Contacts of the helix formed by residues 154 - 168 (chain C) in PDB entry 4R0C
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 PRO 154 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C PHE* 3.5 11.3 - - - -
152C GLY 4.7 0.9 - - - +
153C ARG* 1.3 84.5 - - + +
155C PRO* 1.3 72.4 - - + +
156C ILE 3.3 0.4 - - - -
157C ALA* 3.2 15.3 + - + +
229C GLU* 3.7 43.5 - - + +
232C LEU* 3.6 33.4 - - + +
233C ALA* 4.0 17.3 - - + -
237C THR* 5.0 0.9 - - - +
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Residues in contact with PRO 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C GLY* 3.5 18.3 - - - +
148C PHE* 4.0 11.2 - - + -
149C GLN* 3.7 7.4 - - + +
153C ARG 3.1 6.0 - - - +
154C PRO* 1.3 85.8 - - + +
156C ILE* 1.3 59.9 + - + +
158C GLY* 3.0 3.8 + - - -
159C ILE* 3.0 30.2 + - - +
237C THR* 3.2 30.5 - - + +
452C TYR* 3.4 46.7 - - + -
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Residues in contact with ILE 156 (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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154C PRO 3.3 0.8 - - - -
155C PRO* 1.3 78.6 - - + +
157C ALA* 1.3 60.2 + - - +
159C ILE* 3.7 16.3 - - + +
160C ALA* 2.7 28.4 + - - +
231C ARG* 5.7 0.4 - - - +
232C LEU* 4.0 20.8 - - + +
449C ALA* 3.7 24.7 - - + +
452C TYR* 4.5 10.8 - - + -
453C GLN* 3.6 39.0 - - + +
456C THR* 4.7 3.6 - - + -
464C LEU* 3.5 28.7 - - + -
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Residues in contact with ALA 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C PHE* 4.3 5.2 - - + -
154C PRO* 3.2 14.2 + - + +
155C PRO 3.2 0.4 - - - -
156C ILE* 1.3 79.9 - - - +
158C GLY* 1.3 55.7 + - - +
160C ALA* 4.0 0.6 - - - +
161C THR* 2.9 34.3 + - - -
224C THR* 4.2 5.3 + - + +
228C THR* 4.1 13.0 - - + -
229C GLU* 3.8 38.8 - - + +
232C LEU* 3.5 10.7 - - + +
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Residues in contact with GLY 158 (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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144C ALA* 3.4 20.3 - - - +
148C PHE* 3.7 33.8 - - - -
154C PRO 3.5 4.4 + - - -
155C PRO 3.0 8.6 + - - -
157C ALA* 1.3 78.3 - - - +
159C ILE* 1.3 56.4 + - - +
161C THR* 3.4 4.0 + - - -
162C ALA 3.0 23.2 + - - -
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Residues in contact with ILE 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C ILE* 3.8 34.7 - - + +
142C PRO* 5.0 1.6 - - + -
145C GLY* 4.1 7.6 - - - +
155C PRO 3.0 13.4 + - - +
156C ILE* 3.7 15.0 - - + +
158C GLY* 1.3 74.7 - - - +
160C ALA* 1.3 58.1 + - - +
162C ALA* 3.3 2.1 + - - +
163C PHE* 2.9 28.3 + - + +
445C VAL* 4.5 15.9 - - + -
448C PHE* 3.4 36.3 - - + +
449C ALA* 3.8 15.9 - - + -
452C TYR* 3.8 21.8 - - + -
461C LEU* 5.8 1.1 - - + -
464C LEU* 5.8 1.1 - - + -
465C MET* 5.3 3.4 - - + -
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Residues in contact with ALA 160 (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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156C ILE 2.7 23.6 + - - +
157C ALA* 4.0 4.7 - - - +
159C ILE* 1.3 71.3 - - - +
161C THR* 1.3 66.4 + - - +
163C PHE* 3.4 0.9 + - - +
164C ALA* 3.0 26.0 + - - +
228C THR* 4.5 0.4 - - + -
464C LEU* 3.6 23.8 - - + -
465C MET* 3.5 18.6 - - + +
468C TYR* 4.0 22.6 - - + +
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Residues in contact with THR 161 (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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119C VAL* 3.7 24.9 - - + +
122C VAL* 3.6 20.9 - - + -
123C ALA 4.0 5.4 - - - +
148C PHE* 5.0 2.2 - - + -
157C ALA 2.9 19.7 + - - -
158C GLY* 3.6 6.3 - - - -
160C ALA* 1.3 79.3 - - - +
162C ALA* 1.3 62.9 + - - +
164C ALA* 3.2 3.3 + - - +
