Contacts of the strand formed by residues 222 - 226 (chain A) in PDB entry 1F9O
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 GLN 222 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A CYS 3.6 0.5 - - - +
198A ASP* 2.8 37.4 + - - +
209A LEU* 3.8 28.8 - - + +
219A PRO* 4.7 2.0 - - - +
220A ALA* 2.7 30.8 + - - +
221A LYS* 1.3 73.5 - - - +
223A PHE* 1.3 63.1 + - - +
224A LYS* 3.8 7.4 - - + +
304A GLY 3.1 18.6 - - - +
306A ILE* 3.7 10.2 - - - +
310A TRP* 3.8 13.1 - - + -
312A TRP* 4.9 2.6 + - - -
2B BGC 3.2 32.5 + - - -
3B BGC 4.0 13.9 + - - -
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Residues in contact with PHE 223 (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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94A ASP 3.8 4.7 - - - +
95A GLN* 3.9 18.2 - - + -
96A PRO* 3.6 27.4 - - + -
99A SER* 4.3 7.4 - - - -
100A MET* 4.2 15.9 - - - -
196A CYS 3.0 11.2 - - - +
197A TRP* 3.9 20.6 - + + -
222A GLN* 1.3 78.0 - - - +
224A LYS* 1.3 66.6 + - - +
225A TYR* 3.6 23.1 - + - +
302A TRP* 4.6 2.9 - + - -
303A GLY* 2.9 29.8 - - - -
304A GLY* 3.0 41.8 + - - +
305A GLY 3.4 14.4 - - - -
306A ILE* 4.1 9.0 - - + -
312A TRP* 4.7 1.2 + - - -
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Residues in contact with LYS 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A HIS* 4.8 0.2 - - - -
178A ASN* 5.4 6.4 + - + +
181A GLN* 5.2 1.9 - - - +
194A GLN* 4.1 18.8 + - - +
195A PRO 3.2 20.2 + - - -
196A CYS* 3.1 38.2 + - - +
198A ASP* 4.2 5.1 + - - +
208A PHE* 6.2 0.2 - - - +
209A LEU* 4.1 26.9 - - + +
212A PHE* 6.2 0.8 - - - -
222A GLN* 3.8 18.8 - - + +
223A PHE* 1.3 81.2 - - - +
225A TYR* 1.3 72.5 + - - +
226A THR* 5.5 0.9 - - - +
302A TRP 3.2 7.2 - - - -
303A GLY* 3.9 0.2 - - - -
312A TRP* 3.8 23.8 - - + -
1B V3P 3.6 24.7 + - - +
2B BGC 5.5 1.1 - - - +
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Residues in contact with TYR 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A PRO* 3.8 28.0 - - + -
94A ASP* 2.7 46.8 + - + +
95A GLN* 4.2 2.2 - - + -
153A HIS* 3.7 16.6 - + + +
176A TYR* 4.1 13.7 - + - +
178A ASN* 5.4 0.2 - - - +
196A CYS* 3.4 33.8 - - + +
197A TRP* 4.1 11.1 - - - +
223A PHE* 3.6 20.9 - + + +
224A LYS* 1.3 77.6 - - - +
226A THR* 1.3 64.9 + - - +
301A ALA* 3.1 7.1 - - - +
302A TRP* 2.8 66.1 + - + -
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Residues in contact with THR 226 (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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153A HIS* 3.1 12.7 + - - -
154A TRP* 3.0 37.0 + - + +
178A ASN* 3.0 26.0 + - - +
224A LYS* 5.5 0.5 - - - +
225A TYR* 1.3 76.4 + - - +
227A ASN* 1.3 72.2 + - - +
299A TYR* 3.9 21.1 - - + -
300A TYR 3.9 3.6 - - - +
301A ALA* 4.0 10.1 - - + +
302A TRP* 5.2 1.1 - - - -
1B V3P 4.0 25.8 + - + -
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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