Contacts of the helix formed by residues 128 - 144 (chain C) in PDB entry 1DVM
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 128 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125C ASP* 3.4 16.7 + - - +
127C SER* 1.3 76.3 - - - +
129C VAL* 1.3 63.5 + - - +
130C GLU 3.6 2.0 - - - -
131C ARG* 3.4 45.3 + - + +
132C ALA* 3.1 22.7 + - - +
59D GLN* 3.2 10.2 - - - +
60D ALA* 3.1 34.7 + - - +
63D GLY* 4.7 7.2 - - - -
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Residues in contact with VAL 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C PHE 3.4 18.4 - - - +
127C SER 3.0 8.6 + - - +
128C GLU* 1.3 68.1 - - - +
130C GLU* 1.3 67.1 + - - +
132C ALA* 3.1 5.5 + - - +
133C ARG* 3.0 41.2 + - - +
157C VAL* 3.5 27.1 - - + +
158C GLN* 3.9 7.9 - - - -
159C GLN* 3.9 21.1 - - + +
18D ARG* 4.5 19.7 - - + +
60D ALA 3.9 6.5 + - - +
61D ALA* 5.3 5.4 - - - +
293D LEU 6.0 0.4 - - - +
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Residues in contact with GLU 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C GLU* 3.6 0.6 - - + -
129C VAL* 1.3 78.1 - - - +
131C ARG* 1.3 62.5 + - + +
133C ARG* 3.0 31.7 - - - +
134C PHE* 3.2 14.2 + - + +
10D HIS* 4.5 8.8 - - - -
11D LEU* 3.5 31.8 - - + +
14D ASP* 3.3 26.2 - - - +
18D ARG* 3.0 35.9 + - - +
60D ALA 5.0 1.8 + - - -
62D MET 4.7 0.4 - - - +
63D GLY* 4.4 17.7 - - - +
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Residues in contact with ARG 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C ASP* 4.9 14.5 + - - +
128C GLU* 3.4 47.2 + - + +
130C GLU* 1.3 75.7 - - + +
132C ALA* 1.3 61.0 + - - +
134C PHE* 3.8 13.9 - - + -
135C ILE* 2.8 56.5 + - + +
63D GLY* 6.5 0.4 - - - -
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Residues in contact with ALA 132 (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 VAL* 3.5 28.6 - - + +
125C ASP 3.7 7.4 - - - +
126C PHE* 3.9 18.2 - - + -
128C GLU 3.1 20.2 + - - +
129C VAL* 3.1 8.3 + - - +
131C ARG* 1.3 80.0 - - - +
133C ARG* 1.3 57.5 + - - +
134C PHE 3.2 3.1 + - - -
135C ILE* 3.9 3.6 - - - +
136C ILE* 3.1 30.6 + - - +
157C VAL* 4.5 2.2 - - + -
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Residues in contact with ARG 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C VAL* 3.0 24.9 + - - +
130C GLU* 3.0 31.8 + - - +
132C ALA* 1.3 76.2 - - - +
134C PHE* 1.3 51.8 + - - +
136C ILE* 4.2 11.2 - - - -
137C ASN* 2.7 37.0 + - - +
154C THR* 3.4 31.7 + - - +
155C GLY* 3.7 25.2 + - - -
157C VAL* 2.6 32.5 + - + -
158C GLN* 4.9 1.0 - - - +
14D ASP* 5.2 4.0 + - - +
18D ARG* 3.7 30.6 - - - +
21D GLN* 5.6 2.2 + - - +
254D LEU 5.1 3.8 + - - -
255D SER* 4.6 14.5 - - - -
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Residues in contact with PHE 134 (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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130C GLU* 3.2 17.1 + - + +
131C ARG* 3.5 15.3 - - + +
132C ALA 3.1 0.6 - - - -
133C ARG* 1.3 77.8 - - - +
135C ILE* 1.3 68.7 + - + +
136C ILE 3.0 1.6 - - - -
137C ASN* 3.2 5.2 + - + +
138C ASP* 2.7 70.7 + - + +
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Residues in contact with ILE 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C PHE* 4.7 6.1 - - + -
122C LYS* 6.0 1.3 - - + -
124C VAL* 4.0 28.0 - - + -
125C ASP 5.8 1.3 - - - +
131C ARG* 2.8 53.0 + - + +
132C ALA* 3.9 7.6 - - - +
134C PHE* 1.3 89.5 - - + +
136C ILE* 1.3 56.9 + - - +
138C ASP* 3.9 4.0 - - - +
139C TRP* 3.0 26.9 + - + +
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Residues in contact with ILE 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C PHE* 3.8 49.5 - - + -
124C VAL* 4.7 2.2 - - + -
126C PHE* 4.3 13.9 - - + -
132C ALA 3.1 22.4 - - - +
133C ARG* 4.3 6.7 - - - +
134C PHE 3.0 0.4 - - - -
135C ILE* 1.3 72.5 - - - +
