Contacts of the helix formed by residues 137 - 150 (chain C) in PDB entry 3H1I
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 GLY 137 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64C PHE* 4.6 2.7 - - - -
135C PRO* 3.2 5.2 + - - +
136C TRP* 1.3 80.4 - - - +
138C GLN* 1.3 67.2 + - - +
139C MET 3.3 2.5 - - - -
140C SER* 3.0 8.7 + - - -
141C PHE 2.9 17.0 + - - -
256C ASN* 3.4 22.4 + - - -
258C THR 3.8 4.5 - - - -
259C PRO* 4.2 3.4 - - - -
260C ALA* 3.3 11.2 - - - +
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Residues in contact with GLN 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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137C GLY* 1.3 72.5 - - - +
139C MET* 1.3 67.5 + - - +
141C PHE* 3.2 0.5 + - - +
142C TRP* 2.9 40.0 + - - -
255C GLU* 3.3 19.7 + - + +
256C ASN* 3.7 1.2 + - - -
258C THR* 2.8 40.4 + - + +
259C PRO 3.8 0.2 - - - +
260C ALA* 3.3 0.6 - - - +
261C ASN* 2.8 37.4 + - - +
264C VAL* 2.6 32.3 + - - +
266C PRO* 3.2 26.6 - - + +
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Residues in contact with MET 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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132C TYR* 3.4 32.1 - - + +
138C GLN* 1.3 79.7 - - - +
140C SER* 1.3 69.5 + - - +
141C PHE 2.7 1.7 + - - -
142C TRP* 5.0 1.8 - - - -
143C GLY* 2.8 25.4 + - - +
253C ASP* 2.9 30.1 - - + +
255C GLU* 4.1 18.2 - - + -
256C ASN* 3.2 25.4 + - + +
266C PRO* 5.1 4.0 - - - -
268C HIS 4.5 1.3 - - - +
269C ILE* 4.1 19.1 - - - -
270C LYS 3.4 33.9 - - - +
2001C SMA 4.2 9.9 - - - +
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Residues in contact with SER 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C TYR* 2.7 29.5 + - - -
133C VAL* 3.3 30.7 - - - +
135C PRO* 3.9 1.0 - - - +
136C TRP* 3.3 6.2 + - - -
137C GLY 3.0 28.5 + - - -
139C MET* 1.3 79.1 - - - +
141C PHE* 1.3 62.3 + - - +
143C GLY* 4.1 0.5 - - - -
144C ALA* 3.1 21.7 + - - +
256C ASN* 3.0 13.2 + - - -
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Residues in contact with PHE 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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133C VAL* 5.2 1.8 - - - -
136C TRP* 3.9 26.7 - + - -
137C GLY 2.9 6.1 + - - -
138C GLN 3.5 6.1 - - - +
139C MET 2.7 3.0 + - - -
140C SER* 1.3 72.6 - - - +
142C TRP* 1.3 85.1 + + + +
144C ALA* 2.9 12.5 + - - +
145C THR* 2.9 38.9 + - - -
171C VAL* 3.4 31.4 - - + -
260C ALA* 3.4 28.9 - - + +
262C PRO* 3.7 35.2 - - + -
94R LYS* 3.6 26.0 - - - -
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Residues in contact with TRP 142 (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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138C GLN* 2.9 44.6 + - - +
139C MET* 3.1 3.6 + - - +
141C PHE* 1.3 86.3 - + - +
143C GLY* 1.3 66.8 + - - +
145C THR* 3.1 18.1 + - - -
146C VAL* 2.9 29.4 + - - +
261C ASN 3.0 21.5 + - - -
262C PRO 3.4 22.2 - - - -
264C VAL 3.2 17.8 + - - -
265C THR* 3.1 31.6 - - + -
266C PRO* 3.7 13.9 - - + -
269C ILE* 4.1 20.9 - - + -
94R LYS* 4.6 6.3 - - + -
143R GLY 3.8 20.6 - - - -
144R CYS* 4.4 4.7 - - - -
145R VAL* 3.7 14.1 - - + -
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Residues in contact with GLY 143 (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 PHE* 4.2 2.7 - - - -
132C TYR* 6.1 2.5 - - - -
139C MET* 2.8 18.9 + - - +
140C SER 4.1 0.4 - - - -
142C TRP* 1.3 71.3 - - - +
144C ALA* 1.3 62.8 + - - +
146C VAL 2.8 11.8 + - - -
147C ILE* 2.9 24.1 + - - +
