Contacts of the helix formed by residues 133 - 149 (chain C) in PDB entry 4DVQ
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 ASN 133 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109C CYS* 3.6 22.0 - - - +
110C ARG* 3.6 30.6 + - - +
112C ILE* 5.1 11.5 - - - +
131C LEU 4.1 2.1 + - - -
132C LEU* 1.3 76.3 - - - +
134C GLY* 1.3 67.6 + - - +
135C PRO 3.9 0.2 - - - -
136C GLU* 4.1 7.6 + - - +
137C TRP* 3.6 9.5 + - - -
448C ARG* 2.6 31.8 + - - +
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Residues in contact with GLY 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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107C HIS* 3.5 28.9 + - - +
108C PRO 5.3 2.0 + - - -
109C CYS* 5.3 3.0 - - - -
133C ASN* 1.3 76.8 - - - +
135C PRO* 1.3 70.5 - - - +
137C TRP* 3.0 25.3 + - - +
138C ARG 3.3 3.6 + - - -
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Residues in contact with PRO 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C HIS* 3.8 24.7 - - + +
133C ASN 4.7 0.2 - - - +
134C GLY* 1.3 81.7 - - - +
136C GLU* 1.3 60.4 + - - +
138C ARG* 3.1 3.8 + - + +
139C PHE* 2.8 30.9 + - - +
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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
----------------------------------------------------------
126C LYS* 4.0 28.4 + - - +
132C LEU* 3.4 30.8 - - + +
133C ASN 4.1 5.4 + - - +
134C GLY 3.3 0.6 - - - -
135C PRO* 1.3 78.8 - - - +
137C TRP* 1.3 61.1 + - - +
139C PHE* 3.5 6.0 + - + +
140C ASN* 2.6 41.9 + - - +
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Residues in contact with TRP 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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106C LEU 3.5 23.1 - - - -
107C HIS* 4.4 7.9 - - - -
108C PRO* 3.8 15.5 - - + -
129C VAL* 3.4 25.4 - - + +
132C LEU* 3.7 15.6 - - + +
133C ASN* 3.6 18.1 + - - +
134C GLY 3.0 15.4 + - - +
136C GLU* 1.3 77.7 - - - +
138C ARG* 1.3 80.9 + - + +
140C ASN* 3.2 4.0 + - - +
141C ARG* 2.8 46.7 + - + +
447C MET* 3.6 39.3 - - + -
448C ARG* 3.3 46.7 - - + +
601C HEM 2.9 19.1 + - - -
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Residues in contact with ARG 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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106C LEU* 3.7 37.7 + - - +
107C HIS* 3.5 30.7 - - + +
134C GLY 3.3 1.0 + - - -
135C PRO* 3.1 8.2 + - + +
137C TRP* 1.3 101.4 - - + +
139C PHE* 1.3 65.2 + - - +
141C ARG* 4.3 2.2 - - + +
142C LEU* 3.0 57.9 + - + +
447C MET* 4.0 23.9 - - + +
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Residues in contact with PHE 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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135C PRO 2.8 16.6 + - - +
136C GLU* 3.7 9.2 - - + +
138C ARG* 1.3 79.6 - - - +
140C ASN* 1.3 67.0 + - - +
142C LEU* 3.8 1.1 + - - -
143C ARG* 3.0 74.6 + - - +
298C GLU 4.5 8.1 - - - -
299C LEU* 4.1 15.9 - - + -
300C SER 5.9 0.7 - - - -
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Residues in contact with ASN 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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127C CYS 4.5 3.6 - - - +
129C VAL* 4.0 13.7 - - + -
132C LEU* 3.4 19.7 - - + +
136C GLU* 2.6 39.0 + - - +
137C TRP 3.6 5.8 - - - +
139C PHE* 1.3 81.1 - - - +
141C ARG* 1.3 65.5 + - - +
143C ARG* 3.2 4.7 + - - +
144C LEU* 3.1 26.6 + - + +
299C LEU* 3.9 11.7 - - - +
303C ALA* 3.8 15.8 - - - +
307C ASN* 3.1 27.4 + - - +
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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
----------------------------------------------------------
129C VAL* 3.8 13.0 - - + +
137C TRP* 2.8 40.6 + - + +
138C ARG* 4.0 4.5 - - + +
140C ASN* 1.3 73.2 - - - +
142C LEU* 1.3 59.4 + - + +
144C LEU* 3.0 18.9 + - - +
145C ASN* 2.7 38.7 + - - +
149C LEU* 3.4 28.1 - - - +
