PHE 132 (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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114C VAL* 6.1 0.9 - - + -
117C ALA* 3.5 41.3 - - + -
118C GLU* 3.9 11.4 - - + -
121C ALA* 4.0 6.3 - - + -
128C ALA 3.5 15.0 - - - -
129C ARG 3.2 6.5 + - - +
131C TYR* 1.4 72.8 - - - +
133C GLN* 1.3 58.6 + - - +
135C ALA* 3.3 6.1 + - + +
136C ARG* 2.9 31.0 + - - +
145C VAL* 5.4 1.2 - - - +
148C SER* 3.5 31.4 - - - -
149C PHE* 3.6 44.2 - + + +
152C PHE* 3.4 43.1 - + + -
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Residues in contact with GLN 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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130A ASP* 4.0 18.2 + - - +
131A TYR* 3.7 20.5 + - + -
134A MET* 3.8 27.1 - - - +
129C ARG* 3.0 30.0 + - - +
130C ASP* 3.4 14.5 - - - +
132C PHE* 1.3 77.3 - - - +
134C MET* 1.4 61.4 + - + +
136C ARG* 3.6 20.0 + - - +
137C ALA* 3.0 28.1 + - - +
149C PHE* 3.4 31.7 - - - -
161C LYS* 5.4 2.0 - - - +
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Residues in contact with MET 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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92A SER* 3.8 33.4 - - - +
95A ILE* 3.6 24.0 - - + -
96A GLU* 3.4 30.7 - - + +
116A PHE* 3.6 31.4 - - + -
131A TYR* 4.4 0.7 - - + -
134A MET* 4.0 28.7 - - + -
113C GLN* 3.8 1.8 - - - -
130C ASP 2.9 15.8 + - - +
132C PHE 3.3 0.2 - - - -
133C GLN* 1.4 83.1 - - + +
135C ALA* 1.4 59.5 - - - +
137C ALA* 3.3 1.6 + - - +
138C ASN* 3.0 38.9 + - - +
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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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96A GLU* 5.7 0.2 - - - +
113C GLN* 3.5 40.1 + - + +
114C VAL* 4.2 7.4 - - + +
117C ALA* 5.1 0.9 - - + -
131C TYR 3.1 18.4 + - - +
132C PHE* 3.3 9.2 + - + +
134C MET* 1.4 74.4 - - - +
136C ARG* 1.4 57.2 + - - +
139C CYS* 2.9 35.3 + - - +
145C VAL* 3.5 14.5 - - + +
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Residues in contact with ARG 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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130A ASP* 2.7 30.3 + - - +
131A TYR* 4.5 6.2 + - - -
1202A GOL 3.2 33.4 + - - -
132C PHE 2.9 16.8 + - - +
133C GLN* 3.6 21.3 + - - +
135C ALA* 1.4 75.5 - - - +
137C ALA* 1.3 60.6 + - - +
140C LYS* 3.1 30.3 + - - +
145C VAL* 3.7 11.8 - - + +
146C HIS* 3.4 42.1 + - + +
149C PHE* 3.9 18.6 - - + -
161C LYS* 5.0 0.2 - - - +
165C LEU* 3.5 26.4 - - - +
168C LYS* 3.6 20.0 - - - +
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Residues in contact with ALA 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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116A PHE* 4.0 13.9 - - + -
120A LYS* 3.6 27.7 + - - +
131A TYR* 3.2 28.6 + - + +
1202A GOL 3.9 6.1 + - - -
133C GLN 3.0 15.4 + - - +
134C MET* 3.3 6.9 + - - +
136C ARG* 1.3 76.0 - - - +
138C ASN* 1.3 65.4 + - - +
140C LYS* 4.7 9.2 + - - +
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Residues in contact with ASN 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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88A ILE* 5.4 5.0 - - - +
89A GLY* 4.9 2.3 - - - -
92A SER* 3.1 34.8 + - - -
96A GLU* 5.2 0.6 + - - +
116A PHE* 5.6 0.2 - - - -
100C PRO* 3.7 20.3 - - + +
104C GLY* 3.4 25.5 - - - +
109C PHE* 4.1 7.6 - - + -
113C GLN* 3.0 33.4 + - - +
134C MET* 3.0 18.4 + - - +
137C ALA* 1.3 82.2 - - - +
139C CYS* 1.3 64.3 + - - +
140C LYS* 3.8 1.6 - - - -
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Residues in contact with CYS 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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104C GLY 4.1 10.8 - - - +
106C ASN 5.5 0.4 - - - -
109C PHE* 3.8 20.4 - - - -
110C ALA* 3.6 39.5 - - + -
113C GLN* 4.0 10.5 - - - -
135C ALA 2.9 16.7 + - - +
136C ARG 3.9 1.6 - - - -
138C ASN* 1.3 88.2 - - - +
140C LYS* 1.4 60.1 + - - +
141C LYS* 3.0 10.0 + - - -
142C PHE* 3.2 14.6 + - + +
145C VAL* 3.7 17.5 - - + +
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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