Contacts of the helix formed by residues 135 - 155 (chain C) in PDB entry 3MA0
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 135 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C TYR 4.6 3.8 - - - +
91C ARG* 3.2 28.7 + - - +
132C SER* 3.1 24.9 + - - +
133C PRO 4.9 1.9 - - - -
134C VAL* 1.3 77.7 - - - +
136C ASN* 1.3 64.8 + - - +
137C ASN* 2.9 21.7 + - - +
138C ALA* 3.0 18.6 + - - +
139C LYS* 3.7 3.6 + - - +
169C TRP* 2.9 20.5 + - - +
402C XYP 2.5 25.3 + - - -
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Residues in contact with ASN 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C GLY* 5.7 2.7 - - - +
91C ARG* 5.3 1.4 - - - +
92C MET* 3.8 37.8 + - + +
94C ASN* 3.2 31.5 + - - +
134C VAL 3.9 3.6 + - - -
135C ASP* 1.3 72.5 + - - +
137C ASN* 1.3 62.9 + - - +
139C LYS* 3.2 40.9 + - - +
140C LEU* 3.2 31.6 + - - +
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Residues in contact with ASN 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C ASP* 2.9 46.6 + - - +
91C ARG* 3.5 10.6 - - - +
92C MET 4.3 1.4 + - - -
101C TYR* 3.8 3.1 + - - -
106C ASN* 3.4 21.2 + - - +
135C ASP* 2.9 18.6 + - - +
136C ASN* 1.3 73.4 + - - +
138C ALA* 1.3 56.8 + - - +
140C LEU* 3.0 12.0 + - - +
141C PHE* 2.8 46.7 + - + -
402C XYP 3.0 21.6 + - - +
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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
----------------------------------------------------------
130C GLY* 5.6 0.2 - - - -
131C GLY* 3.8 19.5 + - - +
132C SER 3.2 27.8 - - - +
133C PRO* 5.3 0.2 - - + -
135C ASP* 3.0 9.9 + - + +
137C ASN* 1.3 77.5 - - - +
139C LYS* 1.3 60.9 + - - +
141C PHE* 3.6 13.4 + - - +
142C ARG* 3.2 17.3 + - - +
165C TRP* 3.5 26.4 - - + -
169C TRP* 4.1 3.6 - - + -
195C SER* 5.3 1.6 + - - -
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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
----------------------------------------------------------
313A HIS* 5.7 5.8 - - + +
94C ASN* 5.9 0.2 - - - +
135C ASP 3.7 3.0 + - - +
136C ASN* 3.2 34.7 + - - +
137C ASN 3.1 0.4 - - - -
138C ALA* 1.3 79.8 - - - +
140C LEU* 1.3 77.5 + - - +
142C ARG* 3.4 2.7 + - + +
143C ALA* 2.9 28.1 + - + +
165C TRP* 4.1 13.4 - - + -
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Residues in contact with LEU 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C TYR* 4.8 5.8 - - + +
106C ASN* 3.8 38.8 - - + +
107C GLU* 3.6 29.8 - - + +
136C ASN* 3.2 27.1 + - - +
137C ASN* 3.0 11.7 + - - +
139C LYS* 1.3 95.2 - - - +
141C PHE* 1.3 65.6 + - - +
143C ALA* 3.2 7.6 + - + +
144C GLY 3.0 19.1 + - - -
270C LEU* 6.4 2.0 - - + -
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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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106C ASN* 3.1 45.1 - - + -
109C VAL* 3.8 11.4 - - + -
110C GLY* 3.3 6.0 - - - -
113C GLN* 4.2 4.5 - - - +
137C ASN* 2.8 45.3 + - + +
138C ALA* 3.9 6.1 - - - +
140C LEU* 1.3 71.5 - - - +
142C ARG* 1.3 58.2 + - - +
144C GLY 3.4 0.2 + - - -
145C GLN* 2.8 48.9 + - - +
169C TRP* 3.9 27.8 - + - -
195C SER* 4.3 5.4 - - - +
221C GLN* 3.4 38.4 - - - -
402C XYP 3.8 14.4 - - - -
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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
