Contacts of the helix formed by residues 142 - 151 (chain A) in PDB entry 4L6V
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 GLY 142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139A ILE* 5.0 2.8 + - - +
140A THR* 3.2 4.8 + - - +
141A SER* 1.3 79.5 - - - +
143A LEU* 1.3 59.4 + - - +
144A PHE 3.4 2.7 - - - -
145A TYR* 3.3 30.3 + - - +
146A LEU* 3.0 26.4 + - - +
376A TYR* 5.2 3.8 - - - -
379A GLN* 6.1 0.2 - - - -
385A THR* 3.6 11.5 + - - +
389A LEU* 4.7 4.0 - - - +
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Residues in contact with LEU 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A LEU* 6.6 0.4 - - + -
90A MET* 4.6 35.7 - - + +
114A ALA* 6.1 3.4 - - + -
139A ILE* 4.4 18.5 - - + +
141A SER* 3.6 29.1 - - - +
142A GLY* 1.3 75.7 - - - +
144A PHE* 1.3 64.3 + - + +
146A LEU* 3.1 12.6 + - + +
147A TRP* 2.8 71.3 + - + +
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Residues in contact with PHE 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A GLY* 5.7 2.5 - - - -
98A SER* 4.1 10.3 - - - -
99A ASN* 3.2 28.7 - - - -
100A TYR* 3.3 38.0 - + + -
103A TRP* 3.5 44.9 - + + -
112A PRO* 3.5 22.7 - - + -
113A SER 3.6 16.6 - - - -
114A ALA* 4.8 3.6 - - + -
139A ILE* 3.5 28.5 - - + +
143A LEU* 1.3 80.3 - - + +
145A TYR* 1.3 66.4 + - + +
147A TRP* 3.5 13.8 + + - -
148A ARG 3.4 16.8 + - - -
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Residues in contact with TYR 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A TRP* 3.5 34.1 - + - -
107A PRO 5.8 0.2 - - - -
112A PRO* 3.3 24.4 - - + +
142A GLY* 3.5 23.6 - - - +
143A LEU 3.2 0.6 - - - -
144A PHE* 1.3 76.9 - - + +
146A LEU* 1.3 62.7 + - - +
149A ALA 3.6 2.4 + - - -
376A TYR* 3.5 19.2 - - + -
377A PRO* 3.3 51.4 - - - +
378A TYR* 3.7 16.3 + - + -
379A GLN* 4.1 12.3 - - + -
382A ASP* 2.7 30.9 + - + +
385A THR* 3.6 24.7 - - + -
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Residues in contact with LEU 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A TYR* 4.8 3.1 - - - +
142A GLY 3.0 13.9 + - - +
143A LEU* 3.1 16.1 + - + +
145A TYR* 1.3 75.8 - - - +
147A TRP* 1.3 90.6 + - + +
149A ALA* 3.4 3.1 + - - +
150A SER* 2.7 42.1 + - - +
212A TRP* 6.1 1.8 - - + -
376A TYR* 3.4 39.9 - - + +
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Residues in contact with TRP 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A LEU* 6.3 0.4 - - + -
90A MET* 4.5 14.8 - - + -
91A TYR* 3.2 54.5 - + - -
94A GLY* 4.9 7.9 - - - -
100A TYR* 3.1 45.3 - + + +
143A LEU* 2.8 61.2 + - + +
144A PHE* 3.8 6.7 - + - +
145A TYR 3.4 0.2 - - - -
146A LEU* 1.3 98.5 - - + +
148A ARG* 1.3 57.6 + - - +
150A SER* 3.0 5.7 + - - -
151A GLY 2.9 23.4 + - - -
152A PHE* 3.0 25.2 + + + -
158A LEU* 3.9 21.7 - - + +
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Residues in contact with ARG 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A TYR* 3.2 5.5 + - - +
103A TRP* 3.5 29.4 - - + -
104A LEU* 3.7 29.7 + - + +
107A PRO* 3.5 15.6 - - - +
144A PHE 3.4 8.2 + - - +
146A LEU 3.4 0.4 - - - -
147A TRP* 1.3 77.0 - - - +
149A ALA* 1.3 58.7 + - - +
151A GLY* 2.9 20.4 + - - -
152A PHE 4.5 2.9 - - - +
220A SER* 5.3 0.2 - - - -
223A ILE* 5.5 0.7 - - - +
224A ASN* 2.9 38.4 - - - +
227A LEU* 3.5 41.3 + - + +
228A ASP* 4.3 6.7 + - - -
285A THR* 5.0 4.4 + - - +
377A PRO* 3.8 21.2 - - + +
378A TYR* 3.3 33.0 + - - -
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Residues in contact with ALA 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A TYR 3.6 2.5 + - - +
146A LEU 3.4 2.2 + - - +
147A TRP 3.4 0.4 - - - -
148A ARG* 1.3 77.7 - - - +
150A SER* 1.3 55.7 + - - +
212A TRP* 5.2 3.1 - - - -
216A GLN* 5.2 2.4 - - - +
220A SER* 2.9 24.0 + - - -
224A ASN* 3.5 10.8 - - - -
290A LEU* 4.1 20.4 - - + +
375A PRO 4.8 2.0 - - - +
376A TYR* 3.7 24.7 - - + -
377A PRO* 3.6 23.7 - - + +
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Residues in contact with SER 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A LEU* 2.7 33.8 + - - +
147A TRP* 3.0 12.0 + - - -
148A ARG 3.0 0.8 - - - -
149A ALA* 1.3 75.9 - - - +
151A GLY* 1.3 57.4 + - - +
152A PHE* 3.6 19.6 - - - -
212A TRP* 4.2 22.8 - - - -
215A HIS* 2.9 28.8 + - - -
219A VAL* 3.9 0.5 - - - +
220A SER* 3.1 10.5 + - - -
376A TYR* 5.5 0.2 - - - -
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Residues in contact with GLY 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A ARG 2.9 14.0 + - - -
149A ALA 3.4 0.6 - - - -
150A SER* 1.3 79.1 - - - +
152A PHE* 1.3 65.5 + - - +
153A THR* 3.6 5.1 + - - +
157A GLN* 4.1 8.7 + - - -
219A VAL* 4.1 15.5 - - - +
220A SER* 4.3 8.5 - - - -
223A ILE* 3.7 28.0 - - - +
239A PRO* 4.5 0.3 - - - +
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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