Contacts of the strand formed by residues 231 - 236 (chain A) in PDB entry 1H4R
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 GLU 231 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A ALA* 5.2 6.4 - - - +
224A ILE 3.6 13.0 + - - +
225A ARG* 2.7 45.6 + - - +
229A GLY 3.5 2.8 + - - +
230A THR* 1.3 76.7 - - - +
232A LEU* 1.3 65.5 + - - +
246A PRO* 3.1 27.6 - - + +
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Residues in contact with LEU 232 (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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223A ALA* 3.8 4.7 - - - +
224A ILE* 2.9 44.2 + - + +
226A ASN* 3.6 39.5 - - + +
230A THR* 3.8 16.6 - - + +
231A GLU* 1.3 84.1 - - - +
233A LEU* 1.3 67.6 + - - +
243A ILE* 3.8 21.5 - - + -
244A TYR 3.5 16.4 - - - +
245A ASP* 3.7 20.4 - - - +
246A PRO* 3.8 5.7 - - + +
283A PHE* 5.0 3.8 - - + -
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Residues in contact with LEU 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A TYR* 4.3 13.2 - - + -
222A PHE 3.3 16.6 - - - +
223A ALA* 3.9 13.2 - - + +
224A ILE* 4.1 4.0 - - - -
232A LEU* 1.3 80.2 - - - +
234A LEU* 1.3 59.2 + - - +
242A HIS 3.6 0.2 - - - +
243A ILE* 3.5 6.9 - - - +
244A TYR* 2.8 44.7 + - + -
245A ASP 4.5 2.7 - - - +
246A PRO* 3.9 27.8 - - + -
249A ARG* 3.5 59.2 - - + +
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Residues in contact with LEU 234 (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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220A ASN 3.4 1.2 - - - +
221A TYR* 3.2 5.9 - - - +
222A PHE* 2.8 36.9 + - + +
224A ILE* 3.8 22.5 - - + +
233A LEU* 1.3 72.7 - - - +
235A GLY* 1.3 67.5 + - - +
236A VAL* 3.9 21.8 - - + -
241A LEU* 4.5 20.6 - - + -
242A HIS 3.5 9.6 - - - +
243A ILE* 4.1 13.9 - - + -
244A TYR* 4.7 0.2 - - - -
273A ILE* 5.1 0.4 - - + -
285A PHE* 3.8 31.0 - - + -
296A ILE* 4.0 26.0 - - + -
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Residues in contact with GLY 235 (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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219A VAL* 3.8 15.9 - - - -
220A ASN 3.3 6.3 - - - -
221A TYR* 4.6 1.1 - - - -
233A LEU 3.9 0.8 + - - -
234A LEU* 1.3 74.0 - - - +
236A VAL* 1.3 61.9 + - - +
237A ASP 4.1 0.2 - - - -
241A LEU* 3.3 6.9 - - - +
242A HIS* 2.8 46.1 + - - -
244A TYR* 3.9 11.5 - - - -
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Residues in contact with VAL 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A VAL* 4.7 0.2 - - - -
220A ASN* 2.9 46.5 + - + +
222A PHE* 4.0 16.6 - - + -
234A LEU* 3.9 19.7 - - + -
235A GLY* 1.3 74.9 - - - -
237A ASP* 1.3 62.1 + - - +
240A GLY 3.8 2.9 - - - -
241A LEU* 3.7 24.2 - - + -
258A TRP* 4.2 5.4 - - + -
296A ILE* 4.8 3.4 - - + -
299A LEU* 4.0 23.6 - - + +
300A CYS* 4.1 7.9 - - - +
303A ASN* 3.9 19.5 - - - +
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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