Contacts of the helix formed by residues 143 - 155 (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 ALA 143 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141C LYS 3.7 2.4 + - - -
142C PHE* 1.3 70.5 - - - +
144C PHE* 1.4 57.2 + - - +
146C HIS* 3.1 6.7 + - - +
147C ILE* 3.0 31.1 + - - +
174C ALA* 3.9 10.3 - - - -
175C VAL 2.9 32.5 + - - +
176C PRO* 3.6 17.5 - - + +
179C MET* 4.4 7.2 - - + -
180C LEU* 3.8 21.5 - - + +
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Residues in contact with PHE 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C GLU* 4.2 17.0 - - + -
110C ALA* 3.6 24.9 - - + -
111C ARG* 3.7 26.7 - - + -
114C VAL* 3.8 30.5 - - + -
142C PHE* 3.3 30.8 - + + -
143C ALA* 1.4 77.6 - - - +
145C VAL* 1.3 57.3 + - + +
147C ILE* 3.8 6.5 - - - +
148C SER* 3.0 29.5 + - - -
175C VAL 4.8 0.6 + - - -
176C PRO* 5.6 0.2 - - - +
179C MET* 3.9 26.2 - - + -
195C LEU* 5.6 3.4 - - + -
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Residues in contact with VAL 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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110C ALA* 3.9 9.2 - - + -
114C VAL* 3.7 27.9 - - + +
132C PHE* 5.4 1.1 - - - +
135C ALA* 3.5 35.0 - - + +
136C ARG* 3.7 12.6 - - + +
139C CYS* 3.7 29.4 - - + +
142C PHE* 3.1 20.8 + - + +
144C PHE* 1.3 79.9 - - + +
146C HIS* 1.3 61.0 + - + +
148C SER* 3.4 5.0 + - - -
149C PHE* 3.2 20.8 + - - +
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Residues in contact with HIS 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1202A GOL 3.4 25.4 - - - -
136C ARG* 3.4 31.1 + - + +
140C LYS* 2.7 30.5 + - + -
142C PHE 3.3 24.5 - - - -
143C ALA 3.1 5.3 + - - +
145C VAL* 1.3 74.1 - - + +
147C ILE* 1.4 60.8 + - - +
149C PHE* 3.4 8.5 + - - +
150C ALA* 2.9 28.5 + - - +
165C LEU* 4.5 13.5 + - + +
166C LEU* 4.6 1.9 - - + +
168C LYS* 6.1 0.4 - - - +
169C ALA* 3.6 33.2 + - + +
172C ARG* 6.0 1.8 - - + -
174C ALA* 3.6 15.8 - - + +
180C LEU* 4.6 2.2 - - + -
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Residues in contact with ILE 147 (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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143C ALA 3.0 20.3 + - - +
144C PHE* 4.0 5.8 - - - +
145C VAL 3.3 0.2 - - - -
146C HIS* 1.4 70.9 - - - +
148C SER* 1.3 55.9 + - - +
150C ALA* 3.1 1.6 + - - +
151C GLN* 2.7 35.9 + - + +
166C LEU* 3.8 22.7 - - + -
179C MET* 3.4 54.5 - - + +
180C LEU* 3.9 9.0 - - + +
183C ALA* 4.0 4.9 - - + -
194C LEU* 4.0 20.9 - - + -
195C LEU* 3.8 26.5 - - + -
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Residues in contact with SER 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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114C VAL* 3.3 19.4 - - - +
118C GLU* 2.6 30.9 + - - +
132C PHE* 3.5 20.2 - - - -
144C PHE 3.0 18.8 + - - -
145C VAL 3.5 6.7 - - - -
147C ILE* 1.3 77.0 - - - +
149C PHE* 1.4 56.1 + - - +
151C GLN* 3.4 7.8 + - - +
152C PHE 3.1 22.0 + - - -
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Residues in contact with PHE 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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129C ARG* 4.2 10.5 - - + -
132C PHE* 3.6 43.9 - + + +