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312A HIS 3.0 37.4 + - - +
313A HIS* 4.0 7.4 - - + -
128C LEU* 3.5 22.1 - - - +
129C MET 4.0 0.2 - - - +
130C GLY* 3.3 32.8 - - - +
138C ALA 3.2 18.2 + - - +
139C LYS* 3.7 3.8 - - + +
141C PHE* 1.3 74.5 - - - +
143C ALA* 1.3 59.7 + - - +
145C GLN* 3.2 22.5 + - - -
146C MET* 2.8 45.5 + - - +
163C ASP* 2.9 37.1 + - - -
164C GLN 4.1 1.0 + - - -
165C TRP* 3.5 30.4 - - + -
195C SER* 5.5 0.6 + - - +
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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
----------------------------------------------------------
313A HIS* 4.7 22.5 - - + +
107C GLU* 4.4 14.8 - - - +
139C LYS* 2.9 20.7 + - + +
140C LEU* 3.2 10.3 + - + +
142C ARG* 1.3 75.7 - - - +
144C GLY* 1.3 57.4 + - - +
146C MET* 3.4 2.1 + - - +
147C LYS* 3.0 33.5 + - - +
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Residues in contact with GLY 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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107C GLU* 3.3 27.6 - - - +
111C GLU* 3.5 31.9 + - - +
140C LEU 3.0 11.1 + - - -
141C PHE 3.7 1.8 - - - -
143C ALA* 1.3 74.1 - - - +
145C GLN* 1.3 64.7 + - - +
146C MET 3.5 0.3 + - - -
147C LYS* 3.5 13.4 + - - -
148C VAL* 3.6 4.3 + - - +
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Residues in contact with GLN 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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110C GLY* 3.5 17.0 - - - +
113C GLN* 3.1 23.8 + - + +
114C ALA* 3.5 16.9 - - + +
128C LEU* 5.5 0.9 - - + +
129C MET 5.4 0.2 - - - +
141C PHE* 2.8 31.8 + - - +
142C ARG* 3.2 34.6 + - - +
144C GLY* 1.3 74.1 - - - +
146C MET* 1.3 57.7 + - - +
148C VAL 3.4 1.4 + - - -
149C LEU* 3.0 31.1 + - + +
193C VAL* 3.5 34.0 - - + +
195C SER* 3.2 25.3 + - - +
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Residues in contact with MET 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A HIS* 4.0 28.9 - - + +
313A HIS* 3.8 32.1 - - + +
128C LEU* 3.8 24.9 - - + -
142C ARG* 2.8 36.1 + - - +
143C ALA 4.1 2.7 - - - +
144C GLY 3.3 0.2 - - - -
145C GLN* 1.3 72.6 - - - +
147C LYS* 1.3 60.2 + - - +
149C LEU* 4.1 25.8 - - + +
150C LYS* 2.8 43.5 + - + +
153C VAL* 4.9 10.5 - - + -
160C VAL* 5.2 2.0 - - + -
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Residues in contact with LYS 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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107C GLU* 2.8 28.8 + - - +
111C GLU* 3.2 29.2 + - + +
143C ALA 3.0 17.6 + - - +
144C GLY* 3.8 7.1 - - - +
145C GLN 3.4 0.2 - - - -
146C MET* 1.3 78.1 - - - +
148C VAL* 1.3 62.0 + - + +
150C LYS* 4.4 3.2 - - - +
151C PRO* 3.8 12.8 - - - +
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Residues in contact with VAL 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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111C GLU* 3.7 42.0 - - + +
114C ALA* 3.8 11.0 - - + +
115C LYS* 3.8 33.4 - - + +
118C VAL* 4.2 12.6 - - + -
144C GLY 3.6 2.0 + - - +
145C GLN 3.4 8.4 + - - +
147C LYS* 1.3 77.7 - - + +
149C LEU* 1.3 64.9 + - + +
151C PRO* 3.4 9.4 - - - +
152C TYR* 3.4 18.7 - - + -
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Residues in contact with LEU 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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114C ALA* 3.9 19.1 - - + -
