Contacts of the strand formed by residues 191 - 199 (chain B) in PDB entry 4OE5
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 191 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B SER* 3.3 17.5 - - - -
188B VAL* 3.0 22.0 + - - +
189B PRO* 3.0 8.9 - - - +
190B PRO* 1.3 80.1 - - - +
192B THR* 1.3 60.2 + - - +
193B ASN* 3.4 24.0 + - - -
548B LYS* 5.7 1.8 - - - -
549B GLU 3.0 12.3 - - - -
550B THR* 4.5 7.4 - - - -
551B HIS* 4.5 1.3 - - - -
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Residues in contact with THR 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B SER* 3.3 10.1 - - - +
191B SER* 1.3 70.1 - - - +
193B ASN* 1.3 69.4 + - - +
194B SER* 5.4 2.6 + - - +
547B ILE* 3.8 1.6 - - - +
548B LYS* 3.7 1.0 - - - -
549B GLU* 2.8 42.7 + - + +
551B HIS* 3.0 27.5 + - - -
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Residues in contact with ASN 193 (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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184B GLN* 4.9 0.7 - - - +
185B PRO* 3.9 27.3 - - + +
186B ILE 4.0 15.1 + - - +
187B SER* 2.6 24.4 + - - +
188B VAL* 4.3 3.4 - - - +
191B SER* 3.4 23.4 + - - -
192B THR* 1.3 84.1 - - - +
194B SER* 1.3 65.5 + - - +
546B VAL* 5.7 5.2 - - + -
547B ILE 3.5 6.1 - - - +
548B LYS* 3.7 19.4 - - + +
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Residues in contact with SER 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B GLN* 3.4 13.0 - - - -
185B PRO* 4.0 5.8 - - - +
192B THR* 5.4 3.5 + - - +
193B ASN* 1.3 78.6 - - - +
195B THR* 1.3 65.8 + - - +
196B VAL* 5.1 2.9 - - - +
546B VAL* 3.7 5.7 - - - +
547B ILE* 3.0 49.2 + - - +
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Residues in contact with THR 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B GLU* 5.1 2.4 - - - +
183B GLN 4.6 0.3 + - - -
184B GLN* 2.8 30.6 + - - +
185B PRO* 3.3 23.8 - - - +
194B SER* 1.3 74.3 - - - +
196B VAL* 1.3 64.8 + - - +
197B TYR* 3.6 41.2 + - + +
544B PRO* 4.1 15.7 - - + -
545B GLN 3.4 11.2 - - - +
546B VAL* 4.7 10.0 - - + +
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Residues in contact with VAL 196 (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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498A ARG* 3.3 40.8 - - - +
181B GLU* 6.1 0.4 - - - -
194B SER* 5.1 5.2 - - - +
195B THR* 1.3 76.3 - - - +
197B TYR* 1.3 61.9 + - - +
198B ARG* 3.2 12.2 + - + -
544B PRO* 3.5 0.9 - - - +
545B GLN* 2.8 50.6 + - - +
547B ILE* 3.7 27.8 - - + -
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Residues in contact with TYR 197 (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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498A ARG* 4.3 5.2 + - - -
117B ASP* 4.6 1.0 - - - +
124B ARG* 4.8 10.4 + - - -
180B LEU* 3.4 53.1 + - + +
181B GLU* 3.9 29.0 + - - +
183B GLN* 3.0 24.6 + - - +
184B GLN* 4.1 6.3 - - - -
195B THR* 3.6 35.3 + - + +
196B VAL* 1.3 75.1 - - - +
198B ARG* 1.3 62.3 + - - +
199B GLY 3.8 0.9 + - - -
226B MET* 4.9 4.3 - - + +
539B LEU* 5.0 1.8 - - + -
542B THR* 3.2 16.6 + - + +
544B PRO* 4.2 24.7 - - + -
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Residues in contact with ARG 198 (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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477A GLY 5.5 0.2 + - - -
498A ARG* 3.0 47.3 + - + +
499A ASN* 3.9 24.5 - - - +
501A ALA 3.4 20.6 + - - -
502A GLY* 3.9 10.9 - - - +
117B ASP* 3.9 7.4 - - - +
196B VAL* 3.2 22.0 + - + +
197B TYR* 1.3 71.9 - - - +
199B GLY* 1.3 68.1 + - - +
226B MET 4.4 0.7 - - - -
542B THR* 2.8 17.4 + - - -
543B SER* 2.8 59.9 + - - +
544B PRO 3.7 9.3 + - - -
545B GLN* 3.6 15.2 - - + +
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Residues in contact with GLY 199 (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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499A ASN* 4.5 6.6 + - - -
113B ARG* 4.7 2.5 + - - -
117B ASP* 3.0 23.4 + - - +
197B TYR 3.8 1.6 + - - -
198B ARG* 1.3 85.5 - - - +
200B LEU* 1.3 66.0 + - - +
201B GLU 3.8 0.9 + - - -
226B MET 3.4 21.3 + - - -
227B GLY 4.1 8.1 - - - -
228B ASN* 3.9 4.9 - - - -
541B TRP 4.1 2.0 - - - -
543B SER* 4.9 1.2 + - - -
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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