Contacts of the helix formed by residues 147 - 153 (chain C) in PDB entry 4LDD
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 LEU 147 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73C PHE* 3.7 34.1 - - + -
98C LEU* 3.9 14.8 - - + +
99C GLY* 3.5 14.6 - - - +
100C VAL 3.5 40.6 - - - +
101C ALA* 4.2 3.1 - - + -
111C THR* 4.3 0.7 - - + -
115C ILE* 4.3 13.2 - - + -
145C HIS* 3.0 32.2 + - + +
146C PRO* 1.3 78.4 - - - +
148C ARG* 1.3 60.8 - - - +
149C LEU* 4.6 2.5 - - + +
150C LEU* 3.2 14.9 + - + +
151C ARG 2.9 23.6 + - - -
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Residues in contact with ARG 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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158A LEU* 5.3 14.4 - - - +
160A GLU* 5.5 4.9 + - - -
161A PHE* 5.5 9.7 - - + -
98C LEU 4.9 1.4 + - - -
146C PRO 3.8 3.6 + - - -
147C LEU* 1.3 71.4 - - - +
149C LEU* 1.3 58.3 + - - +
151C ARG* 3.4 27.5 - - - +
152C ILE* 2.9 57.6 + - + +
154C ASN* 3.2 21.2 + - - +
155C GLN* 3.7 31.4 + - - +
156C ALA 5.2 1.7 - - - +
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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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75C LEU* 4.1 6.1 - - + -
98C LEU* 3.6 35.9 - - + -
120C TYR* 3.9 19.7 - - + +
135C VAL* 3.3 43.1 - - + +
137C ARG* 3.5 25.3 - - + +
147C LEU* 3.3 2.1 - - + -
148C ARG* 1.3 77.3 - - - +
150C LEU* 1.3 60.6 + - + +
153C GLY* 3.1 26.3 + - - -
154C ASN* 3.6 16.8 - - - -
155C GLN* 3.2 17.3 + - + +
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Residues in contact with LEU 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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98C LEU* 6.1 1.8 - - + -
111C THR* 4.0 5.8 - - + -
114C ALA* 4.1 17.9 - - + +
115C ILE* 3.8 32.1 - - + -
120C TYR* 4.2 4.0 - - - +
137C ARG* 3.4 29.9 + - - +
141C GLY* 3.3 6.9 - - - -
142C ILE* 2.6 37.9 + - + +
145C HIS* 3.4 42.0 - - + +
147C LEU* 3.2 16.8 + - + +
148C ARG 3.2 0.2 - - - -
149C LEU* 1.3 81.7 - - + +
151C ARG* 1.3 59.1 + - - +
153C GLY 4.4 0.2 + - - -
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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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160A GLU* 3.9 28.8 + - - -
141C GLY* 3.8 11.3 - - - -
142C ILE 3.3 12.3 + - - +
143C PRO* 5.1 1.5 - - + +
144C ASP* 3.9 14.9 - - - +
145C HIS* 3.2 34.7 + - - +
146C PRO* 3.7 15.6 + - - +
147C LEU 2.9 15.5 + - - +
148C ARG* 3.4 38.6 - - - +
150C LEU* 1.3 81.3 - - - +
152C ILE* 1.3 78.0 + - + +
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Residues in contact with ILE 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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141C GLY* 5.2 3.6 - - - -
148C ARG* 2.9 40.8 + - + +
151C ARG* 1.3 105.1 - - - +
153C GLY* 1.3 61.9 + - - +
154C ASN* 3.2 47.5 + - - +
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Residues in contact with GLY 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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136C ASN* 3.3 2.4 - - - +
137C ARG* 2.4 49.2 + - - +
139C GLY 5.8 0.9 - - - -
141C GLY* 5.4 4.3 - - - -
149C LEU 3.1 19.8 + - - -
150C LEU 4.4 1.7 + - - -
151C ARG 3.7 0.8 - - - -
152C ILE* 1.3 79.0 - - - +
154C ASN* 1.3 60.7 + - - +
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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