Contacts of the helix formed by residues 134 - 148 (chain C) in PDB entry 4K9N
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 GLU 134 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B ARG 4.6 5.1 - - - +
104B ILE* 4.6 0.9 - - - +
105B GLY* 3.2 31.5 + - - +
127C TYR* 2.4 35.3 + - - -
129C PRO* 3.9 7.6 - - + -
130C ALA* 2.8 33.4 + - - +
131C SER* 3.2 20.4 + - - +
132C ALA 3.1 0.4 - - - -
133C ALA* 1.3 78.9 - - - +
135C VAL* 1.3 62.5 + - - +
136C PRO* 3.4 0.9 - - - -
137C HIS* 3.1 14.5 + - - +
138C ALA* 2.9 22.0 + - - +
141C ARG* 4.3 1.0 + - - -
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Residues in contact with VAL 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C VAL* 3.7 16.6 - - + -
8C THR* 4.2 4.3 - - + +
129C PRO* 3.9 20.0 - - + -
131C SER 3.9 2.2 - - - +
132C ALA 3.0 19.0 + - - +
134C GLU* 1.3 76.7 - - - +
136C PRO* 1.3 66.9 - - + +
138C ALA* 3.2 1.7 + - - +
139C MET* 2.8 22.5 + - + +
156C LEU* 4.7 3.4 - - + +
158C VAL* 3.9 20.4 - - + -
162C ASP* 3.4 27.6 - - + +
163C TRP* 3.9 24.2 - - + -
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Residues in contact with PRO 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C VAL* 4.0 11.7 - - + -
7C THR* 3.8 31.9 - - + -
8C THR* 3.8 20.9 - - - +
11C LEU* 3.4 14.8 - - + +
132C ALA 4.0 3.8 - - - +
133C ALA 3.7 13.2 - - - +
135C VAL* 1.3 93.3 - - + +
137C HIS* 1.3 57.3 + - - +
139C MET* 3.2 4.1 + - + -
140C SER* 2.9 25.3 + - - -
167C ALA* 4.7 4.3 - - + -
171C SER* 4.1 9.6 - - - +
174C LEU* 3.6 13.2 - - + -
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Residues in contact with HIS 137 (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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105B GLY* 3.3 42.9 - - - -
106B VAL* 3.8 4.7 - - + -
133C ALA 5.0 1.5 + - - +
134C GLU* 3.1 16.6 + - + +
136C PRO* 1.3 80.6 - - - +
138C ALA* 1.3 58.8 + - - +
140C SER* 3.2 5.4 + - - -
141C ARG* 3.0 43.4 + - + +
171C SER* 5.1 2.2 + - - +
174C LEU* 3.6 31.3 - - + +
288D TYR* 6.0 1.6 - - - -
306D ALA 5.4 0.4 - - - -
307D ARG* 2.7 31.7 + - - -
308D ALA 4.6 0.7 - - - -
309D PRO* 4.2 13.1 - - + +
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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
----------------------------------------------------------
125C TRP* 3.7 4.4 - - - -
127C TYR* 3.9 16.4 - - + -
129C PRO* 3.8 14.6 - - + -
134C GLU* 2.9 14.6 + - + +
135C VAL 3.7 7.2 - - - +
137C HIS* 1.3 76.6 + - - +
139C MET* 1.3 58.3 + - - +
141C ARG* 3.3 14.5 + - - +
142C ALA* 2.9 27.7 + - - +
156C LEU* 3.7 26.2 - - + +
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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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8C THR* 3.9 27.4 - - + -
11C LEU* 4.0 14.4 - - + -
12C LEU* 4.3 11.4 - - + -
31C PHE* 5.3 0.2 - - + -
66C PHE* 3.7 28.3 - - + -
93C ILE* 4.4 9.4 - - - -
95C THR* 3.9 17.7 - - + -
135C VAL* 2.8 16.7 + - + +
136C PRO* 3.5 7.4 - - + +
138C ALA* 1.3 72.9 - - - +
140C SER* 1.3 65.2 + - - +
142C ALA* 3.2 3.6 + - - +
143C ILE* 2.9 25.2 + - + +
156C LEU* 3.8 25.3 - - + +
158C VAL* 5.4 0.4 - - + -
163C TRP* 4.4 14.8 - - + -
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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
----------------------------------------------------------
11C LEU* 3.6 15.3 - - - +
136C PRO 2.9 13.3 + - - -
137C HIS* 3.3 10.9 - - - -
139C MET* 1.3 76.5 - - - +
141C ARG* 1.3 62.4 + - - +
143C ILE* 3.2 7.4 + - - +
144C HIS* 3.1 44.5 + - - -
174C LEU* 3.8 29.0 + - - +
177C ARG* 4.3 8.8 + - - -
306D ALA 4.4 1.7 + - - -
308D ALA 5.0 0.3 + - - -
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Residues in contact with ARG 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ILE 4.9 1.6 + - - -
105B GLY* 3.2 25.2 + - - -
107B GLU* 3.2 27.9 + - - +
