Contacts of the helix formed by residues 135 - 145 (chain B) in PDB entry 5A0E
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 135 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A SER* 5.9 0.2 - - - -
140A LYS* 5.1 1.0 - - - +
19B ARG 3.7 16.8 - - - -
20B VAL* 4.1 2.8 - - - +
132B VAL* 4.2 4.9 - - - -
134B GLU* 1.3 81.9 - - - +
136B MET* 1.3 66.7 + - - +
137B ASP* 3.0 15.2 + - - -
138B VAL* 2.9 16.0 + - - +
139B VAL* 3.0 14.6 + - - +
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Residues in contact with MET 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B PRO* 4.1 14.1 - - + -
96B GLY* 3.7 27.4 - - - +
114B ILE* 4.8 0.2 - - - -
115B CYS 3.8 20.0 - - - +
116B THR* 4.4 7.2 - - + -
131B HIS* 6.3 0.9 - - + -
132B VAL* 3.9 23.7 - - + +
134B GLU 3.8 0.8 - - - -
135B GLY* 1.3 77.5 - - - +
137B ASP* 1.3 57.9 + - - +
139B VAL* 3.6 24.3 - - + +
140B LYS* 2.9 46.0 + - + +
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Residues in contact with ASP 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A LYS* 5.5 5.1 + - - -
134B GLU* 5.7 0.9 - - - +
135B GLY* 3.5 14.6 + - - -
136B MET* 1.3 80.4 + - - +
138B VAL* 1.3 72.8 + - - +
140B LYS* 3.3 9.9 + - - +
141B LYS* 3.1 37.1 + - - +
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Residues in contact with VAL 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B VAL* 4.7 3.6 - - + -
17B LEU* 3.6 30.1 - - + +
18B GLY* 3.9 18.2 - - - +
19B ARG 3.6 24.7 - - - +
20B VAL* 3.7 20.4 - - + -
135B GLY* 2.9 8.3 + - - +
137B ASP* 1.3 88.4 + - - +
139B VAL* 1.3 65.2 + - - +
141B LYS* 3.1 11.2 + - - +
142B ILE* 2.9 28.1 + - + +
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Residues in contact with VAL 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B VAL* 4.1 23.1 - - + -
62B CYS* 4.0 12.7 - - + -
114B ILE* 4.1 27.6 - - + -
116B THR* 3.6 28.9 - - + -
135B GLY 3.0 13.2 + - - +
136B MET* 3.3 26.7 + - + +
138B VAL* 1.3 76.8 - - - +
140B LYS* 1.3 55.6 + - - +
142B ILE* 3.1 12.2 + - + +
143B GLU* 2.9 26.7 + - - +
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Residues in contact with LYS 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B SER* 6.0 0.4 - - - +
116B THR* 4.3 15.2 + - + -
136B MET* 2.9 46.7 + - + +
137B ASP* 3.6 9.0 - - - +
138B VAL 3.2 0.4 - - - -
139B VAL* 1.3 75.9 - - - +
141B LYS* 1.3 62.5 + - - +
143B GLU* 2.8 37.5 + - - +
144B SER* 3.1 22.2 + - - -
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Residues in contact with LYS 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B PRO 5.3 1.0 + - - -
17B LEU* 2.9 55.5 + - + +
137B ASP* 3.1 29.0 + - - +
138B VAL* 3.1 9.8 + - - +
140B LYS* 1.3 73.2 - - - +
142B ILE* 1.3 64.8 + - - +
144B SER* 2.7 26.3 + - - +
145B PHE* 3.2 13.2 - - + -
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Residues in contact with ILE 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B VAL* 4.0 27.1 - - + -
17B LEU* 3.9 16.6 - - + -
20B VAL* 4.7 4.7 - - + -
53B PHE* 4.1 23.8 - - + -
56B VAL* 3.5 23.4 - - + +
62B CYS* 3.7 21.5 - - + -
114B ILE* 6.0 0.9 - - + -
138B VAL* 2.9 22.7 + - + +
139B VAL* 3.4 16.4 - - + +
141B LYS* 1.3 75.8 - - - +
143B GLU* 1.3 64.4 + - - +
145B PHE* 2.9 23.6 + - - +
156B ILE* 4.2 14.3 - - + +
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Residues in contact with GLU 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B VAL* 3.6 9.9 - - - -
57B ILE 4.6 2.0 - - - +
58B PRO* 3.6 36.3 - - + +
59B SER* 2.8 27.3 + - - -
62B CYS* 4.2 7.6 - - - -
116B THR* 2.9 24.6 + - + +
139B VAL 2.9 14.8 + - - +
140B LYS* 2.8 42.6 + - - +
141B LYS 3.2 0.2 - - - -
142B ILE* 1.3 76.5 - - - +
144B SER* 1.3 58.9 + - - +
146B GLY* 3.0 21.0 + - - -
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Residues in contact with SER 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B PRO* 5.7 0.2 - - - -
140B LYS 3.1 13.9 + - - -
141B LYS* 2.7 21.7 + - - -
142B ILE 3.1 0.4 - - - -
143B GLU* 1.3 78.3 - - - +
145B PHE* 1.3 72.2 + - - +
146B GLY 3.3 5.6 + - - +
153B SER* 4.7 1.9 + - - -
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Residues in contact with PHE 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ALA* 3.8 19.1 - - + -
17B LEU* 4.0 17.3 - - + -
141B LYS* 3.2 27.1 - - + -
142B ILE* 2.9 11.7 + - - +
144B SER* 1.3 85.0 - - - +
146B GLY* 1.3 59.0 + - - +
152B THR* 3.1 9.0 - - - -
153B SER* 2.9 41.9 + - - +
154B LYS* 3.7 35.0 - - + +
156B ILE* 3.7 30.7 - - + -
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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