Contacts of the helix formed by residues 139 - 146 (chain B) in PDB entry 5T8Y
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 139 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30B PHE* 6.0 1.0 - - - -
33B LEU* 3.6 29.9 - - - +
57B ARG* 3.7 19.9 + - - +
138B LEU* 1.3 73.4 - - - +
140B ASP* 1.3 64.0 + - - +
142B ALA* 3.2 12.0 + - - +
143B VAL* 3.1 26.3 + - - +
503B B12 2.8 34.7 + - - -
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Residues in contact with ASP 140 (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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132B MET* 5.1 0.7 - - - +
136B GLY* 5.8 0.2 - - - -
138B LEU 3.7 2.9 - - - +
139B SER* 1.3 72.0 - - - +
141B ARG* 1.3 61.4 + - - +
143B VAL* 3.9 2.0 - - - +
144B ALA* 3.1 24.8 + - - +
169B LEU* 3.8 15.3 - - + +
170B ALA* 5.2 0.2 - - - -
171B GLU* 2.8 37.5 - - - +
503B B12 2.5 70.6 + - + +
508B PO4 2.9 13.6 + - - -
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Residues in contact with ARG 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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139B SER* 3.2 1.0 + - - -
140B ASP* 1.3 79.1 - - - +
142B ALA* 1.3 57.2 + - - +
144B ALA 3.3 0.7 + - - -
145B GLU* 3.0 26.5 + - - +
156B CYS* 2.7 28.7 + - - +
157B MET* 3.7 14.8 - - - -
158B ILE* 3.4 32.4 - - + +
169B LEU* 4.3 1.1 - - + -
503B B12 3.0 157.5 + - + +
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Residues in contact with ALA 142 (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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30B PHE* 3.6 24.9 - - + -
33B LEU* 4.3 14.6 - - + -
139B SER* 3.2 25.6 + - - +
141B ARG* 1.3 78.5 - - - +
143B VAL* 1.3 64.2 + - - +
145B GLU* 3.5 3.8 + - - +
146B ARG* 3.2 24.3 + - - +
503B B12 3.6 14.8 - - - -
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Residues in contact with VAL 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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25B THR* 4.1 11.9 - - + +
30B PHE* 3.6 27.6 - - + -
70B ILE* 3.7 27.6 - - + -
72B ALA* 4.1 9.6 - - + -
138B LEU* 4.3 20.0 - - + -
139B SER 3.1 18.1 + - - +
140B ASP 3.9 3.4 - - - +
142B ALA* 1.3 76.9 - - - +
144B ALA* 1.3 62.7 + - - +
146B ARG* 3.4 3.9 + - - +
147B ALA* 3.1 21.3 + - - +
171B GLU* 3.8 20.0 - - + +
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Residues in contact with ALA 144 (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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72B ALA* 4.4 5.8 - - + +
140B ASP 3.1 19.3 + - - +
141B ARG 3.3 4.9 + - - +
143B VAL* 1.3 78.2 - - - +
145B GLU* 1.3 61.0 + - - +
147B ALA* 3.0 6.7 + - - -
149B ILE* 3.0 50.4 + - + +
150B GLY 4.4 1.1 - - - -
158B ILE* 4.3 6.3 - - + -
169B LEU* 3.8 23.1 - - + -
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Residues in contact with GLU 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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141B ARG 3.0 16.3 + - - +
142B ALA* 4.0 4.0 - - - +
144B ALA* 1.3 75.8 - - - +
146B ARG* 1.3 58.7 + - - +
147B ALA 3.1 3.3 + - - -
148B GLY* 3.4 5.2 + - - -
150B GLY 3.3 22.0 + - - +
151B PHE* 4.3 3.7 - - - +
152B SER* 2.7 41.5 + - - +
158B ILE* 4.1 3.6 - - + +
183B PRO* 3.4 27.7 - - + +
503B B12 3.6 12.1 - - - +
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Residues in contact with ARG 146 (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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24B PHE 3.9 2.6 - - - +
25B THR* 3.0 27.7 + - - +
26B THR* 2.9 34.0 + - - -
27B ALA* 4.5 0.4 - - - +
28B ASP* 2.9 34.8 + - - +
29B THR 3.4 15.6 + - - -
30B PHE* 3.3 37.1 - - + +
60B PRO* 4.7 0.4 - - - +
142B ALA 3.2 17.1 + - - +
143B VAL 3.4 3.6 + - - +
144B ALA 3.2 0.2 - - - -
145B GLU* 1.3 76.4 - - - +
147B ALA* 1.3 57.2 + - - +
148B GLY 3.5 0.4 - - - -
180B PRO* 5.3 1.2 - - - +
181B ASP 4.3 9.0 - - - +
183B PRO* 4.4 12.5 - - + +
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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