165C ALA* 3.1 18.2 + - - +
220C VAL* 3.8 18.5 - - + +
224C THR* 2.5 34.5 + - - +
468C TYR* 4.3 1.1 + - - -
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Residues in contact with ALA 162 (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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122C VAL* 3.9 19.5 - - + -
126C GLY* 5.7 0.2 - - - -
140C LEU* 4.3 3.8 - - + +
141C ILE* 3.6 35.0 - - + +
144C ALA* 4.0 3.6 - - + -
158C GLY 3.0 16.6 + - - +
159C ILE 3.7 2.0 - - - +
161C THR* 1.3 76.1 - - - +
163C PHE* 1.3 59.2 + - - +
165C ALA* 3.2 3.7 + - - +
166C VAL* 2.8 37.7 + - + +
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Residues in contact with PHE 163 (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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137C TYR* 4.2 3.8 - + - -
141C ILE* 3.9 14.5 - - + +
159C ILE 2.9 17.3 + - - +
160C ALA 3.8 3.1 - - - +
162C ALA* 1.3 75.9 - - - +
164C ALA* 1.3 64.2 + - - +
166C VAL* 4.8 0.4 - - - -
167C SER* 2.9 40.8 + - - -
434C ILE* 3.6 22.2 - - + +
439C MET* 3.6 34.1 - - + -
442C PHE* 4.6 14.8 - + - -
445C VAL* 3.8 42.0 - - + -
461C LEU* 4.7 3.1 - - + -
465C MET* 3.5 42.4 - - + -
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Residues in contact with ALA 164 (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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160C ALA 3.0 17.3 + - - +
161C THR 3.2 4.9 + - - +
163C PHE* 1.3 76.9 - - - +
165C ALA* 1.3 57.8 + - - +
168C GLY* 2.8 30.3 + - - -
169C GLY 3.3 1.9 + - - -
220C VAL* 3.6 21.5 - - + +
434C ILE* 4.2 12.8 - - + -
465C MET* 4.9 1.5 - - - -
468C TYR* 3.7 28.9 - - + -
472C LEU* 4.4 4.1 - - + +
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Residues in contact with ALA 165 (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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122C VAL 4.7 0.2 - - - +
123C ALA* 3.1 46.9 - - + +
126C GLY* 3.1 18.8 - - - +
127C VAL* 3.4 14.7 - - + +
161C THR 3.1 9.6 + - - +
162C ALA 4.1 1.1 - - - +
164C ALA* 1.3 76.8 - - - +
166C VAL* 1.3 66.6 + - - +
169C GLY* 3.4 13.6 + - - +
216C VAL* 4.5 6.1 - - + -
220C VAL* 4.6 2.9 - - + -
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Residues in contact with VAL 166 (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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126C GLY* 3.3 20.1 - - - +
129C SER* 3.4 21.9 + - - +
130C SER* 5.5 3.1 + - - -
136C GLY* 3.8 35.2 - - - +
137C TYR* 3.9 28.6 + - + -
140C LEU* 4.2 7.0 - - + -
141C ILE* 4.6 1.6 - - + -
162C ALA* 2.8 22.0 + - - +
163C PHE* 4.3 2.9 - - - +
165C ALA* 1.3 81.4 - - - +
167C SER* 1.3 61.9 + - - +
169C GLY 4.1 0.2 - - - -
170C PHE* 3.6 18.9 + - - +
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Residues in contact with SER 167 (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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137C TYR* 2.9 24.3 + - - -
163C PHE* 2.9 26.1 + - - -
166C VAL* 1.3 77.8 - - - +
168C GLY* 1.3 62.5 + - - +
169C GLY 3.3 0.2 - - - -
170C PHE* 3.4 9.9 - - - +
433C ASN* 2.6 38.6 + - - +
434C ILE* 3.5 12.3 - - - -
439C MET* 3.2 19.6 - - - +
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Residues in contact with GLY 168 (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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163C PHE 3.7 1.0 + - - -
164C ALA 2.8 18.8 + - - -
167C SER* 1.3 75.6 - - - +
169C GLY* 1.3 56.8 + - - +
170C PHE 3.3 1.1 - - - -
430C SER* 3.0 35.1 - - - -
431C SER* 3.9 1.8 + - - -
434C ILE* 3.9 9.5 - - - +
472C LEU* 4.0 18.9 - - - +
476C TRP* 3.3 10.2 - - - -
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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