125C TRP* 3.5 47.5 - - + +
127C TYR* 3.9 24.2 + - - -
134C GLU* 4.3 0.2 + - - -
137C HIS* 3.0 36.1 + - + +
138C ALA* 3.3 10.3 + - - +
140C SER* 1.3 74.1 + - - +
142C ALA* 1.3 57.5 + - - +
145C MET* 2.8 36.3 + - + +
303D LEU* 5.5 5.1 + - - +
306D ALA* 3.5 29.0 - - + +
307D ARG* 3.7 17.8 - - - +
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Residues in contact with ALA 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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93C ILE* 4.1 14.4 - - + -
125C TRP* 3.7 16.7 - - + -
138C ALA 2.9 12.9 + - - +
139C MET* 3.2 12.8 + - - +
141C ARG* 1.3 74.2 - - - +
143C ILE* 1.3 65.8 + - - +
145C MET* 3.9 0.4 - - - -
146C ALA* 3.0 20.6 + - - +
154C VAL* 3.4 29.4 - - + +
156C LEU* 4.7 11.7 - - + -
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Residues in contact with ILE 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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11C LEU* 4.1 24.7 - - + +
12C LEU* 4.1 23.1 - - + -
15C GLN* 4.0 38.8 - - + +
17C ILE* 4.1 7.6 - - + -
64C PRO* 5.3 2.5 - - + -
93C ILE* 3.8 25.9 - - + +
139C MET* 2.9 23.6 + - + +
140C SER* 3.6 7.6 - - - +
142C ALA* 1.3 75.2 - - - +
144C HIS* 1.3 69.7 + - + +
146C ALA* 3.4 2.1 + - - +
147C SER* 2.8 36.6 + - - +
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Residues in contact with HIS 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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11C LEU* 6.0 0.4 - - - +
15C GLN* 3.5 30.3 + - - +
140C SER* 3.1 40.3 + - - +
141C ARG 4.1 1.8 - - - +
143C ILE* 1.3 79.6 - - + +
145C MET* 1.3 62.1 + - - +
147C SER* 4.3 5.7 - - - -
148C MET* 2.9 43.3 + - + +
174C LEU 5.2 0.6 + - - -
177C ARG* 3.7 36.9 - - - +
179C VAL* 3.4 33.2 - - + +
306D ALA* 4.2 16.2 - - + -
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Residues in contact with MET 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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124C LYS* 2.7 67.9 + - + +
125C TRP* 4.0 20.2 - - + -
141C ARG* 2.8 22.5 + - + +
142C ALA* 4.0 0.9 - - - +
144C HIS* 1.3 77.8 - - - +
146C ALA* 1.3 57.0 + - - +
147C SER 3.4 0.2 + - - -
148C MET* 3.6 13.2 - - + +
154C VAL* 3.8 17.5 - - + -
302D PRO* 3.9 10.3 - - + +
303D LEU* 3.6 30.7 - - + -
306D ALA* 3.6 22.2 - - + -
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Residues in contact with ALA 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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64C PRO* 5.1 0.7 - - + -
91C PRO* 3.4 14.4 - - + +
92C LEU 4.1 3.6 - - - +
93C ILE* 4.0 20.4 - - + -
142C ALA 3.0 17.7 + - - +
143C ILE 3.8 4.0 - - - +
145C MET* 1.3 76.8 - - - +
147C SER* 1.3 60.4 + - - +
151C GLN* 3.4 11.8 - - - +
152C GLY 3.3 39.8 + - - +
154C VAL* 3.6 8.4 - - + +
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Residues in contact with SER 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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64C PRO* 3.5 27.0 - - - +
91C PRO* 4.6 1.3 - - - -
143C ILE* 2.8 25.9 + - - +
144C HIS* 3.2 8.9 + - - -
146C ALA* 1.3 79.1 - - - +
148C MET* 1.3 65.1 + - - +
149C ALA 3.7 0.9 + - - -
151C GLN* 3.0 28.6 + - - +
181C SER* 4.7 2.1 + - - -
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Residues in contact with MET 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C LYS* 2.9 25.6 + - - +
144C HIS* 2.9 28.2 + - + +
145C MET* 3.6 22.0 + - + -
146C ALA 3.6 0.2 - - - -
147C SER* 1.3 77.3 - - - +
149C ALA* 1.3 66.2 + - - +
150C PRO 3.0 7.3 - - - -
151C GLN* 3.2 4.3 + - - -
179C VAL* 3.6 35.4 - - + +
181C SER* 3.9 12.6 - - - +
302D PRO* 3.2 36.6 - - + +
305D ALA* 4.0 2.0 - - - -
306D ALA* 3.9 7.2 - - + +
315D VAL* 3.8 21.5 - - + -
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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