2001C SMA 3.3 35.4 + - - -
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Residues in contact with ALA 144 (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 PHE* 3.7 17.2 - - + -
133C VAL* 3.7 22.4 - - + +
140C SER 3.1 14.6 + - - +
141C PHE* 2.9 14.8 + - - +
143C GLY* 1.3 77.0 - - - +
145C THR* 1.3 50.7 + - - +
146C VAL 3.3 0.2 + - - -
148C THR* 2.4 37.2 + - - +
171C VAL* 4.4 16.8 - - + -
175C THR* 5.5 0.4 - - + -
179C PHE* 4.6 7.4 - - + -
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Residues in contact with THR 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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141C PHE* 2.9 31.2 + - - -
142C TRP* 3.1 20.2 + - + -
144C ALA* 1.3 76.6 - - - +
146C VAL* 1.3 58.4 + - - +
148C THR* 3.8 3.2 + - - -
149C ASN* 3.1 19.0 + - - +
166C TRP* 4.2 8.1 - - + -
171C VAL* 4.0 14.7 - - + +
94R LYS* 4.1 19.3 - - - +
142R LEU 3.0 15.6 - - - +
143R GLY* 3.7 24.7 - - - +
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Residues in contact with VAL 146 (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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142C TRP 2.9 16.9 + - - +
143C GLY 2.8 6.8 + - - +
145C THR* 1.3 78.5 - - - +
147C ILE* 1.3 67.9 - - - +
149C ASN* 2.8 15.8 + - - +
150C LEU* 3.0 12.5 + - + +
269C ILE* 5.2 0.2 - - + -
2001C SMA 3.4 52.9 - - + +
142R LEU* 3.6 37.2 - - + +
144R CYS* 3.9 20.9 - - - -
160R CYS* 4.5 0.2 - - - -
161R HIS* 4.6 0.2 - - + -
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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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129C PHE* 3.3 57.7 - - + -
143C GLY* 2.9 12.7 + - - +
146C VAL* 1.3 70.9 - - - +
148C THR* 1.3 63.3 + - - +
150C LEU* 2.9 34.9 - - + +
151C PHE* 3.7 4.0 - - - -
272C GLU* 5.2 0.7 - - - +
275C PHE* 4.8 2.9 - - + -
2001C SMA 3.5 81.2 - - + +
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Residues in contact with THR 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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129C PHE* 4.4 3.1 - - + -
144C ALA 2.4 28.1 + - - +
145C THR 3.8 0.5 + - - -
147C ILE* 1.3 76.4 - - - +
149C ASN* 1.3 58.4 + - - +
150C LEU 2.7 12.1 + - - -
151C PHE* 2.8 30.3 + - - +
152C SER 4.3 0.2 + - - -
162C VAL* 4.6 6.3 - - - +
165C ALA* 4.0 13.5 - - + -
166C TRP* 2.7 32.1 + - - +
179C PHE* 3.8 22.4 - - + -
2001C SMA 3.8 23.6 - - + -
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Residues in contact with ASN 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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145C THR* 3.1 17.8 - - - +
146C VAL 2.8 11.5 + - - +
148C THR* 1.3 75.9 + - - +
150C LEU* 1.3 52.3 + - - +
151C PHE 3.0 0.2 - - - -
152C SER* 2.5 49.7 + - - +
162C VAL* 4.3 5.0 - - - +
166C TRP* 3.8 17.3 - - - -
2104C UNL 3.2 24.5 + - - -
142R LEU* 2.8 39.1 - - + +
143R GLY* 3.4 7.3 + - - -
2103R UNL 3.8 9.2 + - - -
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Residues in contact with LEU 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 VAL* 3.0 8.9 + - + +
147C ILE* 2.9 41.3 - - + +
148C THR 2.7 4.0 + - - -
149C ASN* 1.3 72.0 - - - +
151C PHE* 1.3 61.4 + - + +
153C ALA* 3.0 29.8 + - - +
154C ILE* 5.4 0.2 - - - +
282C LEU* 3.9 19.5 - - + -
292C VAL* 3.6 30.4 - - + +
295C LEU* 4.3 18.4 - - + -
2001C SMA 4.9 18.4 - - + +
142R LEU* 3.6 21.7 - - + +
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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