118C VAL* 3.7 28.5 - - + -
126C TYR* 4.3 17.0 - - + -
128C LEU* 4.1 25.4 - - + -
145C GLN* 3.0 27.4 + - + +
146C MET* 3.3 19.9 + - + -
148C VAL* 1.3 76.8 - - - +
150C LYS* 1.3 66.5 + - - +
151C PRO 3.3 0.2 - - - -
152C TYR* 2.9 16.8 + - - +
153C VAL* 3.0 20.4 + - + +
158C ILE* 4.7 7.2 - - + -
160C VAL* 6.1 1.3 - - + -
193C VAL* 4.2 12.1 - - + -
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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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229A LYS* 6.0 1.0 - - - +
307A LEU 5.8 1.6 + - - -
308A HIS* 5.9 3.4 + - - -
310A HIS* 5.1 17.5 - - - -
313A HIS* 6.0 4.5 - - + -
146C MET* 2.8 30.2 + - + +
147C LYS* 4.4 3.4 - - - +
149C LEU* 1.3 72.2 - - - +
151C PRO* 1.3 66.8 - - + +
153C VAL* 3.0 7.7 + - - +
154C ASP* 2.8 59.3 + - - +
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Residues in contact with PRO 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 LYS 3.8 9.9 - - - +
148C VAL 3.4 15.9 - - - +
150C LYS* 1.3 97.4 - - + +
152C TYR* 1.3 63.1 + - + +
154C ASP* 4.0 8.2 - - + +
155C SER* 3.0 33.0 + - - -
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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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115C LYS* 6.0 0.5 - - - -
118C VAL* 3.7 41.8 + - + +
122C PRO* 3.4 34.7 - - + +
148C VAL* 3.4 23.3 - - + -
149C LEU* 2.9 7.7 + - - +
151C PRO* 1.3 86.0 - - + +
153C VAL* 1.3 59.1 + - - +
155C SER* 3.5 4.6 + - - -
156C GLY 3.4 1.6 + - - -
157C LYS* 2.9 48.5 + - + -
158C ILE* 3.1 30.5 + - + -
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Residues in contact with VAL 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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226A ALA* 6.2 0.2 - - - +
230A ARG* 5.5 0.3 - - - +
312A HIS* 6.0 4.0 - - + -
146C MET* 4.9 6.5 - - + -
149C LEU* 3.0 22.2 + - + +
150C LYS* 3.0 9.2 + - - +
152C TYR* 1.3 74.6 - - - +
154C ASP* 1.3 70.9 + - - +
156C GLY* 3.0 14.4 + - - -
158C ILE* 3.4 31.5 - - + +
159C LYS* 5.4 0.7 - - - -
160C VAL* 4.3 23.6 - - + +
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Residues in contact with ASP 154 (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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226A ALA 4.6 0.2 - - - +
229A LYS* 3.5 61.4 + - + +
230A ARG* 3.5 5.2 + - - +
233A ALA* 4.4 5.2 - - + -
150C LYS* 2.8 57.3 + - - +
151C PRO* 4.0 7.2 - - + +
153C VAL* 1.3 77.5 - - - +
155C SER* 1.3 59.7 + - - +
156C GLY 3.3 0.2 + - - -
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Residues in contact with SER 155 (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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204A ILE* 3.9 3.6 - - - +
230A ARG* 3.7 3.8 - - - +
233A ALA* 3.8 22.9 - - - -
235A THR* 2.6 41.2 + - - +
151C PRO 3.0 23.0 + - - -
152C TYR 3.5 1.4 + - - -
154C ASP* 1.3 75.4 - - - +
156C GLY* 1.3 61.0 + - - +
157C LYS* 3.5 27.6 + - - +
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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
------------------------------------------------------------
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