Contacts of the helix formed by residues 133 - 151 (chain C) in PDB entry 4M3P
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 SER 133 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C CYS 4.2 0.4 + - - -
132C LYS* 1.3 76.8 - - - +
134C GLU* 1.3 54.9 + - - +
135C THR* 3.4 9.5 + - - -
136C GLU* 3.0 35.5 + - - +
137C VAL* 2.8 33.6 + - - +
169C TRP* 4.7 1.1 - - - -
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Residues in contact with GLU 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C SER* 1.3 73.5 - - - +
135C THR* 1.3 58.3 + - - +
137C VAL* 3.6 1.4 - - - +
138C LYS* 2.9 61.8 + - + +
169C TRP* 3.5 56.2 + - + -
172C GLU* 4.5 0.5 - - - +
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Residues in contact with THR 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C SER* 3.3 9.0 + - - +
134C GLU* 1.3 81.2 - - - +
136C GLU* 1.3 64.8 + - + +
138C LYS* 3.5 5.7 + - - +
139C LYS* 3.1 51.9 + - - +
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Residues in contact with GLU 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C CYS 3.6 6.9 - - - +
132C LYS* 3.4 26.9 - - + +
133C SER* 3.0 39.0 + - - +
135C THR* 1.3 78.1 - - + +
137C VAL* 1.3 65.2 - - - +
139C LYS* 3.4 13.6 + - + +
140C VAL* 3.3 26.0 + - - +
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Residues in contact with VAL 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C THR* 4.5 11.0 - - + +
132C LYS* 3.7 25.8 - - + +
133C SER 2.8 20.9 + - - +
134C GLU 3.6 4.5 - - - +
136C GLU* 1.3 76.3 - - - +
138C LYS* 1.3 63.6 + - - +
140C VAL* 3.0 19.5 + - - +
141C PHE* 3.1 45.1 + - + -
166C GLU* 4.2 12.8 - - + +
169C TRP* 4.1 27.6 - - + -
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Residues in contact with LYS 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C GLU* 2.9 46.1 + - + +
135C THR* 3.9 5.8 - - - +
136C GLU 3.4 0.2 - - - -
137C VAL* 1.3 77.1 - - - +
139C LYS* 1.3 55.9 + - - +
141C PHE* 3.3 5.3 + - - +
142C LEU* 2.9 39.6 + - + +
169C TRP* 3.7 29.6 - - + +
172C GLU* 2.7 34.8 + - - +
173C THR* 3.6 18.6 - - - +
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Residues in contact with LYS 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C THR* 3.1 40.8 + - - +
136C GLU* 3.6 15.9 - - + +
137C VAL 3.3 0.2 - - - -
138C LYS* 1.3 75.0 - - - +
140C VAL* 1.3 58.3 + - + +
142C LEU* 3.3 11.8 + - + +
143C GLN* 2.9 36.0 + - + +
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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
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77C TYR 3.4 25.8 - - - +
125C THR* 4.2 18.4 - - + -
126C PRO* 6.1 0.2 - - + -
132C LYS* 3.8 26.5 - - + -
136C GLU 3.3 14.3 + - - +
137C VAL 3.0 8.9 + - - +
139C LYS* 1.3 79.8 - - + +
141C PHE* 1.3 63.6 + - + +
143C GLN* 3.3 19.8 + - - +
144C GLN* 3.2 29.3 + - - +
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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
----------------------------------------------------------
122C VAL* 4.1 13.8 - - + +
123C SER 3.4 22.2 - - - -
125C THR* 4.4 10.1 - - + -
137C VAL* 3.1 42.1 + - + -
138C LYS* 3.3 7.8 + - - +
139C LYS 3.3 0.2 - - - -
140C VAL* 1.3 75.4 - - + +
142C LEU* 1.3 57.6 + - - +
144C GLN* 3.2 20.5 + - - +
145C LEU* 2.9 28.8 + - - +
161C PHE* 3.8 26.2 - + - -
166C GLU* 3.9 9.6 - - - -
169C TRP 4.3 3.4 - - - -
170C ALA* 3.6 33.0 - - + -
173C THR* 4.0 15.4 - - + +
174C LEU* 4.9 5.9 - - + +
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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
----------------------------------------------------------
138C LYS* 2.9 29.5 + - + +
139C LYS* 3.6 10.5 - - + +
140C VAL 3.3 0.2 - - - -
141C PHE* 1.3 73.9 - - - +
143C GLN* 1.3 65.5 + - - +
145C LEU* 3.3 15.7 + - + +
146C GLU* 3.1 23.9 + - - +
173C THR* 3.8 18.4 - - + +
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Residues in contact with GLN 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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77C TYR* 4.3 21.1 - - + -
