Contacts of the helix formed by residues 137 - 153 (chain C) in PDB entry 4AD7
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 137 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C LEU 2.3 35.5 + - - +
134C TYR 2.9 4.2 + - - +
136C GLN* 1.3 75.3 - - - +
138C ALA* 1.3 56.1 + - - +
139C ARG* 3.2 3.1 - - - -
140C ALA* 2.8 30.4 + - + +
141C PHE* 3.5 16.0 - - + -
170C LEU* 4.1 16.6 - - + +
173C ARG* 2.4 42.8 + - - +
174C LEU* 3.3 14.2 + - - +
177C GLN* 2.8 26.7 + - - +
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Residues in contact with ALA 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C TYR* 2.9 35.2 + - + +
135C THR* 4.2 10.3 - - - +
136C GLN 3.5 2.8 + - - -
137C ASN* 1.3 75.2 - - - +
139C ARG* 1.3 61.6 + - - +
141C PHE* 3.1 13.5 + - - +
142C ARG* 3.0 26.6 + - + +
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Residues in contact with ARG 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C GLN 5.3 0.6 + - - +
137C ASN 3.0 1.3 + - - -
138C ALA* 1.3 77.7 - - - +
140C ALA* 1.3 57.5 + - - +
142C ARG* 3.4 40.1 + - - +
143C ASP* 2.9 56.8 + - - +
173C ARG* 6.2 2.5 - - - +
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Residues in contact with ALA 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C ASN* 2.8 19.8 + - + +
139C ARG* 1.3 79.2 - - - +
141C PHE* 1.3 56.9 + - + +
143C ASP* 3.2 10.5 + - - +
144C LEU* 2.9 27.2 + - - +
166C PHE* 3.7 21.8 - - + -
170C LEU* 4.8 12.1 - - + -
173C ARG* 5.3 11.6 - - - +
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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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119C GLU* 6.0 0.2 - - - -
122C LEU* 4.1 22.4 - - + -
126C PHE* 4.4 4.5 - + - -
133C LEU 4.9 0.9 - - - -
134C TYR* 3.7 33.4 - + + -
137C ASN* 3.5 31.2 - - + -
138C ALA* 3.1 5.3 + - - +
140C ALA* 1.3 72.9 - - + +
142C ARG* 1.3 66.7 + - - +
144C LEU* 3.2 6.7 + - - +
145C TYR* 3.0 32.5 + - + -
166C PHE* 4.3 15.5 - + - -
170C LEU* 4.5 18.2 - - + -
321C LEU* 3.7 31.0 - - + -
325C ILE* 3.6 32.3 - - + -
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Residues in contact with ARG 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C GLU* 3.9 20.1 - - + +
123C GLN* 5.7 5.2 - - - +
138C ALA* 3.0 15.6 + - + +
139C ARG* 3.4 48.7 - - - +
141C PHE* 1.3 75.6 - - - +
143C ASP* 1.3 61.4 + - - +
145C TYR* 3.2 5.0 + - - +
146C SER* 2.9 36.1 + - - +
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Residues in contact with ASP 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C ARG* 2.9 46.0 + - - +
140C ALA* 3.2 11.5 + - - +
142C ARG* 1.3 79.8 + - - +
144C LEU* 1.3 56.6 + - - +
146C SER* 3.3 9.1 + - - -
147C GLU* 2.9 38.6 + - + +
166C PHE* 6.2 0.2 - - + -
169C ARG* 5.9 1.2 + - - -
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Residues in contact with LEU 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C ALA 2.9 13.1 + - - +
141C PHE* 3.2 8.5 + - - +
143C ASP* 1.3 77.4 - - - +
145C TYR* 1.3 59.4 + - + +
147C GLU* 3.2 12.3 + - + +
148C LEU* 2.9 45.7 + - + +
159C LEU* 6.3 0.2 - - + -
162C THR* 5.5 2.2 - - - +
163C LEU* 3.7 31.0 - - + -
166C PHE* 3.5 48.0 - - + -
209C LEU* 4.9 3.6 - - + -
317C VAL* 5.2 1.1 - - + -
321C LEU* 4.1 28.0 - - + -
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Residues in contact with TYR 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C LEU* 3.5 49.2 - - + +
118C SER* 2.8 29.4 + - - -
119C GLU* 3.4 43.3 - - + +
122C LEU* 4.2 10.0 - - + +
141C PHE* 3.0 25.6 + - + -
142C ARG 3.7 1.8 - - - +
144C LEU* 1.3 78.9 - - + +
146C SER* 1.3 57.4 + - - +
148C LEU* 3.3 8.3 + - + +
149C ARG* 2.9 46.6 + - - +
