Contacts of the helix formed by residues 136 - 153 (chain C) in PDB entry 1EAK
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 ASP 136 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C LEU* 1.3 73.7 - - - +
137C PRO* 1.3 78.0 - - + +
138C GLU* 3.0 4.5 + - - +
139C THR* 2.6 53.6 + - - +
140C VAL* 3.1 10.0 + - - +
220C VAL* 5.7 1.6 - - - +
222C ARG* 3.2 46.6 + - + +
232C TYR* 4.1 1.4 - - - -
333C PRO* 4.0 4.9 - - + -
334C GLU* 4.0 17.4 + - + +
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Residues in contact with PRO 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C TYR* 3.5 21.2 - - + -
135C LEU 3.9 0.4 - - - +
136C ASP* 1.3 88.4 - - + +
138C GLU* 1.3 59.4 - - + +
140C VAL 3.3 0.5 + - - -
141C ASP* 2.8 35.4 + - - +
314C TYR* 3.7 38.4 - - + +
333C PRO* 3.4 35.7 - - + +
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Residues in contact with GLU 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C ASP* 3.0 9.9 + - - +
137C PRO* 1.3 79.9 - - + +
139C THR* 1.3 64.5 + - - +
141C ASP* 2.9 12.2 + - - +
142C ASP* 2.8 26.2 + - - +
222C ARG* 3.2 30.6 + - - +
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Residues in contact with THR 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C LEU* 4.1 22.2 - - + -
136C ASP* 2.6 42.3 + - - -
138C GLU* 1.3 71.0 - - - +
140C VAL* 1.3 56.3 + - - +
142C ASP* 3.6 7.0 + - - +
143C ALA* 3.0 26.7 + - - +
146C ARG* 4.9 2.4 + - - +
215C LEU* 3.8 24.5 - - + -
220C VAL* 5.4 0.9 - - + -
222C ARG* 4.6 0.7 + - - -
232C TYR* 2.5 32.8 + - + +
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Residues in contact with VAL 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C TYR* 3.7 24.2 - - + -
132C THR* 4.0 14.8 - - + +
135C LEU* 3.4 39.0 - - + +
136C ASP 3.1 7.2 + - - +
137C PRO 3.5 6.7 - - - +
139C THR* 1.3 73.4 - - - +
141C ASP* 1.3 68.4 + - - +
142C ASP 3.0 2.0 + - - -
143C ALA* 3.1 16.7 + - - +
144C PHE* 3.1 44.8 + - + -
173C PHE* 4.4 4.7 - - + -
397C LEU* 3.8 4.0 - - + -
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Residues in contact with ASP 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C TYR* 4.2 5.7 + - - -
128C ILE* 3.3 17.4 - - - +
131C TYR* 2.6 28.9 + - - -
137C PRO* 2.8 25.7 + - - +
138C GLU* 2.9 13.4 + - - +
140C VAL* 1.3 72.8 - - - +
142C ASP* 1.3 61.6 + - - +
144C PHE* 3.7 2.9 + - - +
145C ALA* 3.2 21.7 + - - +
161C ARG* 3.0 29.5 + - - +
314C TYR* 4.2 7.6 + - - -
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Residues in contact with ASP 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 GLU 2.8 19.1 + - - +
139C THR* 3.7 8.3 - - - +
141C ASP* 1.3 70.7 - - - +
143C ALA* 1.3 54.3 + - - +
145C ALA* 2.7 16.4 + - - +
146C ARG* 2.7 73.0 + - - +
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Residues in contact with ALA 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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135C LEU* 5.5 0.4 - - + -
139C THR* 3.0 17.0 + - + +
140C VAL* 3.1 7.2 + - - +
142C ASP* 1.3 77.6 + - - +
144C PHE* 1.3 63.8 + - - +
146C ARG* 3.5 19.6 + - - +
147C ALA* 2.9 24.4 + - - +
215C LEU* 4.7 6.3 - - + -
397C LEU* 4.2 14.6 - - + -
398C PHE* 3.8 27.8 - - + +
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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
----------------------------------------------------------
126C TYR* 4.6 1.6 - - + -
128C ILE* 3.4 34.5 - - + -
140C VAL* 3.1 27.7 + - + -
141C ASP 4.0 4.0 - - - +
143C ALA* 1.3 74.2 - - - +
145C ALA* 1.3 52.1 - - - +
147C ALA* 3.1 3.7 + - - +
148C PHE* 2.8 43.3 + - + -
171C ILE* 3.4 33.2 - - + -
173C PHE* 3.7 17.5 - + - -
207C PHE* 3.9 14.1 - + - -
397C LEU* 3.4 39.7 - - + -
401C ALA* 3.7 14.8 - - + -
405C PHE* 3.9 15.9 - + + -
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Residues in contact with ALA 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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126C TYR* 4.0 16.5 + - + +