97C GLN* 6.1 0.2 - - - +
139C LYS* 2.9 17.6 + - + +
140C VAL* 3.5 18.4 - - - +
141C PHE 3.3 0.2 - - - -
142C LEU* 1.3 76.5 - - - +
144C GLN* 1.3 62.6 + - + +
146C GLU* 3.7 20.9 - - - +
147C VAL* 4.0 11.1 + - - +
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Residues in contact with GLN 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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75C THR* 5.7 0.9 - - - -
76C PHE* 3.9 15.2 + - - +
77C TYR* 3.8 20.1 + - + -
100C ASN* 4.6 16.3 + - - +
121C GLY 4.3 3.6 - - - +
122C VAL* 3.7 33.0 - - + +
123C SER 4.8 3.6 + - - -
140C VAL* 3.2 38.9 + - - +
141C PHE* 3.2 21.0 + - - +
142C LEU 3.2 0.8 - - - -
143C GLN* 1.3 75.3 - - + +
145C LEU* 1.3 66.8 + - - +
146C GLU 3.2 0.2 - - - -
147C VAL* 3.1 18.2 + - - +
148C PHE* 3.2 24.1 + - + -
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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
----------------------------------------------------------
122C VAL* 5.3 0.6 - - - +
141C PHE 2.9 16.6 + - - +
142C LEU* 3.3 15.2 + - + +
144C GLN* 1.3 77.0 - - - +
146C GLU* 1.3 56.5 + - - +
148C PHE* 3.0 7.9 + - + -
149C MET* 2.8 46.2 + - + +
156C LEU* 3.7 37.0 - - + -
173C THR* 3.6 30.3 - - + +
174C LEU* 4.0 16.2 - - + -
176C ALA* 5.2 2.9 - - + -
177C SER* 3.9 20.2 - - - +
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Residues in contact with GLU 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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97C GLN* 5.8 1.6 - - - +
142C LEU 3.1 15.6 + - - +
143C GLN* 3.7 15.8 - - - +
145C LEU* 1.3 77.2 - - - +
147C VAL* 1.3 63.4 + - + +
149C MET* 3.6 6.4 + - - +
150C LYS* 3.0 27.0 + - + +
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Residues in contact with VAL 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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97C GLN* 4.2 26.0 - - + -
100C ASN* 4.1 19.3 - - + +
101C GLU* 3.8 39.0 - - + +
104C CYS* 4.1 12.1 - - - -
143C GLN 4.0 13.0 - - - +
144C GLN* 3.1 8.8 + - - +
146C GLU* 1.3 79.8 - - + +
148C PHE* 1.3 60.1 + - + +
150C LYS* 3.2 9.4 + - + +
151C LYS* 2.9 32.3 + - + +
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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
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73C THR* 3.6 16.8 - - - -
75C THR* 3.9 13.2 - - + -
100C ASN* 5.5 3.1 - - + -
104C CYS* 3.6 24.7 - - - -
120C GLY* 3.7 16.6 - - - -
121C GLY 3.3 33.9 - - - -
122C VAL* 3.8 16.8 - - + -
144C GLN* 3.2 24.2 + - + -
145C LEU* 3.0 9.3 + - + +
147C VAL* 1.3 79.8 - - + +
149C MET* 1.3 59.0 + - - +
151C LYS* 4.7 0.2 - - - -
152C ASN* 3.1 19.9 + - - -
153C VAL* 3.2 34.1 + - + +
156C LEU* 3.7 22.2 - - + -
174C LEU* 5.5 0.2 - - + -
179C LYS* 4.2 0.5 - - - -
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Residues in contact with MET 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* 2.8 34.1 + - + +
146C GLU* 3.8 6.1 - - - +
148C PHE* 1.3 75.7 - - - +
150C LYS* 1.3 63.4 + - - +
152C ASN* 3.2 14.7 + - - +
177C SER* 3.5 46.0 - - - +
179C LYS* 3.8 21.5 - - - +
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Residues in contact with LYS 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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97C GLN* 5.0 3.2 - - - +
101C GLU* 2.9 29.8 + - + +
146C GLU* 3.0 22.4 + - + +
147C VAL* 3.4 10.1 - - + +
149C MET* 1.3 76.7 - - - +
151C LYS* 1.3 82.1 + - + +
152C ASN* 5.1 0.9 - - - +
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Residues in contact with LYS 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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101C GLU* 3.8 33.8 + - - +
104C CYS* 3.7 30.3 - - + -
105C ASP* 3.1 36.7 + - - +
108C ARG* 5.0 8.1 + - - +
147C VAL* 2.9 22.0 + - + +
148C PHE 4.3 2.5 - - - +
150C LYS* 1.3 93.4 - - + +
152C ASN* 1.3 70.4 + - - +
153C VAL* 3.5 3.6 + - + +
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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