317C VAL* 3.6 18.4 - - + +
318C HIS* 3.6 9.4 + - - +
321C LEU* 4.2 20.0 - - + -
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Residues in contact with SER 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C ARG* 2.9 20.9 + - - +
143C ASP* 3.5 13.4 + - - -
144C LEU 3.2 0.2 - - - -
145C TYR* 1.3 76.3 - - - +
147C GLU* 1.3 59.3 + - - +
149C ARG* 3.1 18.3 + - - +
150C LEU* 2.9 37.0 + - - +
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Residues in contact with GLU 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C ASP* 2.9 24.2 + - + +
144C LEU* 3.2 15.5 + - + +
146C SER* 1.3 77.7 - - - +
148C LEU* 1.3 58.2 + - + +
150C LEU* 3.3 17.5 + - - +
151C TYR* 2.9 29.1 + - - +
156C ASN* 3.8 12.5 + - - +
159C LEU* 4.8 3.7 - - + +
162C THR* 3.7 37.3 - - - +
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Residues in contact with LEU 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C LEU* 4.1 18.4 - - + -
144C LEU* 2.9 37.3 + - + +
145C TYR* 3.7 10.8 - - + +
146C SER 3.3 0.2 - - - -
147C GLU* 1.3 72.6 - - - +
149C ARG* 1.3 58.9 + - - +
151C TYR* 3.4 4.4 + - + +
152C TYR* 2.9 28.2 + - - +
159C LEU* 3.8 30.3 - - + -
163C LEU* 5.3 4.3 - - + -
209C LEU* 5.8 4.0 - - + -
213C ALA* 4.8 5.2 - - + -
217C PHE* 4.1 26.0 - - + -
317C VAL* 4.2 33.7 - - + -
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Residues in contact with ARG 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C GLN* 5.8 9.6 - - + +
115C LEU* 3.7 16.3 - - + +
116C ASN* 3.1 30.1 + - - +
119C GLU* 3.1 28.3 + - - +
145C TYR* 2.9 43.5 + - - +
146C SER* 3.2 17.4 + - - +
148C LEU* 1.3 74.4 - - - +
150C LEU* 1.3 59.3 + - + +
152C TYR* 3.1 11.0 + - + +
153C ARG* 3.0 39.7 + - + +
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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 SER* 2.9 22.4 + - - +
147C GLU* 3.3 20.8 + - - +
149C ARG* 1.3 76.5 - - + +
151C TYR* 1.3 61.4 + - - +
153C ARG* 3.2 31.1 + - - +
154C GLY 3.1 18.2 + - - -
155C ALA* 3.1 26.0 + - + -
156C ASN* 3.5 16.1 + - + -
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Residues in contact with TYR 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 GLU 2.9 16.9 + - - +
148C LEU* 3.6 5.8 - - + +
150C LEU* 1.3 76.0 - - - +
152C TYR* 1.3 61.1 + - - +
154C GLY* 3.3 5.4 + - - -
156C ASN* 3.8 22.4 - - + +
157C LEU 4.1 11.2 - - - -
158C HIS 4.7 0.9 - - - -
159C LEU* 3.6 62.5 - - + +
213C ALA 4.3 3.1 - - - -
214C THR* 3.3 15.3 + - - -
217C PHE* 3.6 33.8 - + + +
218C VAL* 3.2 21.6 - - + +
221C ARG* 3.3 37.4 + - - -
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Residues in contact with TYR 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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108C ASP* 2.6 36.5 + - - -
111C PHE* 3.6 32.8 - + + +
112C GLN* 4.2 19.7 - - + -
115C LEU* 5.7 1.3 - - + -
148C LEU 2.9 14.1 + - - +
149C ARG* 3.1 13.2 + - + +
151C TYR* 1.3 77.6 - - - +
153C ARG* 1.3 71.3 + - + +
154C GLY 3.1 0.4 - - - -
217C PHE* 4.0 28.3 - + + -
220C ALA* 4.1 15.3 - - + -
221C ARG* 3.2 37.5 - - - +
224C VAL* 3.5 19.2 - - + +
314C ILE* 6.2 0.7 - - + -
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Residues in contact with ARG 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C GLN* 6.0 6.3 - - - +
149C ARG* 3.0 24.2 + - + +
150C LEU* 3.2 32.2 + - - +
152C TYR* 1.3 89.3 - - + +
154C GLY* 1.3 57.6 + - - +
155C ALA* 3.1 15.1 + - + +
221C ARG* 4.8 2.7 - - - -
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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
------------------------------------------------------------
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