Contacts of the strand formed by residues 239 - 244 (chain A) in PDB entry 5H8N
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 PHE 239 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A ILE* 2.7 45.6 + - + +
148A LEU* 3.4 36.1 - - + -
176A ASN* 3.6 21.1 - - - -
180A ASN* 4.2 4.9 - - - -
181A TYR* 4.1 16.8 - + - -
237A TYR* 4.0 8.5 - - + -
238A ILE* 1.3 73.8 - - - +
240A ALA* 1.4 81.2 + - + +
241A THR 3.4 0.8 + - - -
273B HIS 4.5 1.6 - - - -
274B GLU 3.8 16.2 - - - -
275B ASN 4.9 1.1 - - - -
276B GLY* 4.2 22.0 - - - -
279B GLU* 3.2 37.9 - - + +
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Residues in contact with ALA 240 (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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134A GLY* 3.6 8.5 - - - -
135A ILE* 4.7 5.6 - - + -
176A ASN* 4.2 7.4 - - - +
238A ILE 4.1 0.6 + - - -
239A PHE* 1.4 101.8 - - + +
241A THR* 1.3 66.6 + - - +
242A THR* 3.4 10.0 + - - +
273B HIS* 3.4 29.5 - - - +
274B GLU* 4.0 15.4 - - + +
279B GLU* 4.4 2.4 + - - -
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Residues in contact with THR 241 (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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132A GLU* 3.3 23.3 + - - +
133A THR 3.3 11.3 + - - -
238A ILE* 3.9 16.5 + - - +
239A PHE 3.4 0.6 - - - -
240A ALA* 1.3 74.3 - - - +
242A THR* 1.3 60.8 + - - +
143B LYS* 5.7 3.8 - - - +
144B TYR* 3.3 23.3 - - + +
273B HIS* 3.3 50.3 + - + +
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Residues in contact with THR 242 (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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115A THR* 3.6 27.4 - - + -
116A ILE* 2.6 30.3 + - - +
132A GLU* 3.6 6.4 - - - +
133A THR* 2.7 38.0 + - + +
134A GLY* 4.1 8.1 - - - -
240A ALA 3.8 11.0 - - - +
241A THR* 1.3 74.9 + - - +
243A GLY* 1.3 59.4 + - - +
144B TYR* 3.3 20.8 + - - -
270B LEU* 4.7 8.8 - - - +
273B HIS* 5.8 0.9 - - - -
274B GLU* 6.5 0.7 - - - -
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Residues in contact with GLY 243 (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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115A THR* 3.7 2.3 - - - -
116A ILE* 2.9 31.6 + - - +
129A PRO* 3.8 16.0 - - - +
131A VAL 3.0 13.7 - - - -
132A GLU* 4.4 0.4 - - - -
133A THR* 3.7 9.0 - - - +
242A THR* 1.3 82.7 + - - +
244A TYR* 1.3 62.6 + - - -
144B TYR* 3.4 4.6 + - - -
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Residues in contact with TYR 244 (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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18A PHE* 3.7 27.7 - + - -
112A GLY 4.1 10.8 - - - +
113A SER* 3.4 52.1 - - - -
114A LEU 3.3 10.1 - - - +
115A THR* 4.1 0.7 - - - -
116A ILE* 3.9 0.9 - - - -
129A PRO* 3.2 4.3 - - - +
130A PHE* 3.0 37.8 + + + -
131A VAL* 2.9 34.9 + - + -
133A THR* 3.7 11.7 - - + -
214A ASP* 2.6 41.2 + - - -
216A ALA* 3.6 7.3 - - + +
217A VAL* 3.5 12.1 - - - +
243A GLY* 1.3 72.4 - - - -
245A GLY* 1.3 58.1 + - - +
301A GLU 4.0 1.6 - - - -
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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