Contacts of the strand formed by residues 292 - 299 (chain o) in PDB entry 6FF7
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 VAL 292 (chain o).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146o ILE* 6.6 0.4 - - + -
147o LYS 3.5 5.6 - - - +
148o ILE* 4.6 5.8 - - + +
188o SER* 3.1 8.6 - - - -
189o PHE* 2.9 53.6 + - + +
278o ILE* 5.2 15.9 - - + +
281o GLN* 5.7 5.6 - - + -
288o PRO* 5.3 1.5 - - + +
290o GLN 3.4 6.3 + - - +
291o LYS* 1.3 72.5 - - - +
293o ILE* 1.3 60.8 + - - +
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Residues in contact with ILE 293 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146o ILE* 3.4 6.1 - - - +
147o LYS* 2.9 44.5 + - + +
186o GLY* 5.0 7.9 - - - +
187o SER 3.5 8.5 - - - +
188o SER* 4.4 1.8 - - - +
291o LYS* 5.5 4.5 - - + -
292o VAL* 1.3 74.8 - - - +
294o ILE* 1.3 63.7 + - - +
295o ALA* 3.1 4.4 + - - +
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Residues in contact with ILE 294 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144o MET* 5.0 10.3 - - + -
145o ASP 3.6 7.9 - - - +
146o ILE* 4.9 0.7 - - - +
184o PHE* 3.8 23.6 - - + +
185o LYS* 3.8 1.7 - - - -
186o GLY* 2.8 32.3 + - - -
187o SER 2.9 16.4 + - - +
188o SER* 4.9 0.4 - - - +
292o VAL 4.4 0.2 + - - -
293o ILE* 1.3 69.1 - - - +
295o ALA* 1.3 63.0 + - - +
296o ASP 3.3 9.8 + - - +
297o CYS* 5.5 1.8 - - + -
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Residues in contact with ALA 295 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145o ASP* 2.8 21.0 + - + +
146o ILE 4.8 0.7 - - - -
147o LYS* 4.2 21.3 - - + -
185o LYS* 5.1 2.6 - - - +
186o GLY* 4.9 4.1 + - - +
293o ILE* 3.1 7.5 + - + -
294o ILE* 1.3 72.2 - - - +
296o ASP* 1.3 60.9 + - + +
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Residues in contact with ASP 296 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144o MET* 3.4 2.1 - - - +
145o ASP* 2.8 41.9 + - + +
185o LYS* 4.9 7.4 - - - -
294o ILE* 3.3 4.5 - - - +
295o ALA* 1.3 80.4 + - + +
297o CYS* 1.3 64.1 + - - +
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Residues in contact with CYS 297 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143o TYR* 3.2 17.3 - - - +
144o MET* 4.2 7.0 - - + -
145o ASP 4.8 0.2 - - - +
176o CYS* 3.3 24.0 - - + +
177o THR* 5.3 0.2 - - - -
184o PHE* 5.1 12.6 - - + -
185o LYS* 5.0 11.8 - - + +
294o ILE* 5.5 2.9 - - + -
296o ASP* 1.3 79.1 - - - +
298o GLY* 1.3 59.6 + - - +
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Residues in contact with GLY 298 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142o VAL* 3.2 8.8 - - - +
143o TYR* 2.9 29.0 + - - +
176o CYS* 3.4 20.5 + - - +
177o THR* 4.5 4.7 - - - -
297o CYS* 1.3 78.7 - - - +
299o GLU* 1.3 60.3 + - - -
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Residues in contact with GLU 299 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141o GLN 3.6 10.8 - - - +
142o VAL* 4.1 3.6 - - + +
143o TYR* 6.4 0.7 - - - -
173o ARG* 5.6 7.9 - - + +
177o THR* 5.2 11.9 - - - +
298o GLY* 1.3 73.9 - - - -
300o TYR* 1.3 64.6 + - - +
301o VAL* 3.6 13.6 + - + +
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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