Contacts of the helix formed by residues 137 - 146 (chain A) in PDB entry 2V5Q
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 SER 137 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A ARG 4.5 2.3 - - - +
136A ARG* 1.3 80.3 - - - +
138A LEU* 1.3 65.3 + - - +
139A LEU* 3.2 17.0 + - - +
140A GLU* 2.6 30.4 + - - +
141A LEU* 3.4 10.6 + - - +
179A LEU 3.6 7.4 + - - -
180A GLY* 3.7 17.6 + - - -
182A LEU 3.3 17.3 - - - -
183A PHE* 4.0 7.4 - - - +
184A LEU* 4.3 8.3 - - - +
79D TYR* 4.6 1.0 + - - -
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Residues in contact with LEU 138 (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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137A SER* 1.3 70.4 - - - +
139A LEU* 1.3 58.9 + - - +
140A GLU 3.4 0.2 - - - -
141A LEU* 3.4 29.0 + - + +
142A HIS* 2.8 31.2 + - - +
156A TYR* 3.9 33.4 - - + -
160A ILE* 3.8 28.9 - - + -
179A LEU* 3.3 29.0 + - + +
182A LEU* 3.0 31.0 + - + +
184A LEU* 4.1 12.1 - - + -
190A VAL* 5.2 2.5 - - + -
240A ILE* 5.0 0.4 - - + -
244A LEU* 4.5 10.8 - - + +
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Residues in contact with LEU 139 (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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137A SER* 3.1 12.8 + - - +
138A LEU* 1.3 77.3 - - - +
140A GLU* 1.3 66.6 + - - +
142A HIS* 3.1 7.3 + - + +
143A LYS* 2.8 65.6 + - + +
179A LEU* 3.3 24.5 + - + +
180A GLY* 3.8 21.1 - - - +
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Residues in contact with GLU 140 (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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136A ARG* 3.4 17.7 - - + +
137A SER* 2.6 42.6 + - - +
139A LEU* 1.3 82.7 - - - +
141A LEU* 1.3 65.5 + - - +
143A LYS* 3.4 8.8 + - + +
144A ARG* 3.2 28.6 + - - +
46D THR* 3.9 11.8 - - + +
78D VAL* 4.2 24.1 - - + +
79D TYR* 3.5 20.6 - - + +
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Residues in contact with LEU 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A SER 3.4 9.1 + - - +
138A LEU* 3.4 34.3 + - + +
140A GLU* 1.3 78.0 - - - +
142A HIS* 1.3 58.5 + - - +
144A ARG* 3.1 3.8 + - - +
145A ARG* 2.9 42.4 + - + +
148A LEU* 4.1 21.1 - - + -
152A GLU* 5.6 0.2 - - - +
156A TYR* 3.6 26.7 - - + +
184A LEU* 4.9 2.7 - - + -
244A LEU* 5.4 2.0 - - + -
318A CYS* 3.2 28.3 - - - +
319A LEU* 3.9 22.7 - - + -
79D TYR* 3.6 9.5 + - - +
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Residues in contact with HIS 142 (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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138A LEU 2.8 21.1 + - - +
139A LEU* 3.5 12.8 - - + +
141A LEU* 1.3 75.6 - - - +
143A LYS* 1.3 66.4 + - + +
145A ARG* 5.0 0.2 - - - -
146A LYS* 2.7 62.7 + - + +
148A LEU* 5.9 0.9 - - - -
179A LEU* 3.6 22.7 - - + -
243A THR* 3.6 28.8 + - + +
244A LEU* 5.5 6.3 - - + +
247A GLY* 3.3 28.2 + - - -
248A LYS* 4.5 1.8 - - - -
249A PRO* 5.6 2.8 - - - +
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Residues in contact with LYS 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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139A LEU* 2.8 53.1 + - + +
140A GLU* 4.8 5.6 + - + -
141A LEU 3.3 0.2 - - - -
142A HIS* 1.3 79.6 - - + +
144A ARG* 1.3 60.0 + - - +
146A LYS* 4.0 22.4 + - - +
44D ASP* 5.7 0.7 - - - +
45D ASN* 3.7 51.8 + - - +
46D THR* 3.7 17.0 - - + -
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Residues in contact with ARG 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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140A GLU 3.2 12.8 + - - +
141A LEU 3.1 6.0 + - - +
142A HIS 3.1 0.8 - - - -
143A LYS* 1.3 76.6 - - - +
145A ARG* 1.3 64.8 + - + +
146A LYS* 5.3 1.6 - - - +
319A LEU 2.8 25.4 - - - +
320A THR* 2.9 45.1 + - + +
23D ARG* 4.5 17.2 + - - +
44D ASP* 5.8 2.0 - - - +
46D THR* 2.8 34.6 + - + +
48D LEU* 3.4 21.3 - - + +
77D ASP* 2.5 45.6 + - - +
79D TYR* 3.3 30.8 - - - -
81D PHE* 4.4 1.6 - - - -
86D LEU* 5.1 0.4 - - - +
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Residues in contact with ARG 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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141A LEU* 2.9 21.4 + - + +
144A ARG* 1.3 78.8 - - - +
146A LYS* 1.3 71.7 + - - +
147A ALA 3.2 12.0 + - - +
148A LEU* 3.8 30.8 - - + +
149A THR* 4.0 2.4 - - - +
152A GLU* 2.8 41.0 + - - -
318A CYS* 2.8 38.6 + - - +
319A LEU 4.4 4.9 - - - -
320A THR 3.6 28.0 - - - -
321A ILE* 3.7 6.6 + - - +
322A PRO* 3.4 37.9 - - - +
323A PRO* 3.9 0.2 - - - +
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Residues in contact with LYS 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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142A HIS* 2.7 50.0 + - + +
143A LYS* 4.0 24.3 + - - +
144A ARG 5.3 0.9 - - - -
145A ARG* 1.3 82.0 - - - +
147A ALA* 1.3 64.9 + - + +
148A LEU* 3.4 7.6 + - - +
243A THR 4.7 0.9 - - - +
244A LEU* 4.3 3.8 - - - +
247A GLY* 3.9 24.7 + - - +
45D ASN* 5.6 2.2 + - - -
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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