447C MET* 3.3 26.8 + - + +
448C ARG 3.7 1.0 - - - -
449C GLN* 2.8 33.5 + - - +
451C LEU* 3.9 17.5 - - - +
601C HEM 2.7 46.0 + - - +
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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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138C ARG* 3.0 62.2 + - + +
139C PHE* 4.4 3.6 - - - +
141C ARG* 1.3 75.7 - - + +
143C ARG* 1.3 67.8 + - - +
144C LEU 3.4 0.2 - - - -
145C ASN* 4.5 10.5 - - - +
146C PRO* 3.7 17.6 - - - +
447C MET* 3.8 27.4 - - + -
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Residues in contact with ARG 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C PHE* 3.0 67.6 + - - +
140C ASN 3.2 2.1 + - - +
141C ARG 3.1 1.2 - - - -
142C LEU* 1.3 86.9 - - + +
144C LEU* 1.3 61.5 + - - +
146C PRO* 4.1 7.0 - - - +
147C ASP* 4.7 3.5 - - - +
293C LEU* 3.4 20.3 - - - +
296C LYS* 5.8 0.7 + - - +
298C GLU* 3.7 52.7 + - + +
299C LEU* 3.8 26.4 - - + +
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Residues in contact with LEU 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C VAL* 3.9 18.8 - - + -
140C ASN 3.1 18.8 - - - +
141C ARG* 3.0 5.2 + - - +
143C ARG* 1.3 78.4 - - - +
145C ASN* 1.3 66.0 + - - +
146C PRO* 3.3 2.5 - - - -
147C ASP* 3.3 3.2 + - - +
148C VAL* 3.1 31.2 + - + +
293C LEU* 3.7 33.2 - - + -
299C LEU* 4.2 9.9 - - + -
307C ASN* 3.4 42.6 - - + +
311C LEU* 5.4 2.2 - - + -
451C LEU* 4.0 26.7 - - + -
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Residues in contact with ASN 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C ARG* 2.7 59.0 + - - +
142C LEU* 4.5 16.4 - - - +
144C LEU* 1.3 75.8 - - - +
146C PRO* 1.3 72.0 - - + +
149C LEU* 3.1 30.1 + - + +
150C SER* 3.1 9.1 + - - +
447C MET* 4.7 10.7 + - - +
451C LEU* 3.9 7.2 - - - +
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Residues in contact with PRO 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 3.7 19.1 - - - +
143C ARG* 4.1 5.2 - - - +
144C LEU 3.5 6.1 - - - +
145C ASN* 1.3 95.5 - - + +
147C ASP* 1.3 59.4 + - - +
150C SER* 2.6 32.6 + - - -
153C ALA* 3.2 7.3 + - - +
296C LYS* 4.5 17.5 - - - +
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Residues in contact with ASP 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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143C ARG 4.7 2.8 - - - +
144C LEU 3.3 2.6 + - - +
145C ASN 3.3 0.6 - - - -
146C PRO* 1.3 81.2 - - - +
148C VAL* 1.3 60.2 + - + +
153C ALA* 3.3 16.9 - - - +
286C TYR* 4.6 1.7 + - - -
289C ILE* 3.5 25.0 - - + +
292C GLU* 3.5 35.7 - - + +
293C LEU* 4.0 23.4 - - + +
296C LYS* 2.7 39.7 + - - +
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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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144C LEU* 3.1 29.1 + - + +
147C ASP* 1.3 80.3 - - + +
149C LEU* 1.3 59.5 + - - +
150C SER 3.9 0.2 - - - -
153C ALA* 4.6 2.5 - - - -
154C VAL* 5.2 0.2 - - - +
157C PHE* 3.9 19.9 - - - -
204C LEU* 5.8 0.2 - - + -
289C ILE* 3.3 33.2 - - + +
293C LEU* 4.9 3.1 - - + -
311C LEU* 4.1 27.1 - - + -
451C LEU* 3.6 33.7 - - + +
452C GLY* 4.7 4.0 - - - -
454C ARG* 4.9 1.0 - - - +
455C LEU* 4.9 8.2 + - + +
601C HEM 5.2 2.2 - - + -
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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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141C ARG* 3.4 29.2 - - - +
145C ASN* 3.1 17.8 + - + +
148C VAL* 1.3 78.1 - - - +
150C SER* 1.3 59.8 + - - +
154C VAL* 4.7 0.7 - - - -
449C GLN* 4.5 12.6 - - + +
450C CYS 3.8 15.9 - - - +
451C LEU* 3.5 22.4 - - + +
453C ARG* 4.3 10.1 - - + +
454C ARG* 2.6 74.8 + - + +
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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
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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