141C ASP 3.2 12.7 + - - +
142C ASP* 2.7 21.9 + - - +
144C PHE* 1.3 74.3 - - - +
146C ARG* 1.3 62.3 + - - +
148C PHE* 3.1 8.3 + - - +
149C GLN* 3.0 22.3 + - - +
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Residues in contact with ARG 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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139C THR* 4.9 2.2 + - - +
142C ASP* 2.7 46.5 + - - +
143C ALA* 3.8 15.8 - - - +
145C ALA* 1.3 72.4 - - - +
147C ALA* 1.3 59.4 + - - +
149C GLN* 3.3 16.6 - - - +
150C VAL* 3.0 21.0 - - - +
215C LEU* 4.3 22.0 - - - +
396C SER* 5.3 0.2 + - - -
398C PHE* 3.4 45.2 - - + +
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Residues in contact with ALA 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 2.9 19.1 + - - +
144C PHE 3.3 5.6 - - - +
146C ARG* 1.3 75.5 - - - +
148C PHE* 1.3 64.2 + - - +
150C VAL* 3.2 16.6 + - - +
151C TRP* 3.7 11.6 + - - -
398C PHE* 3.5 18.8 - - + +
401C ALA* 3.7 8.3 - - + -
402C ALA* 3.4 30.3 - - - +
405C PHE* 3.7 6.8 - - + -
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Residues in contact with PHE 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C TYR* 3.4 53.2 - + + -
144C PHE 2.8 31.9 + - - -
145C ALA* 3.1 6.7 + - - +
147C ALA* 1.3 67.7 - - - +
149C GLN* 1.3 56.8 + - - +
150C VAL 2.7 15.9 + - - -
151C TRP* 3.0 12.7 + - - +
152C SER* 3.4 1.9 + - - -
159C PHE* 3.3 59.8 - + + -
169C ILE* 3.8 24.0 - - + -
171C ILE* 3.7 2.7 - - + -
405C PHE* 3.2 49.1 - + + -
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Residues in contact with GLN 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 ALA 3.0 13.1 + - - +
146C ARG* 3.3 16.6 - - - +
148C PHE* 1.3 74.5 - - - +
150C VAL* 1.3 57.3 + - + +
151C TRP 3.1 0.4 - - - -
152C SER* 3.1 17.5 + - - -
153C ASP* 2.4 65.3 + - - +
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Residues in contact with VAL 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 ARG 3.0 20.0 - - - +
147C ALA* 3.3 12.8 - - - +
148C PHE 2.7 1.2 + - - -
149C GLN* 1.3 80.5 - - + +
151C TRP* 1.3 63.7 - - + +
153C ASP* 4.3 11.4 - - - +
154C VAL* 4.5 2.3 - - - +
398C PHE* 3.6 25.4 - - + -
402C ALA* 4.9 1.3 - - + -
420C LEU* 4.8 5.6 - - + -
431C PHE* 3.9 16.8 - - + -
433C LEU* 3.3 43.8 - - + +
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Residues in contact with TRP 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 ALA 3.7 17.0 + - - -
148C PHE* 3.7 7.0 - - - +
150C VAL* 1.3 84.1 - - + +
152C SER* 1.3 62.7 + - - +
153C ASP 3.3 1.6 - - - -
154C VAL* 3.3 8.6 - - - +
155C THR* 2.9 25.8 + - - +
157C LEU* 5.3 1.6 - - + -
159C PHE* 4.3 13.9 - + + -
402C ALA* 3.1 20.6 + - - +
405C PHE* 4.1 15.9 - - + -
406C GLY* 3.5 23.7 - - - +
409C MET* 5.0 3.8 - - + -
411C LEU* 3.5 18.8 - - + -
420C LEU* 3.5 24.6 - - + +
421C MET* 4.2 5.2 - - + -
433C LEU* 3.7 28.5 - - + -
437C ASP* 4.2 9.0 - - + -
441C ILE* 3.4 54.7 - - + -
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Residues in contact with SER 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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148C PHE 3.4 4.9 + - - -
149C GLN* 3.1 38.1 + - - -
151C TRP* 1.3 75.3 - - - +
153C ASP* 1.3 60.2 + - - +
154C VAL 2.9 6.0 + - - -
155C THR* 2.7 23.7 + - - +
157C LEU* 3.0 28.7 - - - -
158C ARG* 5.0 2.0 - - - -
159C PHE* 4.4 8.7 - - - -
448C SER* 4.5 3.5 - - - -
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Residues in contact with ASP 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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149C GLN* 2.4 56.6 + - - +
150C VAL* 4.4 6.8 - - - +
151C TRP 3.3 0.4 - - - -
152C SER* 1.3 76.4 + - - +
154C VAL* 1.3 66.0 + - + +
448C SER* 3.5 15.8 + - - -
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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