133C GLN* 3.4 44.4 - - - -
136C ARG* 3.9 22.0 - - + -
145C VAL 3.2 10.6 + - - +
146C HIS* 3.6 9.6 - - - +
147C ILE 3.3 0.2 - - - -
148C SER* 1.4 73.4 - - - +
150C ALA* 1.3 66.1 + - - +
152C PHE* 3.2 6.3 + + - +
153C GLU* 3.0 45.6 + - + +
161C LYS* 5.0 6.3 - - - -
165C LEU* 3.7 28.3 - - + -
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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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146C HIS 2.9 17.8 + - - +
147C ILE 3.6 4.0 - - - +
149C PHE* 1.3 75.2 - - - +
151C GLN* 1.4 57.0 + - - +
153C GLU* 3.4 1.1 + - - -
154C LEU* 3.0 18.4 + - - +
162C SER* 2.7 41.5 + - - +
165C LEU* 3.9 13.6 - - + +
166C LEU* 3.7 14.1 - - + -
194C LEU* 3.6 14.4 - - + -
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Residues in contact with GLN 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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147C ILE* 2.7 21.3 + - + +
148C SER* 3.5 9.2 - - - +
149C PHE 3.3 0.2 - - - -
150C ALA* 1.4 67.7 - - - +
152C PHE* 1.3 60.7 - - - +
154C LEU* 3.3 5.6 + - - +
155C SER* 2.9 40.3 + - - +
192C LYS 3.0 22.8 + - - +
193C GLN* 3.4 24.3 + - - +
194C LEU* 2.8 43.6 + - + +
195C LEU 4.6 0.5 + - - -
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Residues in contact with PHE 152 (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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121C ALA* 4.0 21.5 - - + -
125C PRO* 3.3 29.2 - - + -
128C ALA* 4.2 1.3 - - + -
129C ARG* 3.9 40.4 - - + -
132C PHE* 3.4 43.1 - + + -
148C SER 3.1 7.5 + - - +
149C PHE* 3.2 12.8 + + - +
151C GLN* 1.3 75.3 - - - +
153C GLU* 1.4 80.7 + - - +
155C SER* 3.3 9.3 + - - -
156C GLN* 3.1 48.7 + - + +
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Residues in contact with GLU 153 (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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129C ARG* 2.7 33.7 + - - -
149C PHE* 3.0 31.3 + - + +
150C ALA 3.7 7.4 - - - +
152C PHE* 1.4 77.9 - - - +
154C LEU* 1.3 60.2 + - - +
156C GLN* 3.2 9.3 + - - +
158C ASN* 2.8 74.0 + - - +
161C LYS* 3.8 15.8 - - + +
162C SER* 4.0 8.5 - - - +
165C LEU* 3.7 17.9 - - + -
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Residues in contact with LEU 154 (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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150C ALA 3.0 17.4 + - - +
151C GLN* 3.6 7.2 - - - +
152C PHE 3.3 0.2 - - - -
153C GLU* 1.3 75.5 - - - +
155C SER* 1.4 56.6 + - - +
157C GLY* 2.9 21.4 + - - +
158C ASN 4.4 2.5 - - - +
159C VAL* 4.0 21.0 - - + +
162C SER* 3.8 8.9 - - - +
187C LEU* 3.7 21.5 - - + -
191C LYS 3.6 17.9 - - - +
192C LYS* 3.5 26.2 - - - +
194C LEU* 4.0 28.5 - - + -
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Residues in contact with SER 155 (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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151C GLN* 2.9 31.3 + - - +
152C PHE* 3.6 9.9 - - - -
154C LEU* 1.4 75.2 - - - +
156C GLN* 1.4 65.1 + - - +
157C GLY 3.3 1.0 + - - -
192C LYS 5.2 0.2 + - - -
193C GLN* 5.2 2.6 + - - -
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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