Contacts of the helix formed by residues 136 - 151 (chain C) in PDB entry 4U2M
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 ARG 136 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127B THR* 4.4 21.9 + - + +
134C PHE 3.2 1.0 - - - -
135C THR* 1.3 78.0 + - - +
137C HIS* 1.3 65.8 + - - +
138C ALA 3.4 2.0 + - - -
139C SER* 3.4 12.5 + - - -
140C ASP* 3.0 34.7 + - - +
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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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11C LEU* 4.2 5.4 - - + -
45C CYS* 3.8 15.5 - - + -
76C PHE* 3.5 42.2 + + - -
77C MET* 2.8 26.7 + - - -
80C ALA* 3.7 18.4 - - + -
134C PHE* 3.2 27.8 + - + +
135C THR 3.4 0.2 - - - -
136C ARG* 1.3 79.0 - - - +
138C ALA* 1.3 58.6 + - - +
140C ASP* 3.0 14.1 + - + +
141C VAL* 2.9 50.6 + - + +
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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
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7C SER* 3.6 33.8 - - - +
8C GLN* 3.6 26.5 - - + +
11C LEU* 3.9 19.8 - - + +
80C ALA* 5.0 1.2 - - - +
134C PHE 4.8 0.4 + - - -
135C THR 4.9 3.3 + - - +
136C ARG 3.4 1.2 - - - -
137C HIS* 1.3 78.5 - - - +
139C SER* 1.3 62.0 + - - +
141C VAL* 3.3 5.8 + - - +
142C LEU* 3.1 19.4 + - - +
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Residues in contact with SER 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C SER* 3.0 21.9 + - - -
135C THR 5.6 0.7 + - - -
136C ARG* 3.4 12.9 + - - -
138C ALA* 1.3 76.6 - - - +
140C ASP* 1.3 66.4 + - - +
142C LEU* 3.4 2.0 + - - +
143C LEU* 3.0 25.3 + - - +
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Residues in contact with ASP 140 (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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136C ARG* 3.0 32.3 + - - +
137C HIS* 3.0 14.5 + - - +
139C SER* 1.3 74.7 - - - +
141C VAL* 1.3 67.6 + - + +
143C LEU* 3.4 12.6 + - - +
144C ASN* 2.9 36.3 + - - +
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Residues in contact with VAL 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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10C VAL* 6.3 0.4 - - + -
11C LEU* 4.4 15.9 - - + -
14C LEU* 4.6 8.7 - - + -
41C VAL* 5.0 7.2 - - + -
44C ALA* 4.0 11.1 - - + +
45C CYS* 3.7 14.1 - - - -
77C MET 4.4 3.1 - - - +
137C HIS* 2.9 47.7 + - + +
138C ALA 3.6 7.6 - - - +
140C ASP* 1.3 77.9 - - + +
142C LEU* 1.3 58.1 + - - +
144C ASN* 3.2 5.2 + - - +
145C LEU* 2.8 46.7 + - + +
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Residues in contact with LEU 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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6C HIS* 3.8 15.3 - - + -
7C SER* 3.9 17.7 - - - +
10C VAL* 4.1 24.0 - - + -
138C ALA 3.1 13.1 + - - +
139C SER* 3.9 3.6 - - - +
140C ASP 3.3 0.2 - - - -
141C VAL* 1.3 77.2 - - - +
143C LEU* 1.3 67.9 + - - +
145C LEU* 3.2 14.6 + - + +
146C ASN 2.9 18.7 + - - -
172C VAL* 5.2 3.1 - - + -
213C MET 3.6 15.0 - - - +
214C TYR* 3.3 30.1 - - + +
215C THR 4.1 2.5 - - - +
216C SER* 3.7 22.9 - - - +
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Residues in contact with LEU 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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139C SER 3.0 18.7 + - - +
140C ASP* 3.6 11.4 - - - +
142C LEU* 1.3 76.4 - - - +
144C ASN* 1.3 65.3 + - - +
146C ASN* 3.2 12.8 + - + +
147C ARG* 2.9 42.1 + - + +
214C TYR 5.0 1.6 - - - -
