Contacts of the strand formed by residues 237 - 241 (chain B) in PDB entry 1H8O
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 THR 237 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138B PRO* 4.2 2.7 - - - -
139B GLY 3.9 7.9 + - - -
141B GLU* 2.4 31.9 + - - -
151B LEU* 3.8 38.3 - - + +
152B SER 5.8 3.6 - - - +
167B TRP* 5.7 1.3 - - + -
223B ALA 3.7 0.7 - - - +
224B VAL* 3.2 2.9 - - - +
225B TYR* 2.8 38.4 + - + +
236B GLY* 1.3 75.8 - - - -
238B LEU* 1.3 59.2 + - - +
239B VAL* 3.8 1.5 + - + -
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Residues in contact with LEU 238 (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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138B PRO* 4.0 18.5 - - + +
139B GLY 3.2 16.5 + - - +
140B GLY* 3.0 5.4 - - - +
141B GLU* 3.0 27.8 + - - +
222B SER 5.6 0.4 - - - -
223B ALA* 3.5 24.0 - - - +
224B VAL* 4.2 11.9 - - + +
237B THR* 1.3 70.9 + - - +
239B VAL* 1.3 67.5 + - - +
240B THR* 3.8 17.9 - - - +
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Residues in contact with VAL 239 (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 GLU* 3.7 13.5 - - + +
143B VAL* 3.8 24.5 - - + -
149B VAL* 4.6 11.4 - - + -
151B LEU* 3.6 32.3 - - + -
214B LEU* 5.4 1.1 - - + -
217B LEU* 4.8 4.5 - - + -
221B ASP 4.5 5.4 - - - +
222B SER* 3.4 3.5 - - - -
223B ALA 2.8 31.9 + - - +
225B TYR* 3.9 24.9 - - + -
237B THR* 4.8 1.8 - - + -
238B LEU* 1.3 79.0 - - - +
240B THR* 1.3 66.7 + - - +
241B VAL* 4.4 8.5 - - + -
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Residues in contact with THR 240 (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 GLU 3.2 10.0 + - - -
142B LEU* 3.4 27.2 - - + +
143B VAL* 2.8 28.5 + - - +
222B SER* 3.8 7.0 - - - +
238B LEU* 3.8 22.3 - - - +
239B VAL* 1.3 78.2 + - - +
241B VAL* 1.3 65.1 + - - +
242B SER* 4.2 11.9 - - - +
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Residues in contact with VAL 241 (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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143B VAL* 3.3 13.2 - - + +
144B ARG 4.0 2.7 - - - +
145B PRO* 3.6 38.4 - - + -
217B LEU* 4.0 18.6 - - + -
218B THR 3.7 30.1 - - - +
219B SER* 4.4 10.8 + - - +
221B ASP* 4.3 8.1 - - + -
222B SER* 3.0 22.0 + - - +
239B VAL* 4.4 6.1 - - + -
240B THR* 1.3 77.5 - - - +
242B SER* 1.3 71.2 + - - +
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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