Contacts of the strand formed by residues 193 - 199 (chain A) in PDB entry 4OG2
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 LYS 193 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191A ILE* 4.4 0.3 - - - +
192A LYS* 1.3 80.9 - - + +
194A VAL* 1.3 65.4 + - - +
222A GLU* 2.8 41.6 + - - +
224A VAL* 3.8 14.3 - - + +
246A LEU 3.8 12.3 + - - +
247A LYS* 3.6 20.2 - - + +
248A PRO* 3.9 12.6 - - + -
249A ASP* 2.8 34.8 + - - +
250A LEU* 3.2 6.8 + - - +
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Residues in contact with VAL 194 (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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191A ILE* 4.4 3.1 - - + -
193A LYS* 1.3 80.9 - - - +
195A ALA* 1.3 65.8 + - - +
196A VAL* 4.2 4.9 - - + -
216A VAL* 3.9 20.6 - - + -
221A LEU* 3.8 33.7 - - + -
222A GLU 2.8 11.9 + - - +
223A LEU* 3.5 7.6 - - - +
224A VAL* 2.9 27.8 + - - +
250A LEU* 3.3 24.0 - - + +
252A ILE* 3.9 30.3 - - + -
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Residues in contact with ALA 195 (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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194A VAL* 1.3 73.7 - - - +
196A VAL* 1.3 62.2 + - - +
197A PHE* 4.3 3.1 - - + -
224A VAL* 4.2 3.4 - - + -
225A THR* 3.7 25.4 - - + -
243A ALA* 3.9 18.6 - - + -
248A PRO* 3.9 18.3 - - + +
250A LEU 2.9 6.3 + - - -
251A VAL* 3.2 12.0 - - + +
252A ILE 2.9 24.8 + - - -
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Residues in contact with VAL 196 (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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194A VAL* 4.2 11.9 - - + -
195A ALA* 1.3 78.3 - - - +
197A PHE* 1.3 65.5 + - - +
209A THR* 3.2 27.1 - - - +
212A PHE* 5.3 2.2 - - + -
213A GLN* 4.0 20.2 - - + +
216A VAL* 4.9 3.4 - - + -
223A LEU* 3.5 24.2 - - + -
225A THR 3.0 12.2 + - - +
226A VAL* 3.2 8.3 - - + -
227A GLN* 2.8 32.4 + - - +
252A ILE* 3.5 24.0 - - + +
254A SER* 6.0 0.2 - - - +
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Residues in contact with PHE 197 (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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195A ALA* 4.3 7.4 - - + -
196A VAL* 1.3 82.2 - - - +
198A PHE* 1.3 62.7 + - - +
227A GLN* 3.2 22.2 - - + -
229A PHE* 3.8 18.2 - + + -
236A PHE* 6.1 0.2 - + - -
239A GLN* 3.7 29.4 - - + -
240A ALA* 4.0 8.3 - - - -
243A ALA* 3.5 31.4 - - + -
251A VAL* 3.7 33.9 - - + -
252A ILE 2.8 10.6 + - - +
253A ILE* 4.4 4.3 - - + -
254A SER* 2.9 24.4 + - - -
263A LEU* 3.8 26.7 - - + -
267A LEU* 4.2 9.2 - - + -
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Residues in contact with PHE 198 (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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197A PHE* 1.3 77.7 - - - +
199A ALA* 1.3 67.6 + - - +
200A GLN* 3.4 17.0 + - + -
205A SER 4.2 1.3 - - - +
206A LYS* 3.6 30.5 - - + -
209A THR* 3.6 36.6 - - + -
213A GLN* 4.8 0.9 - - - -
226A VAL* 3.5 32.3 - - + -
227A GLN 2.9 9.9 + - - -
228A LYS* 3.4 38.0 - - + -
229A PHE* 3.0 29.4 + - - -
254A SER* 3.2 11.2 - - - +
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Residues in contact with ALA 199 (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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198A PHE* 1.3 74.7 - - - +
200A GLN* 1.3 64.7 + - - +
201A ASN* 3.2 6.2 + - - +
202A ASP* 3.3 11.7 + - + +
205A SER* 3.5 24.2 - - - +
206A LYS* 4.0 0.5 - - - +
229A PHE* 3.2 25.3 - - + +
231A THR* 3.6 31.4 - - + +
254A SER 2.9 8.5 + - - +
255A GLY* 4.1 2.0 - - - -
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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