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Residues in contact with ASN 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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44C ALA* 3.0 35.1 + - + +
140C ASP* 2.9 28.5 + - - +
141C VAL 3.8 1.8 - - - +
143C LEU* 1.3 78.0 - - - +
145C LEU* 1.3 65.8 + - - +
147C ARG* 3.2 36.7 + - + +
148C LEU* 2.9 27.6 + - + +
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Residues in contact with LEU 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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10C VAL* 5.1 0.9 - - + -
14C LEU* 4.3 15.0 - - + -
40C ALA* 3.6 40.8 - - + +
41C VAL* 4.4 4.3 - - + +
44C ALA* 4.0 7.4 - - + +
141C VAL* 2.8 39.2 + - + +
142C LEU* 3.2 17.2 + - + +
144C ASN* 1.3 74.3 - - - +
146C ASN* 1.3 56.2 + - - +
148C LEU* 3.3 10.1 + - + +
149C ARG 2.9 21.7 + - - -
169C HIS* 3.6 11.9 - - - +
172C VAL* 3.9 25.4 - - + -
214C TYR* 3.7 14.6 - - + -
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Residues in contact with ASN 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 LEU 2.9 7.4 + - - +
143C LEU* 3.2 14.4 + - + +
145C LEU* 1.3 73.2 - - - +
147C ARG* 1.3 61.9 + - - +
149C ARG* 3.0 37.2 + - - +
150C SER* 2.8 34.3 + - - -
214C TYR* 3.3 32.5 - - + +
215C THR* 3.6 21.6 - - - +
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Residues in contact with ARG 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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50C LYS* 5.3 11.0 - - - +
143C LEU* 2.9 32.0 + - + +
144C ASN* 3.2 35.7 + - - +
146C ASN* 1.3 74.0 - - + +
148C LEU* 1.3 66.4 + - + +
150C SER* 3.3 10.4 + - - -
151C ARG* 3.2 25.1 + - - +
153C ILE* 5.4 0.4 - - - +
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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
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40C ALA* 3.6 28.7 - - - +
43C ALA* 4.0 15.0 - - + +
44C ALA* 4.1 5.4 - - - +
50C LYS* 4.0 30.7 - - + +
144C ASN* 2.9 19.8 + - + +
145C LEU* 3.4 16.6 - - + +
146C ASN 3.2 0.2 - - - -
147C ARG* 1.3 78.5 - - + +
149C ARG* 1.3 64.1 + - - +
151C ARG 3.3 1.0 + - - -
152C ASP 3.1 3.3 + - - -
153C ILE* 2.8 66.9 + - + +
154C LEU* 4.8 1.3 - - + -
169C HIS* 3.9 4.9 - - - +
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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
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145C LEU 2.9 14.2 + - - +
146C ASN* 3.0 36.7 + - - +
148C LEU* 1.3 77.2 - - - +
150C SER* 1.3 62.3 + - - +
152C ASP* 3.0 14.2 + - - +
155C THR* 4.4 5.2 - - + +
166C PHE* 5.9 0.2 - - - -
167C ARG* 3.8 26.1 + - + +
168C ALA* 5.0 0.2 - - - -
169C HIS* 3.7 9.8 - - + -
210C LEU* 3.5 25.7 - - - +
211C ASP* 3.0 35.8 + - - +
214C TYR* 3.6 38.7 - - + +
215C THR* 5.2 1.0 - - - +
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Residues in contact with SER 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C ASN* 2.8 22.5 + - - -
147C ARG* 3.4 13.1 - - - -
149C ARG* 1.3 74.9 - - - +
151C ARG* 1.3 67.7 + - - +
152C ASP* 3.7 0.7 + - - +
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Residues in contact with ARG 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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50C LYS* 6.3 1.1 - - - +
147C ARG 3.2 12.4 + - - +
149C ARG 3.2 0.4 - - - -
150C SER* 1.3 82.7 + - - +
152C ASP* 1.3 70.0 + - - +
153C ILE* 3.3 30.7 + - + +
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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