137C ASN* 1.3 66.6 + - - +
138C ASP 3.1 0.7 - - - -
139C TRP* 2.8 17.0 + - - +
140C VAL* 3.2 12.2 + - + +
151C LEU* 4.2 4.9 - - + -
154C THR* 3.7 21.3 - - + -
157C VAL* 4.3 19.5 - - + -
164C VAL* 4.8 6.7 - - + -
166C VAL* 4.2 15.5 - - + -
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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
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133C ARG* 2.7 24.1 + - - +
134C PHE* 3.2 7.3 + - + +
136C ILE* 1.3 79.1 - - - +
138C ASP* 1.3 57.5 + - - +
140C VAL* 3.3 11.8 + - - +
141C LYS* 2.9 22.5 + - - +
149C SER 3.5 20.2 - - - +
150C HIS* 3.7 9.1 - - + +
151C LEU* 2.5 36.3 + - - +
154C THR* 3.1 22.1 + - - +
257D GLN* 5.9 3.0 - - - +
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Residues in contact with ASP 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C PHE* 2.7 56.3 + - + +
135C ILE* 3.9 4.7 - - - +
137C ASN* 1.3 72.2 - - - +
139C TRP* 1.3 53.1 + - - +
141C LYS* 3.2 30.0 + - - +
142C THR* 2.5 48.8 + - - +
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Residues in contact with TRP 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C THR* 2.9 25.9 + - + -
95C ASP 3.8 7.2 + - - -
96C ALA* 3.5 26.6 - - + +
98C PHE* 3.9 12.8 - + + -
119C SER* 5.3 2.7 - - - -
122C LYS* 3.4 42.0 - - + -
135C ILE 3.0 14.5 + - - +
136C ILE 2.8 11.0 + - - +
138C ASP* 1.3 75.0 - - - +
140C VAL* 1.3 70.1 + - + +
142C THR* 3.6 4.7 - - - -
143C HIS* 2.6 68.0 + + - -
166C VAL* 6.1 0.2 - - + -
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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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94C THR* 4.1 8.3 - - + -
98C PHE* 6.0 0.2 - - + -
136C ILE* 3.2 12.5 + - + +
137C ASN* 3.4 7.9 - - - +
138C ASP 3.2 0.2 - - - -
139C TRP* 1.3 81.8 - - + +
141C LYS* 1.3 58.6 + - - +
143C HIS 3.0 4.5 + - - -
144C THR* 2.9 33.5 + - + +
148C ILE* 3.6 26.7 - - + +
149C SER 5.4 0.7 - - - -
150C HIS 5.3 0.2 - - - +
151C LEU* 3.6 31.6 - - + -
166C VAL* 3.9 13.7 - - + -
168C ALA* 3.3 28.9 - - + -
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Residues in contact with LYS 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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137C ASN 2.9 16.2 + - - +
138C ASP* 3.6 25.8 + - - +
140C VAL* 1.3 77.6 - - - +
142C THR* 1.3 63.9 + - + +
143C HIS 3.4 0.2 + - - -
144C THR 3.5 0.7 + - - -
146C GLY* 2.6 45.6 + - - +
148C ILE 3.0 11.2 + - - -
149C SER* 3.6 31.2 - - - +
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Residues in contact with THR 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 ASP* 2.5 38.6 + - - +
139C TRP* 3.4 7.6 + - - -
141C LYS* 1.3 79.9 - - + +
143C HIS* 1.3 72.1 + - - +
144C THR 3.7 0.2 + - - -
145C LYS* 3.9 10.0 + - - +
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Residues in contact with HIS 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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92C SER* 4.4 3.8 + - - -
93C THR 3.6 20.4 + - - +
94C THR* 3.2 25.2 + - - +
139C TRP* 2.6 70.0 - + - +
140C VAL 3.0 3.7 + - - +
142C THR* 1.3 90.3 + - - +
144C THR* 1.3 59.1 + - - +
145C LYS* 3.3 9.7 + - - +
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Residues in contact with THR 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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92C SER* 4.1 16.1 - - - +
94C THR* 4.2 3.4 - - + -
140C VAL* 2.9 17.9 + - + +
141C LYS 3.5 2.5 + - - -
142C THR 3.5 0.4 - - - -
143C HIS* 1.3 79.3 - - - +
145C LYS* 1.3 59.1 + - - +
146C GLY 3.0 4.3 - - - -
147C MET* 2.7 35.3 + - - +
148C ILE* 2.8 44.5 + - + -
168C ALA* 3.9 38.6 - - + +
169C LEU 5.0 0.9 - - - -
170C TYR* 4.8 3.8 - - - -
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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